Starting phenix.real_space_refine
on Wed Feb 14 08:10:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/02_2024/8hf4_34712_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/02_2024/8hf4_34712.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/02_2024/8hf4_34712.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/02_2024/8hf4_34712.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/02_2024/8hf4_34712_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/02_2024/8hf4_34712_updated.pdb"
  }
  resolution = 2.8
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      30      5.16       5
     C    5732      2.51       5
     N    1462      2.21       5
     O    1686      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  469": "OE1" <-> "OE2"
    Residue "B TYR  196": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  373": "OE1" <-> "OE2"
    Residue "B TYR  568": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  657": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 8916
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "B"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.76, per 1000 atoms: 0.53
  Number of scatterers: 8916
  At special positions: 0
  Unit cell: (82.368, 81.51, 140.712, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       6     15.00
     O    1686      8.00
     N    1462      7.00
     C    5732      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.18
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      42 helices and 5 sheets defined
      63.9% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 3.511A  pdb=" N   VAL A 162 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LYS A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 158 through 163'
    Processing helix  chain 'A' and resid 168 through 194
      removed outlier: 3.503A  pdb=" N   LEU A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A 189 " --> pdb=" O   GLY A 185 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLN A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   SER A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 251
      removed outlier: 3.720A  pdb=" N   ASP A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   HIS A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 259
      removed outlier: 3.938A  pdb=" N   ALA A 258 " --> pdb=" O   MET A 254 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   THR A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 254 through 259'
    Processing helix  chain 'A' and resid 262 through 287
      removed outlier: 3.761A  pdb=" N   ALA A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER A 274 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ILE A 275 " --> pdb=" O   ASP A 271 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   ASP A 277 " --> pdb=" O   ASN A 273 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   ALA A 278 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU A 279 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   ALA A 280 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   SER A 281 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   THR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   ILE A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 303
    Processing helix  chain 'A' and resid 305 through 324
      removed outlier: 3.640A  pdb=" N   MET A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU A 313 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ALA A 314 " --> pdb=" O   MET A 310 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   LEU A 315 " --> pdb=" O   THR A 311 " (cutoff:3.500A)
      Proline residue:  A 316  - end of helix
    Processing helix  chain 'A' and resid 326 through 360
      removed outlier: 4.115A  pdb=" N   GLU A 330 " --> pdb=" O   MET A 326 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS A 331 " --> pdb=" O   LYS A 327 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE A 354 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   GLU A 355 " --> pdb=" O   ILE A 351 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   THR A 356 " --> pdb=" O   ASN A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 416
      removed outlier: 3.693A  pdb=" N   ASP A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 463
      removed outlier: 3.544A  pdb=" N   TYR A 433 " --> pdb=" O   THR A 429 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
      removed outlier: 3.733A  pdb=" N   ILE A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   THR A 446 " --> pdb=" O   ILE A 442 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   LYS A 447 " --> pdb=" O   ASN A 443 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU A 460 " --> pdb=" O   ASN A 456 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   VAL A 461 " --> pdb=" O   ARG A 457 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   TYR A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LEU A 463 " --> pdb=" O   ASN A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 530
    Processing helix  chain 'A' and resid 553 through 559
    Processing helix  chain 'A' and resid 574 through 579
    Processing helix  chain 'A' and resid 589 through 597
    Processing helix  chain 'A' and resid 624 through 637
    Processing helix  chain 'A' and resid 654 through 665
    Processing helix  chain 'A' and resid 678 through 682
      removed outlier: 3.745A  pdb=" N   GLU A 682 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 678 through 682'
    Processing helix  chain 'A' and resid 701 through 705
    Processing helix  chain 'A' and resid 710 through 716
    Processing helix  chain 'B' and resid 158 through 162
    Processing helix  chain 'B' and resid 166 through 194
      removed outlier: 3.533A  pdb=" N   ASN B 170 " --> pdb=" O   GLY B 166 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE B 183 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY B 185 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU B 189 " --> pdb=" O   GLY B 185 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLN B 190 " --> pdb=" O   SER B 186 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   SER B 191 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE B 192 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 199
      No H-bonds generated for 'chain 'B' and resid 196 through 199'
    Processing helix  chain 'B' and resid 202 through 250
      removed outlier: 3.702A  pdb=" N   ILE B 207 " --> pdb=" O   SER B 203 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 208 " --> pdb=" O   THR B 204 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   SER B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE B 210 " --> pdb=" O   GLY B 206 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY B 211 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASP B 240 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 259
      removed outlier: 3.831A  pdb=" N   ALA B 258 " --> pdb=" O   MET B 254 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 254 through 259'
    Processing helix  chain 'B' and resid 262 through 303
      removed outlier: 5.084A  pdb=" N   ASP B 277 " --> pdb=" O   ASN B 273 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   ALA B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   LEU B 279 " --> pdb=" O   ILE B 275 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   ALA B 280 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   SER B 281 " --> pdb=" O   ASP B 277 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ILE B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL B 299 " --> pdb=" O   ILE B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 311
    Processing helix  chain 'B' and resid 314 through 324
    Processing helix  chain 'B' and resid 326 through 352
      removed outlier: 4.074A  pdb=" N   GLU B 330 " --> pdb=" O   MET B 326 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS B 331 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 359
    Processing helix  chain 'B' and resid 363 through 416
      removed outlier: 3.719A  pdb=" N   GLN B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLN B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 463
      removed outlier: 3.978A  pdb=" N   VAL B 432 " --> pdb=" O   ASN B 428 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   TYR B 433 " --> pdb=" O   THR B 429 " (cutoff:3.500A)
      Proline residue:  B 437  - end of helix
      removed outlier: 4.056A  pdb=" N   THR B 446 " --> pdb=" O   ILE B 442 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LYS B 447 " --> pdb=" O   ASN B 443 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 454 " --> pdb=" O   THR B 450 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLU B 460 " --> pdb=" O   ASN B 456 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   VAL B 461 " --> pdb=" O   ARG B 457 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   TYR B 462 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LEU B 463 " --> pdb=" O   ASN B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 531
    Processing helix  chain 'B' and resid 548 through 550
      No H-bonds generated for 'chain 'B' and resid 548 through 550'
    Processing helix  chain 'B' and resid 553 through 559
    Processing helix  chain 'B' and resid 574 through 578
    Processing helix  chain 'B' and resid 589 through 597
    Processing helix  chain 'B' and resid 603 through 606
      No H-bonds generated for 'chain 'B' and resid 603 through 606'
    Processing helix  chain 'B' and resid 624 through 637
    Processing helix  chain 'B' and resid 654 through 665
    Processing helix  chain 'B' and resid 679 through 683
      removed outlier: 4.156A  pdb=" N   ARG B 683 " --> pdb=" O   THR B 679 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 679 through 683'
    Processing helix  chain 'B' and resid 701 through 707
    Processing helix  chain 'B' and resid 710 through 716
    Processing sheet with id=  A, first strand: chain 'A' and resid 485 through 487
      removed outlier: 3.644A  pdb=" N   SER A 542 " --> pdb=" O   THR A 485 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LYS A 487 " --> pdb=" O   GLU A 540 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU A 540 " --> pdb=" O   LYS A 487 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 695 through 699
      removed outlier: 6.992A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   GLU A 698 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   VAL A 687 " --> pdb=" O   GLU A 698 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS A 686 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU A 671 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   PHE A 515 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   PHE A 673 " --> pdb=" O   PHE A 515 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 489 through 491
      removed outlier: 3.838A  pdb=" N   VAL A 489 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 503 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   TYR A 491 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   SER A 501 " --> pdb=" O   TYR A 491 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'B' and resid 485 through 487
      removed outlier: 3.542A  pdb=" N   SER B 542 " --> pdb=" O   THR B 485 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 695 through 699
      removed outlier: 7.010A  pdb=" N   VAL B 689 " --> pdb=" O   VAL B 696 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   GLU B 698 " --> pdb=" O   VAL B 687 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL B 687 " --> pdb=" O   GLU B 698 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   VAL B 688 " --> pdb=" O   LYS B 512 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ALA B 514 " --> pdb=" O   VAL B 688 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   LEU B 690 " --> pdb=" O   ALA B 514 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL B 516 " --> pdb=" O   LEU B 690 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU B 671 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   PHE B 515 " --> pdb=" O   LEU B 671 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   PHE B 673 " --> pdb=" O   PHE B 515 " (cutoff:3.500A)

    489 hydrogen bonds defined for protein.
    1458 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: 2.46

  Time building geometry restraints manager: 3.50 seconds

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

  Histogram of bond lengths:
        1.19 -     1.37: 2896
        1.37 -     1.54: 6074
        1.54 -     1.72: 22
        1.72 -     1.89: 56
        1.89 -     2.07: 2
  Bond restraints: 9050
  Sorted by residual:
  bond pdb=" C4  AGS A 801 "
       pdb=" C5  AGS A 801 "
    ideal  model  delta    sigma   weight residual
    1.386  1.458 -0.072 1.00e-02 1.00e+04 5.25e+01
  bond pdb=" C4  AGS B 801 "
       pdb=" C5  AGS B 801 "
    ideal  model  delta    sigma   weight residual
    1.386  1.458 -0.072 1.00e-02 1.00e+04 5.21e+01
  bond pdb=" PG  AGS A 801 "
       pdb=" S1G AGS A 801 "
    ideal  model  delta    sigma   weight residual
    1.949  2.070 -0.121 2.00e-02 2.50e+03 3.63e+01
  bond pdb=" PG  AGS B 801 "
       pdb=" S1G AGS B 801 "
    ideal  model  delta    sigma   weight residual
    1.949  2.069 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" C5  AGS B 801 "
       pdb=" C6  AGS B 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.469 -0.060 1.00e-02 1.00e+04 3.61e+01
  ... (remaining 9045 not shown)

  Histogram of bond angle deviations from ideal:
       99.36 -   106.62: 166
      106.62 -   113.88: 5379
      113.88 -   121.14: 4728
      121.14 -   128.40: 1973
      128.40 -   135.67: 32
  Bond angle restraints: 12278
  Sorted by residual:
  angle pdb=" C5  AGS A 801 "
        pdb=" C4  AGS A 801 "
        pdb=" N3  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     126.80  118.84    7.96 7.41e-01 1.82e+00 1.16e+02
  angle pdb=" C5  AGS B 801 "
        pdb=" C4  AGS B 801 "
        pdb=" N3  AGS B 801 "
      ideal   model   delta    sigma   weight residual
     126.80  118.87    7.93 7.41e-01 1.82e+00 1.15e+02
  angle pdb=" C4  AGS B 801 "
        pdb=" C5  AGS B 801 "
        pdb=" N7  AGS B 801 "
      ideal   model   delta    sigma   weight residual
     110.73  106.97    3.76 4.52e-01 4.89e+00 6.92e+01
  angle pdb=" C5  AGS B 801 "
        pdb=" N7  AGS B 801 "
        pdb=" C8  AGS B 801 "
      ideal   model   delta    sigma   weight residual
     103.67  107.21   -3.54 4.26e-01 5.51e+00 6.92e+01
  angle pdb=" C4  AGS A 801 "
        pdb=" C5  AGS A 801 "
        pdb=" N7  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     110.73  106.97    3.76 4.52e-01 4.89e+00 6.91e+01
  ... (remaining 12273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.82: 5110
       23.82 -    47.64: 347
       47.64 -    71.46: 20
       71.46 -    95.27: 11
       95.27 -   119.09: 2
  Dihedral angle restraints: 5490
    sinusoidal: 2196
      harmonic: 3294
  Sorted by residual:
  dihedral pdb=" C   PHE B 673 "
           pdb=" N   PHE B 673 "
           pdb=" CA  PHE B 673 "
           pdb=" CB  PHE B 673 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.61  -10.99     0      2.50e+00 1.60e-01 1.93e+01
  dihedral pdb=" O1A AGS A 801 "
           pdb=" O3A AGS A 801 "
           pdb=" PA  AGS A 801 "
           pdb=" PB  AGS A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   51.36 -119.09     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" O1A AGS B 801 "
           pdb=" O3A AGS B 801 "
           pdb=" PA  AGS B 801 "
           pdb=" PB  AGS B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   51.35 -119.08     1      3.00e+01 1.11e-03 1.59e+01
  ... (remaining 5487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1387
       0.076 -    0.151: 89
       0.151 -    0.227: 19
       0.227 -    0.302: 3
       0.302 -    0.378: 4
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" CA  SER B 519 "
            pdb=" N   SER B 519 "
            pdb=" C   SER B 519 "
            pdb=" CB  SER B 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  LYS B 528 "
            pdb=" N   LYS B 528 "
            pdb=" C   LYS B 528 "
            pdb=" CB  LYS B 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" CB  ILE A 600 "
            pdb=" CA  ILE A 600 "
            pdb=" CG1 ILE A 600 "
            pdb=" CG2 ILE A 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.66e+00
  ... (remaining 1499 not shown)

  Planarity restraints: 1522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 187 "    0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   TYR B 187 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TYR B 187 "    0.021 2.00e-02 2.50e+03
        pdb=" N   TYR B 188 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 563 "    0.036 5.00e-02 4.00e+02   5.43e-02 4.72e+00
        pdb=" N   PRO B 564 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 564 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 564 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 436 "   -0.035 5.00e-02 4.00e+02   5.30e-02 4.50e+00
        pdb=" N   PRO B 437 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 437 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 437 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1519 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1020
        2.75 -     3.28: 9219
        3.28 -     3.82: 14402
        3.82 -     4.36: 15681
        4.36 -     4.90: 27952
  Nonbonded interactions: 68274
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 653 "
            pdb=" OG1 THR B 656 "
     model   vdw
     2.207 2.440
  nonbonded pdb=" OG1 THR A 524 "
            pdb=" O2G AGS A 801 "
     model   vdw
     2.247 2.440
  nonbonded pdb=" OG1 THR B 175 "
            pdb=" OE1 GLN B 226 "
     model   vdw
     2.263 2.440
  nonbonded pdb=" O   SER B 519 "
            pdb=" O1B AGS B 801 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ILE B 207 "
            pdb=" N   SER B 209 "
     model   vdw
     2.293 2.520
  ... (remaining 68269 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          4.150
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     25.970
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.050
  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:12.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
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      :  0.006   0.121   9050  Z= 0.372
  Angle     :  0.755   9.449  12278  Z= 0.509
  Chirality :  0.048   0.378   1502
  Planarity :  0.004   0.054   1522
  Dihedral  : 14.956 119.092   3366
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.72 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  1.41 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.26), residues: 1122
  helix:  2.75 (0.20), residues: 686
  sheet:  1.12 (0.69), residues: 72
  loop : -1.50 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 408 
 HIS   0.002   0.001   HIS B 248 
 PHE   0.030   0.001   PHE B 673 
 TYR   0.013   0.001   TYR B 562 
 ARG   0.003   0.000   ARG A 677 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 1.152 
Fit side-chains
REVERT: A  683 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8097 (mtp85)
REVERT: B  529 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8609 (mtt)
  outliers start: 11
  outliers final: 1
  residues processed: 99
  average time/residue: 0.9101
  time to fit residues: 98.5656
Evaluate side-chains
  55 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain B residue  529 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 84 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    0.1980
   chunk 101 optimal weight:    8.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 566 GLN
B 566 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9050  Z= 0.173
  Angle     :  0.549   9.656  12278  Z= 0.283
  Chirality :  0.040   0.360   1502
  Planarity :  0.003   0.039   1522
  Dihedral  :  8.026 136.612   1261
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.79 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.26), residues: 1122
  helix:  2.82 (0.20), residues: 700
  sheet:  0.60 (0.65), residues: 80
  loop : -1.49 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 408 
 HIS   0.002   0.001   HIS A 490 
 PHE   0.012   0.001   PHE B 309 
 TYR   0.019   0.001   TYR A 559 
 ARG   0.002   0.000   ARG A 677 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
REVERT: A  193 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8480 (mp)
REVERT: A  409 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7967 (tpp)
REVERT: A  604 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8611 (pt)
REVERT: A  676 HIS cc_start: 0.8782 (m170) cc_final: 0.8496 (m-70)
REVERT: B  201 MET cc_start: 0.6449 (mmm) cc_final: 0.5944 (mmm)
REVERT: B  458 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8462 (mp)
  outliers start: 20
  outliers final: 6
  residues processed: 76
  average time/residue: 0.8333
  time to fit residues: 70.5931
Evaluate side-chains
  65 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 84 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 101 optimal weight:    7.9990
   chunk 110 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 81 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 566 GLN
B 566 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9050  Z= 0.171
  Angle     :  0.502  10.137  12278  Z= 0.258
  Chirality :  0.038   0.267   1502
  Planarity :  0.003   0.038   1522
  Dihedral  :  8.206 140.112   1252
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.12 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.26), residues: 1122
  helix:  2.99 (0.20), residues: 686
  sheet:  0.48 (0.64), residues: 80
  loop : -1.41 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 248 
 PHE   0.008   0.001   PHE B 673 
 TYR   0.015   0.001   TYR A 559 
 ARG   0.002   0.000   ARG A 677 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  604 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8609 (pt)
REVERT: A  676 HIS cc_start: 0.8782 (m170) cc_final: 0.8537 (m-70)
REVERT: B  201 MET cc_start: 0.7096 (mmm) cc_final: 0.6393 (mmm)
  outliers start: 25
  outliers final: 7
  residues processed: 70
  average time/residue: 0.8703
  time to fit residues: 67.6027
Evaluate side-chains
  60 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 102 optimal weight:    0.4980
   chunk 108 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 90 optimal weight:    8.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
B 538 GLN
B 566 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9050  Z= 0.165
  Angle     :  0.485   8.186  12278  Z= 0.250
  Chirality :  0.038   0.193   1502
  Planarity :  0.003   0.037   1522
  Dihedral  :  8.116 142.759   1252
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.55 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.26), residues: 1122
  helix:  3.04 (0.19), residues: 686
  sheet:  0.40 (0.63), residues: 80
  loop : -1.43 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 248 
 PHE   0.007   0.001   PHE B 673 
 TYR   0.012   0.001   TYR B 187 
 ARG   0.001   0.000   ARG A 677 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 1.045 
Fit side-chains
REVERT: A  326 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7659 (ptp)
REVERT: A  604 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8630 (pt)
REVERT: A  676 HIS cc_start: 0.8773 (m170) cc_final: 0.8559 (m-70)
REVERT: B  201 MET cc_start: 0.7438 (mmm) cc_final: 0.7042 (mtp)
REVERT: B  310 MET cc_start: 0.8753 (ttt) cc_final: 0.8213 (tmm)
  outliers start: 21
  outliers final: 10
  residues processed: 75
  average time/residue: 0.8310
  time to fit residues: 69.0570
Evaluate side-chains
  66 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 0 optimal weight:    0.0020
   chunk 55 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.8592

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

Flipped N/Q/H residues before XYZ refinement:
B 200 GLN
B 538 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9050  Z= 0.150
  Angle     :  0.479   6.736  12278  Z= 0.248
  Chirality :  0.037   0.183   1502
  Planarity :  0.003   0.035   1522
  Dihedral  :  8.085 144.927   1252
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.96 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.26), residues: 1122
  helix:  3.07 (0.19), residues: 686
  sheet:  0.40 (0.64), residues: 80
  loop : -1.47 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 408 
 HIS   0.003   0.001   HIS B 248 
 PHE   0.013   0.001   PHE B 250 
 TYR   0.012   0.001   TYR A 559 
 ARG   0.001   0.000   ARG B 386 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  201 MET cc_start: 0.8446 (mpp) cc_final: 0.8171 (mpp)
REVERT: A  326 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7675 (ptp)
REVERT: A  604 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8631 (pt)
REVERT: A  676 HIS cc_start: 0.8758 (m170) cc_final: 0.8543 (m-70)
REVERT: B  201 MET cc_start: 0.7527 (mmm) cc_final: 0.7027 (mtp)
REVERT: B  676 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.8278 (t70)
  outliers start: 21
  outliers final: 13
  residues processed: 70
  average time/residue: 0.8888
  time to fit residues: 68.7310
Evaluate side-chains
  67 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 108 optimal weight:    9.9990
   chunk 89 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9980
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
B 538 GLN
B 566 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9050  Z= 0.254
  Angle     :  0.533   7.517  12278  Z= 0.277
  Chirality :  0.039   0.181   1502
  Planarity :  0.003   0.033   1522
  Dihedral  :  8.213 151.201   1252
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.77 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.26), residues: 1122
  helix:  2.92 (0.19), residues: 686
  sheet:  0.24 (0.63), residues: 80
  loop : -1.50 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 408 
 HIS   0.004   0.001   HIS A 248 
 PHE   0.012   0.001   PHE B 250 
 TYR   0.014   0.001   TYR B 187 
 ARG   0.002   0.000   ARG A 334 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 51
  time to evaluate  : 1.346 
Fit side-chains
REVERT: B  201 MET cc_start: 0.7912 (mmm) cc_final: 0.7604 (mtp)
REVERT: B  409 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7997 (tpp)
  outliers start: 30
  outliers final: 14
  residues processed: 73
  average time/residue: 0.9123
  time to fit residues: 73.8494
Evaluate side-chains
  65 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  409 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0970
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 368 GLN
B 538 GLN
B 566 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9050  Z= 0.142
  Angle     :  0.481   7.499  12278  Z= 0.249
  Chirality :  0.037   0.179   1502
  Planarity :  0.003   0.036   1522
  Dihedral  :  8.171 153.111   1252
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 18.69 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.26), residues: 1122
  helix:  3.07 (0.19), residues: 686
  sheet:  0.26 (0.64), residues: 80
  loop : -1.49 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 408 
 HIS   0.003   0.001   HIS B 248 
 PHE   0.007   0.001   PHE B 673 
 TYR   0.011   0.001   TYR A 559 
 ARG   0.002   0.000   ARG A 606 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.886 
Fit side-chains
REVERT: B  201 MET cc_start: 0.7925 (mmm) cc_final: 0.7559 (mtp)
  outliers start: 14
  outliers final: 12
  residues processed: 66
  average time/residue: 0.8851
  time to fit residues: 64.6224
Evaluate side-chains
  63 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  407 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0670
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9980
   chunk 98 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
B 538 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9050  Z= 0.142
  Angle     :  0.477   7.850  12278  Z= 0.246
  Chirality :  0.037   0.193   1502
  Planarity :  0.003   0.037   1522
  Dihedral  :  8.132 155.409   1252
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.39 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.26), residues: 1122
  helix:  3.14 (0.19), residues: 686
  sheet:  0.29 (0.64), residues: 80
  loop : -1.50 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 408 
 HIS   0.003   0.001   HIS B 248 
 PHE   0.007   0.001   PHE B 673 
 TYR   0.011   0.001   TYR B 187 
 ARG   0.002   0.000   ARG B 202 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.994 
Fit side-chains
REVERT: B  201 MET cc_start: 0.7940 (mmm) cc_final: 0.7672 (mtp)
  outliers start: 14
  outliers final: 12
  residues processed: 68
  average time/residue: 0.8539
  time to fit residues: 64.3485
Evaluate side-chains
  64 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  407 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 100 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 95 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    1.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9050  Z= 0.219
  Angle     :  0.525   8.521  12278  Z= 0.269
  Chirality :  0.039   0.208   1502
  Planarity :  0.003   0.037   1522
  Dihedral  :  8.231 158.789   1252
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.09 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.26), residues: 1122
  helix:  2.99 (0.19), residues: 686
  sheet:  0.20 (0.64), residues: 80
  loop : -1.48 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 248 
 PHE   0.007   0.001   PHE B 673 
 TYR   0.011   0.001   TYR B 187 
 ARG   0.002   0.000   ARG B 677 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 1.087 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8064 (mmm) cc_final: 0.7773 (mtp)
  outliers start: 17
  outliers final: 14
  residues processed: 67
  average time/residue: 0.8433
  time to fit residues: 62.7247
Evaluate side-chains
  65 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  407 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 73 optimal weight:    0.5980
   chunk 111 optimal weight:   10.0000
   chunk 102 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 94 optimal weight:    9.9990
   overall best weight:    1.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9050  Z= 0.179
  Angle     :  0.513   8.782  12278  Z= 0.262
  Chirality :  0.038   0.243   1502
  Planarity :  0.003   0.035   1522
  Dihedral  :  8.266 160.612   1252
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.60 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.26), residues: 1122
  helix:  3.03 (0.19), residues: 684
  sheet:  0.20 (0.64), residues: 80
  loop : -1.50 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 248 
 PHE   0.007   0.001   PHE B 673 
 TYR   0.010   0.001   TYR B 187 
 ARG   0.001   0.000   ARG A 677 

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.948 
Fit side-chains
REVERT: B  201 MET cc_start: 0.8138 (mmm) cc_final: 0.7832 (mtp)
  outliers start: 14
  outliers final: 13
  residues processed: 63
  average time/residue: 1.0498
  time to fit residues: 72.5774
Evaluate side-chains
  63 residues out of total 990 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  250 PHE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  407 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0060
   chunk 11 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.086758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.066584 restraints weight = 21673.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 3.19
r_work: 0.3042 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9050  Z= 0.142
  Angle     :  0.503   9.824  12278  Z= 0.254
  Chirality :  0.037   0.251   1502
  Planarity :  0.003   0.036   1522
  Dihedral  :  8.236 162.262   1252
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.49 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.26), residues: 1122
  helix:  3.12 (0.19), residues: 684
  sheet:  0.25 (0.64), residues: 80
  loop : -1.51 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 408 
 HIS   0.002   0.001   HIS A 248 
 PHE   0.007   0.001   PHE B 673 
 TYR   0.008   0.001   TYR A 559 
 ARG   0.001   0.000   ARG A 677 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2289.06 seconds
wall clock time: 42 minutes 1.34 seconds (2521.34 seconds total)