Starting phenix.real_space_refine
on Thu May  1 02:02:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x07_32919/05_2025/7x07_32919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x07_32919/05_2025/7x07_32919.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x07_32919/05_2025/7x07_32919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x07_32919/05_2025/7x07_32919.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x07_32919/05_2025/7x07_32919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x07_32919/05_2025/7x07_32919.cif"
  }
  resolution = 3.78
  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=   0.019
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: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6489      2.51       5
     N    1782      2.21       5
     O    1806      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10125
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 633, 5046
          Classifications: {'peptide': 633}
          Link IDs: {'PTRANS': 22, 'TRANS': 610}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 633, 5051
          Classifications: {'peptide': 633}
          Link IDs: {'PTRANS': 22, 'TRANS': 610}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'7PO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.74, per 1000 atoms: 0.67
  Number of scatterers: 10125
  At special positions: 0
  Unit cell: (74.7, 118.69, 147.74, 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      48     16.00
     O    1806      8.00
     N    1782      7.00
     C    6489      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.76
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2370

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 4 sheets defined
      51.6% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 83
      removed outlier: 3.913A  pdb=" N   LEU A  72 " --> pdb=" O   ASN A  68 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLN A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 96
      removed outlier: 3.741A  pdb=" N   LEU A  93 " --> pdb=" O   ARG A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.574A  pdb=" N   TYR A 110 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 124
      removed outlier: 4.397A  pdb=" N   CYS A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 140
      removed outlier: 3.650A  pdb=" N   GLY A 131 " --> pdb=" O   PRO A 127 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   TRP A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 168
      removed outlier: 3.872A  pdb=" N   ARG A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   LEU A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 175
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 4.055A  pdb=" N   SER A 184 " --> pdb=" O   TYR A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 198
    Processing helix  chain 'A' and resid 201 through 206
    Processing helix  chain 'A' and resid 217 through 232
      removed outlier: 4.089A  pdb=" N   ALA A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   TYR A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
      removed outlier: 3.574A  pdb=" N   ILE A 246 " --> pdb=" O   TRP A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
      removed outlier: 3.632A  pdb=" N   PHE A 265 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
      removed outlier: 3.856A  pdb=" N   TYR A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 3.706A  pdb=" N   LEU A 306 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 347
    Processing helix  chain 'A' and resid 347 through 353
      removed outlier: 4.003A  pdb=" N   ILE A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 371
      removed outlier: 3.825A  pdb=" N   GLU A 371 " --> pdb=" O   LYS A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 394
      removed outlier: 3.908A  pdb=" N   ALA A 384 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 404
      removed outlier: 4.320A  pdb=" N   ILE A 402 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 431
      removed outlier: 3.647A  pdb=" N   LEU A 412 " --> pdb=" O   GLU A 408 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU A 427 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLN A 430 " --> pdb=" O   PHE A 426 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 511
    Processing helix  chain 'A' and resid 512 through 521
    Processing helix  chain 'A' and resid 552 through 557
      removed outlier: 4.169A  pdb=" N   VAL A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 583
      removed outlier: 3.606A  pdb=" N   ALA A 578 " --> pdb=" O   GLN A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 591
    Processing helix  chain 'A' and resid 606 through 608
      No H-bonds generated for 'chain 'A' and resid 606 through 608'
    Processing helix  chain 'A' and resid 609 through 621
    Processing helix  chain 'A' and resid 639 through 650
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 3.794A  pdb=" N   LEU A 663 " --> pdb=" O   ARG A 660 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS A 665 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 701
      removed outlier: 4.476A  pdb=" N   LYS A 696 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 718
    Processing helix  chain 'A' and resid 719 through 721
      No H-bonds generated for 'chain 'A' and resid 719 through 721'
    Processing helix  chain 'B' and resid 68 through 83
      removed outlier: 3.830A  pdb=" N   LEU B  72 " --> pdb=" O   ASN B  68 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLN B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   TRP B  77 " --> pdb=" O   GLN B  73 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU B  78 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU B  79 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ARG B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU B  81 " --> pdb=" O   TRP B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 118 through 123
      removed outlier: 3.741A  pdb=" N   ILE B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 118 through 123'
    Processing helix  chain 'B' and resid 127 through 139
      removed outlier: 3.715A  pdb=" N   TRP B 132 " --> pdb=" O   ARG B 128 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLN B 133 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLN B 136 " --> pdb=" O   TRP B 132 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TRP B 137 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU B 139 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 146
    Processing helix  chain 'B' and resid 155 through 160
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 192 through 199
      removed outlier: 3.688A  pdb=" N   SER B 196 " --> pdb=" O   ASN B 192 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR B 198 " --> pdb=" O   ASP B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 206
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 227 through 237
    Processing helix  chain 'B' and resid 250 through 255
    Processing helix  chain 'B' and resid 267 through 289
    Processing helix  chain 'B' and resid 289 through 297
      removed outlier: 3.922A  pdb=" N   ILE B 293 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 312
    Processing helix  chain 'B' and resid 318 through 323
      removed outlier: 4.121A  pdb=" N   LEU B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 318 through 323'
    Processing helix  chain 'B' and resid 327 through 337
      removed outlier: 3.946A  pdb=" N   LEU B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 353
      removed outlier: 4.319A  pdb=" N   LEU B 345 " --> pdb=" O   ALA B 341 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   MET B 346 " --> pdb=" O   SER B 342 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 345 " (cutoff:3.500A)
      Proline residue:  B 350  - end of helix
    Processing helix  chain 'B' and resid 362 through 371
    Processing helix  chain 'B' and resid 373 through 378
    Processing helix  chain 'B' and resid 382 through 391
      removed outlier: 4.218A  pdb=" N   ALA B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 426
      removed outlier: 4.350A  pdb=" N   ALA B 413 " --> pdb=" O   VAL B 409 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY B 414 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR B 415 " --> pdb=" O   GLU B 411 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE B 423 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLN B 424 " --> pdb=" O   HIS B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 432
    Processing helix  chain 'B' and resid 512 through 522
      removed outlier: 4.224A  pdb=" N   LEU B 516 " --> pdb=" O   GLY B 512 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE B 517 " --> pdb=" O   LYS B 513 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG B 518 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 556
    Processing helix  chain 'B' and resid 564 through 568
    Processing helix  chain 'B' and resid 572 through 574
      No H-bonds generated for 'chain 'B' and resid 572 through 574'
    Processing helix  chain 'B' and resid 575 through 583
      removed outlier: 3.799A  pdb=" N   VAL B 583 " --> pdb=" O   ILE B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 621
      removed outlier: 3.658A  pdb=" N   ARG B 612 " --> pdb=" O   GLY B 608 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET B 618 " --> pdb=" O   GLY B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 649
    Processing helix  chain 'B' and resid 661 through 665
      removed outlier: 3.737A  pdb=" N   LYS B 665 " --> pdb=" O   SER B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 706
      removed outlier: 3.874A  pdb=" N   LEU B 690 " --> pdb=" O   SER B 686 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER B 691 " --> pdb=" O   ALA B 687 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE B 706 " --> pdb=" O   GLN B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 721
      removed outlier: 3.548A  pdb=" N   LEU B 713 " --> pdb=" O   MET B 709 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN B 714 " --> pdb=" O   GLN B 710 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   GLU B 715 " --> pdb=" O   ARG B 711 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE B 719 " --> pdb=" O   GLU B 715 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469
      removed outlier: 4.836A  pdb=" N   LEU A 493 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ALA A 491 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   VAL A 482 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL A 489 " --> pdb=" O   VAL A 482 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 467 through 469
      removed outlier: 3.844A  pdb=" N   TYR B 532 " --> pdb=" O   ILE B 475 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 539 through 543
      removed outlier: 6.466A  pdb=" N   PHE B 540 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ASP B 629 " --> pdb=" O   PHE B 540 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE B 542 " --> pdb=" O   ASP B 629 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 671

    330 hydrogen bonds defined for protein.
    915 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: 2.36

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1626
        1.30 -     1.43: 2748
        1.43 -     1.56: 5880
        1.56 -     1.69: 0
        1.69 -     1.83: 80
  Bond restraints: 10334
  Sorted by residual:
  bond pdb=" C   PRO B 143 "
       pdb=" O   PRO B 143 "
    ideal  model  delta    sigma   weight residual
    1.238  1.170  0.068 1.37e-02 5.33e+03 2.48e+01
  bond pdb=" N   ARG B 236 "
       pdb=" CA  ARG B 236 "
    ideal  model  delta    sigma   weight residual
    1.459  1.519 -0.060 1.23e-02 6.61e+03 2.38e+01
  bond pdb=" C   VAL A 224 "
       pdb=" O   VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.231  1.278 -0.047 1.02e-02 9.61e+03 2.11e+01
  bond pdb=" C   ALA B 626 "
       pdb=" O   ALA B 626 "
    ideal  model  delta    sigma   weight residual
    1.235  1.184  0.051 1.15e-02 7.56e+03 1.99e+01
  bond pdb=" N   THR B 506 "
       pdb=" CA  THR B 506 "
    ideal  model  delta    sigma   weight residual
    1.455  1.510 -0.055 1.27e-02 6.20e+03 1.86e+01
  ... (remaining 10329 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 13410
        3.46 -     6.92: 549
        6.92 -    10.39: 10
       10.39 -    13.85: 0
       13.85 -    17.31: 1
  Bond angle restraints: 13970
  Sorted by residual:
  angle pdb=" N   ILE B 637 "
        pdb=" CA  ILE B 637 "
        pdb=" C   ILE B 637 "
      ideal   model   delta    sigma   weight residual
     109.34   92.03   17.31 2.08e+00 2.31e-01 6.93e+01
  angle pdb=" N   ILE A 320 "
        pdb=" CA  ILE A 320 "
        pdb=" C   ILE A 320 "
      ideal   model   delta    sigma   weight residual
     112.17  105.61    6.56 9.50e-01 1.11e+00 4.77e+01
  angle pdb=" N   ILE B 151 "
        pdb=" CA  ILE B 151 "
        pdb=" C   ILE B 151 "
      ideal   model   delta    sigma   weight residual
     112.90  106.87    6.03 9.60e-01 1.09e+00 3.95e+01
  angle pdb=" N   ALA B 168 "
        pdb=" CA  ALA B 168 "
        pdb=" C   ALA B 168 "
      ideal   model   delta    sigma   weight residual
     112.68  104.44    8.24 1.33e+00 5.65e-01 3.84e+01
  angle pdb=" N   VAL B 102 "
        pdb=" CA  VAL B 102 "
        pdb=" C   VAL B 102 "
      ideal   model   delta    sigma   weight residual
     111.91  106.50    5.41 8.90e-01 1.26e+00 3.70e+01
  ... (remaining 13965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 5475
       17.58 -    35.15: 605
       35.15 -    52.73: 113
       52.73 -    70.30: 19
       70.30 -    87.88: 14
  Dihedral angle restraints: 6226
    sinusoidal: 2544
      harmonic: 3682
  Sorted by residual:
  dihedral pdb=" CA  LEU B  96 "
           pdb=" C   LEU B  96 "
           pdb=" N   HIS B  97 "
           pdb=" CA  HIS B  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.40   28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  ALA B 170 "
           pdb=" C   ALA B 170 "
           pdb=" N   TYR B 171 "
           pdb=" CA  TYR B 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.04   26.96     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  SER B 636 "
           pdb=" C   SER B 636 "
           pdb=" N   ILE B 637 "
           pdb=" CA  ILE B 637 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.47   26.53     0      5.00e+00 4.00e-02 2.81e+01
  ... (remaining 6223 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 921
       0.067 -    0.134: 511
       0.134 -    0.201: 119
       0.201 -    0.267: 7
       0.267 -    0.334: 1
  Chirality restraints: 1559
  Sorted by residual:
  chirality pdb=" CA  ILE B 637 "
            pdb=" N   ILE B 637 "
            pdb=" C   ILE B 637 "
            pdb=" CB  ILE B 637 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CB  THR A 225 "
            pdb=" CA  THR A 225 "
            pdb=" OG1 THR A 225 "
            pdb=" CG2 THR A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  ILE A 657 "
            pdb=" N   ILE A 657 "
            pdb=" C   ILE A 657 "
            pdb=" CB  ILE A 657 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1556 not shown)

  Planarity restraints: 1774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 143 "   -0.018 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   PRO B 143 "    0.065 2.00e-02 2.50e+03
        pdb=" O   PRO B 143 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ALA B 144 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 641 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   GLY B 641 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLY B 641 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS B 642 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 622 "   -0.018 2.00e-02 2.50e+03   3.53e-02 1.24e+01
        pdb=" C   ARG B 622 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ARG B 622 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PRO B 623 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1771 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 298
        2.70 -     3.25: 9979
        3.25 -     3.80: 14719
        3.80 -     4.35: 20324
        4.35 -     4.90: 32170
  Nonbonded interactions: 77490
  Sorted by model distance:
  nonbonded pdb=" N   ILE B 637 "
            pdb=" O   ILE B 637 "
     model   vdw
     2.145 2.496
  nonbonded pdb=" C   SER B 636 "
            pdb=" O   ILE B 637 "
     model   vdw
     2.211 3.270
  nonbonded pdb=" NH1 ARG B 275 "
            pdb=" O   ASP B 312 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   GLY A 188 "
            pdb=" NH2 ARG A 191 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" OE2 GLU B 155 "
            pdb=" OG  SER B 213 "
     model   vdw
     2.335 3.040
  ... (remaining 77485 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 67 through 721)
  selection = (chain 'B' and resid 67 through 721)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.770
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
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      :  0.013   0.068  10334  Z= 0.947
  Angle     :  1.657  17.311  13970  Z= 1.222
  Chirality :  0.077   0.334   1559
  Planarity :  0.008   0.046   1774
  Dihedral  : 15.382  87.879   3856
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  8.11 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  5.53 %
    Favored  : 92.50 %
  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: -4.75 (0.20), residues: 1258
  helix: -3.09 (0.15), residues: 739
  sheet: -3.69 (0.77), residues: 40
  loop : -2.93 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.005   TRP B 524 
 HIS   0.020   0.004   HIS B 621 
 PHE   0.042   0.005   PHE B 204 
 TYR   0.036   0.006   TYR B 174 
 ARG   0.015   0.002   ARG B 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22326 (  330)
  hydrogen bonds       : angle       8.65644 (  915)
  covalent geometry    : bond        0.01267 (10334)
  covalent geometry    : angle       1.65724 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  114 LEU cc_start: 0.9135 (tp) cc_final: 0.8910 (tt)
REVERT: B  160 LEU cc_start: 0.8818 (tp) cc_final: 0.8434 (tt)
REVERT: B  493 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7664 (mp)
REVERT: B  501 MET cc_start: 0.7923 (tpp) cc_final: 0.7208 (mmm)
REVERT: B  615 MET cc_start: 0.7873 (mtt) cc_final: 0.7389 (mtt)
REVERT: B  663 LEU cc_start: 0.9145 (tp) cc_final: 0.8939 (tt)
  outliers start: 21
  outliers final: 8
  residues processed: 161
  average time/residue: 0.2271
  time to fit residues: 51.4615
Evaluate side-chains
  120 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.2980
   chunk 95 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 98 optimal weight:    0.5980
   chunk 38 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 73 optimal weight:    0.5980
   chunk 114 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 430 GLN
B 433 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.226298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.182171 restraints weight = 11858.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.177826 restraints weight = 18568.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.175831 restraints weight = 18394.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10334  Z= 0.145
  Angle     :  0.705  10.372  13970  Z= 0.376
  Chirality :  0.042   0.149   1559
  Planarity :  0.004   0.037   1774
  Dihedral  :  7.808  59.404   1454
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.92 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.50 %
    Favored  : 88.10 %
  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: -3.89 (0.22), residues: 1258
  helix: -2.34 (0.17), residues: 765
  sheet: -2.00 (1.23), residues: 22
  loop : -2.80 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 664 
 HIS   0.010   0.001   HIS B 621 
 PHE   0.017   0.001   PHE B 673 
 TYR   0.015   0.001   TYR A 559 
 ARG   0.007   0.001   ARG B 660 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  330)
  hydrogen bonds       : angle       5.34503 (  915)
  covalent geometry    : bond        0.00329 (10334)
  covalent geometry    : angle       0.70488 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.5857 (tpt) cc_final: 0.5655 (mmm)
REVERT: A  505 ILE cc_start: 0.5152 (OUTLIER) cc_final: 0.4889 (mt)
REVERT: A  674 ASP cc_start: 0.4740 (p0) cc_final: 0.4355 (p0)
REVERT: B  114 LEU cc_start: 0.9164 (tp) cc_final: 0.8837 (tt)
REVERT: B  380 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7270 (tt0)
REVERT: B  493 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7574 (mp)
REVERT: B  501 MET cc_start: 0.8020 (tpp) cc_final: 0.7389 (mmm)
REVERT: B  621 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7722 (m-70)
REVERT: B  663 LEU cc_start: 0.9107 (tp) cc_final: 0.8902 (tp)
  outliers start: 15
  outliers final: 9
  residues processed: 136
  average time/residue: 0.2096
  time to fit residues: 41.3385
Evaluate side-chains
  124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  324 ARG
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 119 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 4 optimal weight:    0.0670
   chunk 69 optimal weight:    0.4980
   chunk 61 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 37 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6922

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

Flipped N/Q/H residues before XYZ refinement:
** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 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 = 0.4466 r_free = 0.4466 target = 0.225509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.180471 restraints weight = 12062.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.176364 restraints weight = 19172.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.169478 restraints weight = 17094.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10334  Z= 0.141
  Angle     :  0.639  10.480  13970  Z= 0.337
  Chirality :  0.042   0.214   1559
  Planarity :  0.004   0.037   1774
  Dihedral  :  7.238  59.432   1445
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.39 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.87 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.56 (0.22), residues: 1258
  helix: -2.08 (0.18), residues: 768
  sheet: -2.60 (0.96), residues: 34
  loop : -2.59 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 664 
 HIS   0.016   0.002   HIS B 669 
 PHE   0.032   0.001   PHE A 681 
 TYR   0.014   0.001   TYR B 620 
 ARG   0.010   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03324 (  330)
  hydrogen bonds       : angle       4.77892 (  915)
  covalent geometry    : bond        0.00327 (10334)
  covalent geometry    : angle       0.63942 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8747 (tt)
REVERT: A  322 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8588 (tp)
REVERT: A  505 ILE cc_start: 0.5355 (OUTLIER) cc_final: 0.5108 (mt)
REVERT: B  380 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7199 (tt0)
REVERT: B  493 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7554 (mp)
REVERT: B  501 MET cc_start: 0.8035 (tpp) cc_final: 0.7093 (mmt)
REVERT: B  527 TYR cc_start: 0.7197 (m-80) cc_final: 0.6969 (m-80)
REVERT: B  683 LYS cc_start: 0.8339 (tptm) cc_final: 0.8124 (tptt)
  outliers start: 22
  outliers final: 12
  residues processed: 144
  average time/residue: 0.2133
  time to fit residues: 45.1693
Evaluate side-chains
  120 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  324 ARG
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    0.2980
   chunk 1 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0470
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.226299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.179821 restraints weight = 11975.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.177638 restraints weight = 20594.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.173810 restraints weight = 16407.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10334  Z= 0.130
  Angle     :  0.620  11.467  13970  Z= 0.324
  Chirality :  0.041   0.143   1559
  Planarity :  0.004   0.037   1774
  Dihedral  :  6.967  55.353   1445
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.76 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.46 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.22), residues: 1258
  helix: -2.00 (0.18), residues: 780
  sheet: -2.63 (0.93), residues: 34
  loop : -2.67 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP B 664 
 HIS   0.011   0.001   HIS B 669 
 PHE   0.015   0.001   PHE A 252 
 TYR   0.010   0.001   TYR B 181 
 ARG   0.006   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03033 (  330)
  hydrogen bonds       : angle       4.59978 (  915)
  covalent geometry    : bond        0.00301 (10334)
  covalent geometry    : angle       0.62019 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8596 (tp)
REVERT: A  346 MET cc_start: 0.8093 (ttm) cc_final: 0.7834 (ttm)
REVERT: A  505 ILE cc_start: 0.5446 (OUTLIER) cc_final: 0.5235 (mt)
REVERT: A  559 TYR cc_start: 0.7594 (t80) cc_final: 0.7384 (t80)
REVERT: B   81 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8708 (tp)
REVERT: B  114 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8629 (tt)
REVERT: B  380 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7116 (tt0)
REVERT: B  493 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7510 (mp)
REVERT: B  501 MET cc_start: 0.8109 (tpp) cc_final: 0.7422 (mmt)
REVERT: B  663 LEU cc_start: 0.9171 (tp) cc_final: 0.8932 (tp)
  outliers start: 27
  outliers final: 14
  residues processed: 133
  average time/residue: 0.2150
  time to fit residues: 41.5360
Evaluate side-chains
  116 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  324 ARG
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 69 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 47 optimal weight:    0.2980
   chunk 118 optimal weight:    0.6980
   chunk 113 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 36 optimal weight:   10.0000
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4473 r_free = 0.4473 target = 0.226137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.184120 restraints weight = 11916.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.181321 restraints weight = 19180.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.179330 restraints weight = 16950.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10334  Z= 0.131
  Angle     :  0.607  11.262  13970  Z= 0.317
  Chirality :  0.041   0.135   1559
  Planarity :  0.004   0.073   1774
  Dihedral  :  6.782  55.574   1445
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.55 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.93 %
    Favored  : 80.69 %
  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: -3.36 (0.23), residues: 1258
  helix: -1.86 (0.18), residues: 779
  sheet: -2.58 (0.93), residues: 34
  loop : -2.63 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.001   TRP B 664 
 HIS   0.005   0.001   HIS B 621 
 PHE   0.019   0.001   PHE B 644 
 TYR   0.010   0.001   TYR B 181 
 ARG   0.006   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02930 (  330)
  hydrogen bonds       : angle       4.49220 (  915)
  covalent geometry    : bond        0.00306 (10334)
  covalent geometry    : angle       0.60726 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8767 (tt)
REVERT: A  322 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8604 (tp)
REVERT: B   81 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8759 (tp)
REVERT: B  114 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8710 (tt)
REVERT: B  380 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7107 (tt0)
REVERT: B  493 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7506 (mp)
REVERT: B  501 MET cc_start: 0.8321 (tpp) cc_final: 0.8106 (tpp)
REVERT: B  663 LEU cc_start: 0.9158 (tp) cc_final: 0.8942 (tp)
  outliers start: 36
  outliers final: 19
  residues processed: 132
  average time/residue: 0.1891
  time to fit residues: 37.7986
Evaluate side-chains
  124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 13 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.223121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.178497 restraints weight = 12012.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.176453 restraints weight = 19744.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.174106 restraints weight = 14763.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10334  Z= 0.179
  Angle     :  0.645  11.541  13970  Z= 0.331
  Chirality :  0.044   0.280   1559
  Planarity :  0.004   0.065   1774
  Dihedral  :  6.874  56.738   1443
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.03 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.68 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.30 (0.23), residues: 1258
  helix: -1.79 (0.18), residues: 780
  sheet: -2.64 (0.81), residues: 42
  loop : -2.64 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP B 664 
 HIS   0.006   0.001   HIS B 621 
 PHE   0.016   0.002   PHE B 644 
 TYR   0.023   0.001   TYR B 620 
 ARG   0.006   0.000   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03029 (  330)
  hydrogen bonds       : angle       4.52688 (  915)
  covalent geometry    : bond        0.00425 (10334)
  covalent geometry    : angle       0.64537 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8828 (tt)
REVERT: A  322 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8658 (tp)
REVERT: A  338 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.7834 (m)
REVERT: A  346 MET cc_start: 0.8168 (ttm) cc_final: 0.7943 (ttm)
REVERT: A  403 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6418 (mtt)
REVERT: B   81 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8741 (tp)
REVERT: B  114 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8642 (tt)
REVERT: B  380 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7157 (tt0)
REVERT: B  493 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7677 (mp)
REVERT: B  663 LEU cc_start: 0.9064 (tp) cc_final: 0.8825 (tp)
  outliers start: 34
  outliers final: 22
  residues processed: 131
  average time/residue: 0.1810
  time to fit residues: 35.8281
Evaluate side-chains
  126 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 123 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.4457 r_free = 0.4457 target = 0.223495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.179152 restraints weight = 12099.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.176331 restraints weight = 18712.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.172171 restraints weight = 16533.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10334  Z= 0.167
  Angle     :  0.629  11.234  13970  Z= 0.324
  Chirality :  0.043   0.189   1559
  Planarity :  0.004   0.062   1774
  Dihedral  :  6.807  58.464   1443
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.62 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.18 (0.23), residues: 1258
  helix: -1.69 (0.18), residues: 780
  sheet: -2.53 (0.93), residues: 34
  loop : -2.61 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.002   TRP B 664 
 HIS   0.006   0.001   HIS B 669 
 PHE   0.014   0.001   PHE B 644 
 TYR   0.016   0.001   TYR B 620 
 ARG   0.008   0.000   ARG B 660 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02944 (  330)
  hydrogen bonds       : angle       4.45985 (  915)
  covalent geometry    : bond        0.00395 (10334)
  covalent geometry    : angle       0.62873 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 101
  time to evaluate  : 3.242 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6303 (tp)
REVERT: A  319 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8803 (tt)
REVERT: A  322 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8663 (tp)
REVERT: A  403 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.6425 (mtt)
REVERT: A  517 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5921 (t80)
REVERT: B   81 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8831 (tp)
REVERT: B  114 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8720 (tt)
REVERT: B  380 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7179 (tt0)
REVERT: B  501 MET cc_start: 0.8239 (tpp) cc_final: 0.7648 (mmt)
REVERT: B  618 MET cc_start: 0.7331 (ttt) cc_final: 0.7061 (ttt)
  outliers start: 38
  outliers final: 24
  residues processed: 130
  average time/residue: 0.2518
  time to fit residues: 50.2369
Evaluate side-chains
  129 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 122 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 103 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 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 = 0.4439 r_free = 0.4439 target = 0.221119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.175403 restraints weight = 12055.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.173230 restraints weight = 18421.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.166864 restraints weight = 19836.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10334  Z= 0.207
  Angle     :  0.666  11.427  13970  Z= 0.341
  Chirality :  0.044   0.181   1559
  Planarity :  0.004   0.061   1774
  Dihedral  :  6.882  59.931   1441
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.56 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.18 (0.23), residues: 1258
  helix: -1.69 (0.18), residues: 780
  sheet: -2.48 (0.82), residues: 42
  loop : -2.62 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP B 664 
 HIS   0.007   0.001   HIS B 621 
 PHE   0.017   0.002   PHE B 644 
 TYR   0.014   0.001   TYR B 620 
 ARG   0.008   0.000   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03081 (  330)
  hydrogen bonds       : angle       4.55688 (  915)
  covalent geometry    : bond        0.00494 (10334)
  covalent geometry    : angle       0.66576 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 101
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6564 (tp)
REVERT: A  319 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8715 (tt)
REVERT: A  322 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8563 (tp)
REVERT: A  338 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.7855 (m)
REVERT: A  403 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.6442 (mtt)
REVERT: B  114 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8713 (tt)
REVERT: B  380 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7218 (tt0)
  outliers start: 36
  outliers final: 24
  residues processed: 129
  average time/residue: 0.1881
  time to fit residues: 36.6222
Evaluate side-chains
  128 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  482 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0070
   chunk 71 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 95 optimal weight:    0.5980
   chunk 93 optimal weight:    5.9990
   chunk 109 optimal weight:    0.1980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 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 = 0.4474 r_free = 0.4474 target = 0.225624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.180186 restraints weight = 11963.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.177290 restraints weight = 18617.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.176135 restraints weight = 15955.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10334  Z= 0.117
  Angle     :  0.618  11.008  13970  Z= 0.317
  Chirality :  0.041   0.157   1559
  Planarity :  0.004   0.051   1774
  Dihedral  :  6.478  58.124   1441
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.03 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.97 (0.23), residues: 1258
  helix: -1.52 (0.19), residues: 780
  sheet: -2.12 (0.93), residues: 34
  loop : -2.55 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.001   TRP B 664 
 HIS   0.009   0.001   HIS B 669 
 PHE   0.013   0.001   PHE A 175 
 TYR   0.032   0.001   TYR A 174 
 ARG   0.006   0.000   ARG B  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02823 (  330)
  hydrogen bonds       : angle       4.38586 (  915)
  covalent geometry    : bond        0.00274 (10334)
  covalent geometry    : angle       0.61798 (13970)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6384 (tp)
REVERT: A  319 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8694 (tt)
REVERT: A  322 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8618 (tp)
REVERT: A  403 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7283 (ttt)
REVERT: B  114 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8728 (tt)
REVERT: B  380 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7168 (tt0)
REVERT: B  618 MET cc_start: 0.7199 (ttt) cc_final: 0.6905 (ttt)
  outliers start: 32
  outliers final: 22
  residues processed: 133
  average time/residue: 0.1835
  time to fit residues: 36.9608
Evaluate side-chains
  128 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 50.5698 > 50:
  distance: 86 - 91:   7.154
  distance: 91 - 92:  16.384
  distance: 92 - 93:  26.446
  distance: 92 - 95:  15.044
  distance: 93 - 94:  25.686
  distance: 93 - 101:   6.646
  distance: 95 - 96:  11.935
  distance: 96 - 97:  14.102
  distance: 96 - 98:  22.489
  distance: 97 - 99:  16.361
  distance: 98 - 100:  20.243
  distance: 99 - 100:  22.514
  distance: 101 - 102:   7.876
  distance: 102 - 103:  33.337
  distance: 102 - 105:  15.762
  distance: 103 - 104:  10.006
  distance: 103 - 112:  21.715
  distance: 105 - 106:   9.574
  distance: 106 - 107:  13.460
  distance: 107 - 108:   9.255
  distance: 108 - 109:   8.425
  distance: 109 - 110:  11.984
  distance: 109 - 111:  11.043
  distance: 112 - 113:  19.581
  distance: 112 - 118:  18.180
  distance: 113 - 114:   5.268
  distance: 113 - 116:  17.116
  distance: 114 - 115:  19.695
  distance: 114 - 119:  15.570
  distance: 115 - 133:  22.605
  distance: 116 - 117:   6.027
  distance: 117 - 118:  28.370
  distance: 119 - 120:  32.131
  distance: 120 - 121:  33.065
  distance: 120 - 123:  27.315
  distance: 121 - 122:  12.106
  distance: 121 - 125:  13.008
  distance: 123 - 124:  16.121
  distance: 125 - 126:  21.778
  distance: 126 - 127:   6.429
  distance: 126 - 129:  16.060
  distance: 127 - 128:  13.823
  distance: 127 - 133:  26.853
  distance: 129 - 130:  11.520
  distance: 130 - 131:   3.590
  distance: 130 - 132:  13.448
  distance: 133 - 134:  19.536
  distance: 134 - 135:  15.458
  distance: 134 - 137:  17.316
  distance: 135 - 136:  22.660
  distance: 135 - 147:  27.051
  distance: 137 - 138:   6.752
  distance: 138 - 139:   6.061
  distance: 138 - 140:   6.528
  distance: 139 - 141:   8.003
  distance: 140 - 142:  26.606
  distance: 140 - 143:  16.011
  distance: 141 - 142:  24.508
  distance: 142 - 144:  19.790
  distance: 143 - 145:  15.362
  distance: 144 - 146:   8.953
  distance: 145 - 146:   3.451
  distance: 147 - 148:  13.039
  distance: 148 - 149:  17.307
  distance: 148 - 151:   8.551
  distance: 149 - 150:  22.376
  distance: 149 - 156:  25.448
  distance: 151 - 152:  12.918
  distance: 152 - 153:   8.425
  distance: 153 - 154:  11.317
  distance: 154 - 155:  11.104
  distance: 156 - 157:  13.798
  distance: 157 - 158:  13.194
  distance: 157 - 160:   7.994
  distance: 158 - 159:  18.234
  distance: 158 - 168:   8.847
  distance: 160 - 161:  14.223
  distance: 161 - 162:  15.292
  distance: 161 - 163:  17.665
  distance: 162 - 164:  15.274
  distance: 163 - 165:  12.077
  distance: 164 - 166:  16.784
  distance: 165 - 166:  21.994
  distance: 166 - 167:   7.289
  distance: 168 - 169:   8.004
  distance: 169 - 170:  15.510
  distance: 169 - 172:  17.786
  distance: 170 - 171:   6.440
  distance: 170 - 178:   8.107
  distance: 172 - 173:  24.815
  distance: 173 - 174:  15.428
  distance: 173 - 175:  25.663
  distance: 174 - 176:  14.057
  distance: 175 - 177:  10.086
  distance: 176 - 177:  18.527
  distance: 178 - 179:  12.286
  distance: 179 - 180:   9.080
  distance: 179 - 182:  11.554
  distance: 180 - 181:  14.780
  distance: 180 - 185:  18.257
  distance: 182 - 183:  10.782
  distance: 182 - 184:  10.238