Starting phenix.real_space_refine
on Tue Mar  3 22:06:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6j5w_0683/03_2026/6j5w_0683.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6j5w_0683/03_2026/6j5w_0683.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6j5w_0683/03_2026/6j5w_0683.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6j5w_0683/03_2026/6j5w_0683.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6j5w_0683/03_2026/6j5w_0683.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6j5w_0683/03_2026/6j5w_0683.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      57      5.16       5
     C    5677      2.51       5
     N    1548      2.21       5
     O    1701      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8985
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 2455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2455
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 10, 'TRANS': 295}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 6503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 816, 6503
          Classifications: {'peptide': 816}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 788}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.25, per 1000 atoms: 0.25
  Number of scatterers: 8985
  At special positions: 0
  Unit cell: (87.28, 93.826, 123.283, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     P       2     15.00
     O    1701      8.00
     N    1548      7.00
     C    5677      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 369.2 milliseconds
  

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2110

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 7 sheets defined
      43.7% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'B' and resid 16 through 39
      removed outlier: 3.564A  pdb=" N   LYS B  20 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP B  25 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B  36 " --> pdb=" O   ARG B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 57
      removed outlier: 3.757A  pdb=" N   ILE B  53 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 114
      removed outlier: 4.180A  pdb=" N   GLU B 103 " --> pdb=" O   HIS B  99 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR B 105 " --> pdb=" O   VAL B 101 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 108 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ALA B 112 " --> pdb=" O   ILE B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 117
      No H-bonds generated for 'chain 'B' and resid 115 through 117'
    Processing helix  chain 'B' and resid 161 through 182
      removed outlier: 3.733A  pdb=" N   ILE B 172 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA B 173 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA B 175 " --> pdb=" O   GLU B 171 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA B 182 " --> pdb=" O   TYR B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 195
      No H-bonds generated for 'chain 'B' and resid 193 through 195'
    Processing helix  chain 'B' and resid 247 through 264
      removed outlier: 3.912A  pdb=" N   VAL B 251 " --> pdb=" O   GLU B 247 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER B 253 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE B 256 " --> pdb=" O   TYR B 252 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ILE B 261 " --> pdb=" O   CYS B 257 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 289
      removed outlier: 3.624A  pdb=" N   LEU B 282 " --> pdb=" O   GLY B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 301
    Processing helix  chain 'B' and resid 309 through 322
      removed outlier: 3.603A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 345
      removed outlier: 3.542A  pdb=" N   VAL B 336 " --> pdb=" O   LYS B 332 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA B 337 " --> pdb=" O   MET B 333 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LYS B 338 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 4.027A  pdb=" N   VAL A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU A  11 " --> pdb=" O   THR A   7 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE A  16 " --> pdb=" O   LYS A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 42
      removed outlier: 4.414A  pdb=" N   LYS A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLN A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU A  31 " --> pdb=" O   TYR A  27 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ASP A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU A  34 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR A  40 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
      removed outlier: 3.628A  pdb=" N   GLU A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 4.121A  pdb=" N   LEU A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A  69 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR A  70 " --> pdb=" O   ARG A  66 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU A  71 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ASP A  78 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   CYS A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A  81 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 99
      removed outlier: 3.729A  pdb=" N   SER A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 112
      removed outlier: 3.814A  pdb=" N   LYS A 110 " --> pdb=" O   PRO A 106 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A 112 " --> pdb=" O   GLN A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 175
      removed outlier: 4.334A  pdb=" N   ILE A 170 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   TRP A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LEU A 174 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
      removed outlier: 3.813A  pdb=" N   SER A 180 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 200
      removed outlier: 3.938A  pdb=" N   ILE A 198 " --> pdb=" O   GLY A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 227 through 235
    Processing helix  chain 'A' and resid 245 through 257
      removed outlier: 3.737A  pdb=" N   LYS A 252 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 282
      removed outlier: 3.574A  pdb=" N   LYS A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
      removed outlier: 3.752A  pdb=" N   VAL A 301 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'A' and resid 321 through 332
    Processing helix  chain 'A' and resid 341 through 343
      No H-bonds generated for 'chain 'A' and resid 341 through 343'
    Processing helix  chain 'A' and resid 344 through 353
    Processing helix  chain 'A' and resid 358 through 371
      removed outlier: 3.914A  pdb=" N   CYS A 371 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 390
      removed outlier: 3.703A  pdb=" N   ILE A 382 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 410
      removed outlier: 3.765A  pdb=" N   VAL A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLN A 405 " --> pdb=" O   MET A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 421
      removed outlier: 3.736A  pdb=" N   LYS A 416 " --> pdb=" O   PRO A 412 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   SER A 417 " --> pdb=" O   SER A 413 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   CYS A 418 " --> pdb=" O   HIS A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 425
      removed outlier: 3.570A  pdb=" N   TYR A 425 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 422 through 425'
    Processing helix  chain 'A' and resid 433 through 441
      removed outlier: 3.703A  pdb=" N   GLY A 439 " --> pdb=" O   GLN A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 464
      removed outlier: 3.912A  pdb=" N   CYS A 461 " --> pdb=" O   SER A 457 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   PHE A 462 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 501
      removed outlier: 3.566A  pdb=" N   ARG A 492 " --> pdb=" O   HIS A 488 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP A 493 " --> pdb=" O   ASP A 489 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A 494 " --> pdb=" O   MET A 490 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LYS A 501 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 558
    Processing helix  chain 'A' and resid 574 through 579
    Processing helix  chain 'A' and resid 580 through 582
      No H-bonds generated for 'chain 'A' and resid 580 through 582'
    Processing helix  chain 'A' and resid 603 through 607
      removed outlier: 3.961A  pdb=" N   GLU A 607 " --> pdb=" O   ARG A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 632
      removed outlier: 3.852A  pdb=" N   ILE A 630 " --> pdb=" O   GLN A 627 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   VAL A 631 " --> pdb=" O   PRO A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 657
      removed outlier: 4.472A  pdb=" N   GLY A 655 " --> pdb=" O   LYS A 652 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU A 657 " --> pdb=" O   ILE A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 683
      removed outlier: 3.796A  pdb=" N   LYS A 681 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ASN A 682 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 699
      removed outlier: 3.666A  pdb=" N   ILE A 699 " --> pdb=" O   GLY A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 704
      removed outlier: 3.685A  pdb=" N   LEU A 704 " --> pdb=" O   GLU A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 709
      removed outlier: 3.996A  pdb=" N   ILE A 708 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ASN A 709 " --> pdb=" O   SER A 706 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 705 through 709'
    Processing helix  chain 'A' and resid 728 through 733
    Processing helix  chain 'A' and resid 780 through 785
      removed outlier: 4.102A  pdb=" N   TRP A 784 " --> pdb=" O   GLN A 780 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 785 " --> pdb=" O   GLU A 781 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 780 through 785'
    Processing helix  chain 'A' and resid 808 through 815
    Processing sheet with id=AA1, first strand: chain 'B' and resid 72 through 79
      removed outlier: 3.566A  pdb=" N   ARG B  82 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 127
      removed outlier: 4.177A  pdb=" N   GLY B 125 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 197 through 199
    Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 219
      removed outlier: 6.469A  pdb=" N   ILE A 216 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 7.700A  pdb=" N   ASP A 267 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   VAL A 218 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE A 264 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   THR A 295 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   MET A 266 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   HIS A 313 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ALA A 186 " --> pdb=" O   HIS A 313 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 432
    Processing sheet with id=AA6, first strand: chain 'A' and resid 515 through 517
      removed outlier: 3.536A  pdb=" N   VAL A 536 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   LEU A 591 " --> pdb=" O   ASP A 616 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASP A 640 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 746
      removed outlier: 3.583A  pdb=" N   SER A 770 " --> pdb=" O   LEU A 744 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   LEU A 796 " --> pdb=" O   THR A 822 " (cutoff:3.500A)

    261 hydrogen bonds defined for protein.
    729 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: 1.31

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2633
        1.33 -     1.46: 1752
        1.46 -     1.58: 4683
        1.58 -     1.70: 3
        1.70 -     1.82: 83
  Bond restraints: 9154
  Sorted by residual:
  bond pdb=" C4  ADP A 901 "
       pdb=" C5  ADP A 901 "
    ideal  model  delta    sigma   weight residual
    1.490  1.453  0.037 2.00e-02 2.50e+03 3.34e+00
  bond pdb=" CB  CYS B 257 "
       pdb=" SG  CYS B 257 "
    ideal  model  delta    sigma   weight residual
    1.808  1.751  0.057 3.30e-02 9.18e+02 2.94e+00
  bond pdb=" CA  GLU B 156 "
       pdb=" CB  GLU B 156 "
    ideal  model  delta    sigma   weight residual
    1.528  1.556 -0.027 1.67e-02 3.59e+03 2.66e+00
  bond pdb=" CG1 ILE A 614 "
       pdb=" CD1 ILE A 614 "
    ideal  model  delta    sigma   weight residual
    1.513  1.451  0.062 3.90e-02 6.57e+02 2.49e+00
  bond pdb=" C   ALA B 182 "
       pdb=" N   PHE B 183 "
    ideal  model  delta    sigma   weight residual
    1.329  1.282  0.047 3.03e-02 1.09e+03 2.40e+00
  ... (remaining 9149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 12119
        3.46 -     6.93: 205
        6.93 -    10.39: 37
       10.39 -    13.85: 5
       13.85 -    17.31: 2
  Bond angle restraints: 12368
  Sorted by residual:
  angle pdb=" C   GLU B  80 "
        pdb=" N   ASP B  81 "
        pdb=" CA  ASP B  81 "
      ideal   model   delta    sigma   weight residual
     121.54  131.85  -10.31 1.91e+00 2.74e-01 2.91e+01
  angle pdb=" C   SER B 208 "
        pdb=" N   ASP B 209 "
        pdb=" CA  ASP B 209 "
      ideal   model   delta    sigma   weight residual
     121.54  131.84  -10.30 1.91e+00 2.74e-01 2.91e+01
  angle pdb=" C   ILE B 152 "
        pdb=" N   VAL B 153 "
        pdb=" CA  VAL B 153 "
      ideal   model   delta    sigma   weight residual
     121.97  131.52   -9.55 1.80e+00 3.09e-01 2.81e+01
  angle pdb=" N   VAL B 153 "
        pdb=" CA  VAL B 153 "
        pdb=" C   VAL B 153 "
      ideal   model   delta    sigma   weight residual
     109.34   98.98   10.36 2.08e+00 2.31e-01 2.48e+01
  angle pdb=" CA  LEU A 623 "
        pdb=" CB  LEU A 623 "
        pdb=" CG  LEU A 623 "
      ideal   model   delta    sigma   weight residual
     116.30  133.61  -17.31 3.50e+00 8.16e-02 2.45e+01
  ... (remaining 12363 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.03: 5044
       15.03 -    30.05: 407
       30.05 -    45.08: 98
       45.08 -    60.11: 10
       60.11 -    75.14: 3
  Dihedral angle restraints: 5562
    sinusoidal: 2307
      harmonic: 3255
  Sorted by residual:
  dihedral pdb=" CA  ILE B 152 "
           pdb=" C   ILE B 152 "
           pdb=" N   VAL B 153 "
           pdb=" CA  VAL B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.50   52.50     0      5.00e+00 4.00e-02 1.10e+02
  dihedral pdb=" CA  CYS A 649 "
           pdb=" C   CYS A 649 "
           pdb=" N   PHE A 650 "
           pdb=" CA  PHE A 650 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.38   50.62     0      5.00e+00 4.00e-02 1.03e+02
  dihedral pdb=" CA  GLU B 156 "
           pdb=" C   GLU B 156 "
           pdb=" N   GLU B 157 "
           pdb=" CA  GLU B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  130.41   49.59     0      5.00e+00 4.00e-02 9.84e+01
  ... (remaining 5559 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 922
       0.061 -    0.122: 390
       0.122 -    0.183: 60
       0.183 -    0.244: 15
       0.244 -    0.305: 4
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" CB  ILE A 419 "
            pdb=" CA  ILE A 419 "
            pdb=" CG1 ILE A 419 "
            pdb=" CG2 ILE A 419 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" CB  ILE A 582 "
            pdb=" CA  ILE A 582 "
            pdb=" CG1 ILE A 582 "
            pdb=" CG2 ILE A 582 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CG  LEU A 494 "
            pdb=" CB  LEU A 494 "
            pdb=" CD1 LEU A 494 "
            pdb=" CD2 LEU A 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 1388 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 649 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   CYS A 649 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   CYS A 649 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PHE A 650 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  80 "   -0.013 2.00e-02 2.50e+03   2.75e-02 7.54e+00
        pdb=" C   GLU B  80 "    0.047 2.00e-02 2.50e+03
        pdb=" O   GLU B  80 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ASP B  81 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  43 "    0.041 5.00e-02 4.00e+02   6.17e-02 6.10e+00
        pdb=" N   PRO B  44 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B  44 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B  44 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1733
        2.77 -     3.30: 8320
        3.30 -     3.83: 14108
        3.83 -     4.37: 16463
        4.37 -     4.90: 27777
  Nonbonded interactions: 68401
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 151 "
            pdb=" OG  SER B 158 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OD1 ASP A 267 "
            pdb=" OG1 THR A 295 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   LEU B 123 "
            pdb=" OH  TYR A 721 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG  SER A 773 "
            pdb=" OG  SER A 800 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   ASN B 116 "
            pdb=" OG  SER A 773 "
     model   vdw
     2.346 3.040
  ... (remaining 68396 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.750
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
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      :  0.008   0.062   9154  Z= 0.329
  Angle     :  1.206  17.313  12368  Z= 0.624
  Chirality :  0.067   0.305   1391
  Planarity :  0.007   0.062   1576
  Dihedral  : 11.811  75.137   3452
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 11.04 %
    Favored  : 88.51 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  5.54 %
    Favored  : 93.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.65 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.62 (0.20), residues: 1114
  helix: -3.61 (0.15), residues: 427
  sheet: -3.22 (0.39), residues: 113
  loop : -2.53 (0.24), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  66 
 TYR   0.037   0.003   TYR A 109 
 PHE   0.028   0.004   PHE B 120 
 TRP   0.027   0.004   TRP A  96 
 HIS   0.012   0.002   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00775 ( 9154)
  covalent geometry    : angle       1.20563 (12368)
  hydrogen bonds       : bond        0.19512 (  261)
  hydrogen bonds       : angle       7.62688 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 201
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 ASP cc_start: 0.8393 (t0) cc_final: 0.8187 (t0)
REVERT: B  171 GLU cc_start: 0.8479 (tp30) cc_final: 0.8264 (tp30)
REVERT: B  247 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7547 (tm-30)
REVERT: B  335 GLN cc_start: 0.8658 (tt0) cc_final: 0.8068 (tt0)
REVERT: B  342 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7734 (tp-100)
REVERT: A   20 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8416 (ttpt)
REVERT: A   29 LYS cc_start: 0.9008 (tmmt) cc_final: 0.8486 (mmtm)
REVERT: A  169 LYS cc_start: 0.8449 (mptt) cc_final: 0.8000 (mmtm)
REVERT: A  277 TRP cc_start: 0.5944 (t60) cc_final: 0.5649 (t60)
REVERT: A  498 ILE cc_start: 0.9302 (tp) cc_final: 0.9030 (tp)
REVERT: A  506 ASN cc_start: 0.7681 (t0) cc_final: 0.6718 (p0)
REVERT: A  548 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8784 (t0)
REVERT: A  572 ASP cc_start: 0.8039 (t0) cc_final: 0.7685 (t0)
REVERT: A  612 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9042 (tt)
REVERT: A  828 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7716 (mp0)
  outliers start: 9
  outliers final: 1
  residues processed: 210
  average time/residue: 0.1048
  time to fit residues: 29.4583
Evaluate side-chains
  115 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  548 ASN
Chi-restraints excluded: chain A residue  612 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0570
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    0.4980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
B 119 ASN
B 174 ASN
B 180 HIS
A  42 GLN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 434 GLN
A 450 ASN
A 548 ASN
A 643 ASN
A 742 HIS
A 761 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.134512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.111375 restraints weight = 16063.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.115003 restraints weight = 8333.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.117494 restraints weight = 5266.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.119077 restraints weight = 3809.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.120394 restraints weight = 3040.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9154  Z= 0.124
  Angle     :  0.731  11.873  12368  Z= 0.368
  Chirality :  0.046   0.178   1391
  Planarity :  0.005   0.047   1576
  Dihedral  :  7.635  50.150   1227
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.62 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 10.09 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.69 (0.23), residues: 1114
  helix: -2.54 (0.20), residues: 450
  sheet: -2.80 (0.40), residues: 123
  loop : -2.18 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 695 
 TYR   0.027   0.002   TYR A  27 
 PHE   0.015   0.001   PHE A 748 
 TRP   0.014   0.001   TRP A 825 
 HIS   0.009   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9154)
  covalent geometry    : angle       0.73086 (12368)
  hydrogen bonds       : bond        0.04013 (  261)
  hydrogen bonds       : angle       5.11078 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8194 (tt0) cc_final: 0.7867 (tp30)
REVERT: B   37 ASP cc_start: 0.8464 (t0) cc_final: 0.8185 (t0)
REVERT: B  102 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7726 (pttm)
REVERT: B  339 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7650 (mm-30)
REVERT: A   29 LYS cc_start: 0.8742 (tmmt) cc_final: 0.8201 (mmtm)
REVERT: A  169 LYS cc_start: 0.8278 (mptt) cc_final: 0.7771 (mtmt)
REVERT: A  185 MET cc_start: 0.7400 (mmm) cc_final: 0.7184 (mmt)
REVERT: A  277 TRP cc_start: 0.5905 (t60) cc_final: 0.5658 (t60)
REVERT: A  391 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.7019 (ptp90)
REVERT: A  498 ILE cc_start: 0.9211 (tp) cc_final: 0.8909 (tp)
REVERT: A  612 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8856 (tt)
REVERT: A  622 ASN cc_start: 0.8344 (p0) cc_final: 0.7603 (p0)
REVERT: A  634 LYS cc_start: 0.7070 (mppt) cc_final: 0.6805 (mmtt)
REVERT: A  828 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7824 (mp0)
  outliers start: 30
  outliers final: 11
  residues processed: 177
  average time/residue: 0.0979
  time to fit residues: 23.9152
Evaluate side-chains
  128 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  804 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 105 optimal weight:    0.0870
   chunk 42 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 84 optimal weight:    0.7980
   chunk 1 optimal weight:    8.9990
   chunk 74 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
A  42 GLN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 506 ASN
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 672 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.131715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108260 restraints weight = 16030.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.111871 restraints weight = 8295.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.114348 restraints weight = 5258.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116040 restraints weight = 3825.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.117082 restraints weight = 3045.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9154  Z= 0.141
  Angle     :  0.721  11.474  12368  Z= 0.359
  Chirality :  0.047   0.210   1391
  Planarity :  0.004   0.043   1576
  Dihedral  :  7.073  51.678   1221
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.98 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 11.97 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.24), residues: 1114
  helix: -1.88 (0.22), residues: 449
  sheet: -2.53 (0.42), residues: 129
  loop : -1.88 (0.28), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 695 
 TYR   0.021   0.001   TYR A  27 
 PHE   0.017   0.002   PHE A 633 
 TRP   0.011   0.001   TRP B 162 
 HIS   0.010   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9154)
  covalent geometry    : angle       0.72103 (12368)
  hydrogen bonds       : bond        0.03476 (  261)
  hydrogen bonds       : angle       4.67798 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 128
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8104 (tt0) cc_final: 0.7838 (tp30)
REVERT: B   37 ASP cc_start: 0.8506 (t0) cc_final: 0.8181 (t0)
REVERT: B  269 MET cc_start: 0.6139 (ttt) cc_final: 0.5909 (tmm)
REVERT: A   64 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8249 (t0)
REVERT: A  169 LYS cc_start: 0.8362 (mptt) cc_final: 0.7776 (mtmt)
REVERT: A  498 ILE cc_start: 0.9252 (tp) cc_final: 0.9019 (tp)
REVERT: A  606 MET cc_start: 0.9040 (ttp) cc_final: 0.8705 (ttm)
REVERT: A  612 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9013 (tt)
REVERT: A  622 ASN cc_start: 0.8246 (p0) cc_final: 0.7532 (p0)
REVERT: A  634 LYS cc_start: 0.7049 (mppt) cc_final: 0.6716 (mmtt)
REVERT: A  817 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.5244 (p90)
REVERT: A  828 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7897 (mp0)
  outliers start: 38
  outliers final: 22
  residues processed: 155
  average time/residue: 0.0952
  time to fit residues: 20.6248
Evaluate side-chains
  134 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  126 CYS
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  817 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 53 optimal weight:    7.9990
   chunk 106 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 78 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0020
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.107833 restraints weight = 16303.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.111381 restraints weight = 8338.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.113833 restraints weight = 5273.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.115374 restraints weight = 3810.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.116591 restraints weight = 3047.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9154  Z= 0.148
  Angle     :  0.708  11.289  12368  Z= 0.352
  Chirality :  0.047   0.168   1391
  Planarity :  0.004   0.043   1576
  Dihedral  :  6.897  52.789   1221
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.16 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 12.76 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.25), residues: 1114
  helix: -1.34 (0.24), residues: 435
  sheet: -2.25 (0.45), residues: 123
  loop : -1.60 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 326 
 TYR   0.018   0.001   TYR A  27 
 PHE   0.030   0.002   PHE B 139 
 TRP   0.011   0.001   TRP B 162 
 HIS   0.009   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9154)
  covalent geometry    : angle       0.70775 (12368)
  hydrogen bonds       : bond        0.03238 (  261)
  hydrogen bonds       : angle       4.47457 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 127
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 ASP cc_start: 0.8476 (t0) cc_final: 0.8089 (t0)
REVERT: B  269 MET cc_start: 0.6412 (ttt) cc_final: 0.5600 (ptm)
REVERT: A   39 LYS cc_start: 0.7909 (mptt) cc_final: 0.7685 (mptt)
REVERT: A   64 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8272 (t0)
REVERT: A  169 LYS cc_start: 0.8349 (mptt) cc_final: 0.7811 (mtmt)
REVERT: A  498 ILE cc_start: 0.9301 (tp) cc_final: 0.9096 (tp)
REVERT: A  599 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6692 (pt)
REVERT: A  606 MET cc_start: 0.9142 (ttp) cc_final: 0.8824 (ttm)
REVERT: A  612 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8997 (tt)
REVERT: A  622 ASN cc_start: 0.8230 (p0) cc_final: 0.7515 (p0)
REVERT: A  817 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.5343 (p90)
REVERT: A  828 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7902 (mp0)
  outliers start: 43
  outliers final: 26
  residues processed: 156
  average time/residue: 0.0938
  time to fit residues: 20.3385
Evaluate side-chains
  145 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  126 CYS
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  817 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0470
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.134239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.111121 restraints weight = 16097.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.114837 restraints weight = 8202.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.117390 restraints weight = 5134.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.118932 restraints weight = 3682.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.120104 restraints weight = 2941.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9154  Z= 0.114
  Angle     :  0.662  11.269  12368  Z= 0.330
  Chirality :  0.044   0.156   1391
  Planarity :  0.004   0.042   1576
  Dihedral  :  6.478  53.023   1221
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.62 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 13.95 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.26), residues: 1114
  helix: -0.99 (0.24), residues: 442
  sheet: -2.15 (0.47), residues: 121
  loop : -1.39 (0.29), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 695 
 TYR   0.015   0.001   TYR A  27 
 PHE   0.014   0.001   PHE A 748 
 TRP   0.018   0.001   TRP A 277 
 HIS   0.006   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9154)
  covalent geometry    : angle       0.66181 (12368)
  hydrogen bonds       : bond        0.02818 (  261)
  hydrogen bonds       : angle       4.20208 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 137
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 ASP cc_start: 0.8520 (t0) cc_final: 0.8039 (t0)
REVERT: B  269 MET cc_start: 0.6133 (ttt) cc_final: 0.5867 (ptm)
REVERT: B  326 ARG cc_start: 0.7500 (mtp85) cc_final: 0.7276 (ptm160)
REVERT: A   29 LYS cc_start: 0.9062 (tmmt) cc_final: 0.8547 (mmtm)
REVERT: A  599 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6478 (pt)
REVERT: A  606 MET cc_start: 0.8950 (ttp) cc_final: 0.8665 (ttm)
REVERT: A  622 ASN cc_start: 0.7872 (p0) cc_final: 0.7176 (p0)
REVERT: A  649 CYS cc_start: 0.7546 (p) cc_final: 0.7288 (p)
REVERT: A  817 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.4991 (p90)
REVERT: A  828 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7814 (mp0)
  outliers start: 38
  outliers final: 23
  residues processed: 164
  average time/residue: 0.0871
  time to fit residues: 20.4358
Evaluate side-chains
  140 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  817 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 514 HIS
A 672 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.102678 restraints weight = 16450.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.106198 restraints weight = 8556.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.108628 restraints weight = 5452.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.110257 restraints weight = 3949.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.111328 restraints weight = 3154.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9154  Z= 0.225
  Angle     :  0.775  11.092  12368  Z= 0.387
  Chirality :  0.050   0.183   1391
  Planarity :  0.004   0.040   1576
  Dihedral  :  6.940  55.510   1221
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.61 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 14.84 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.26), residues: 1114
  helix: -1.12 (0.24), residues: 451
  sheet: -2.03 (0.45), residues: 139
  loop : -1.52 (0.29), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  82 
 TYR   0.016   0.002   TYR A  27 
 PHE   0.030   0.002   PHE B 139 
 TRP   0.014   0.002   TRP A 277 
 HIS   0.009   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 9154)
  covalent geometry    : angle       0.77492 (12368)
  hydrogen bonds       : bond        0.03427 (  261)
  hydrogen bonds       : angle       4.53879 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 107
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8258 (tt0) cc_final: 0.7971 (tp30)
REVERT: B   37 ASP cc_start: 0.8530 (t0) cc_final: 0.7950 (t0)
REVERT: B  253 SER cc_start: 0.9380 (m) cc_final: 0.8671 (t)
REVERT: B  269 MET cc_start: 0.6124 (ttt) cc_final: 0.5890 (ptm)
REVERT: A   64 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8300 (t0)
REVERT: A  170 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8689 (tt)
REVERT: A  391 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6563 (ptp90)
REVERT: A  599 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.6744 (pt)
REVERT: A  612 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8964 (tt)
REVERT: A  622 ASN cc_start: 0.8167 (p0) cc_final: 0.7483 (p0)
REVERT: A  649 CYS cc_start: 0.7746 (p) cc_final: 0.7509 (p)
REVERT: A  759 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8328 (m)
REVERT: A  817 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.5545 (p90)
REVERT: A  828 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7960 (mp0)
  outliers start: 44
  outliers final: 26
  residues processed: 142
  average time/residue: 0.0890
  time to fit residues: 18.2050
Evaluate side-chains
  132 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  514 HIS
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  817 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 514 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.129560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.106335 restraints weight = 16324.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.109809 restraints weight = 8649.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.112197 restraints weight = 5568.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.113825 restraints weight = 4058.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.114835 restraints weight = 3241.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9154  Z= 0.142
  Angle     :  0.725  16.140  12368  Z= 0.355
  Chirality :  0.047   0.165   1391
  Planarity :  0.004   0.041   1576
  Dihedral  :  6.666  54.662   1221
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.35 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 15.03 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.26), residues: 1114
  helix: -0.86 (0.25), residues: 446
  sheet: -1.88 (0.46), residues: 139
  loop : -1.41 (0.29), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 299 
 TYR   0.015   0.001   TYR A  27 
 PHE   0.023   0.002   PHE B 139 
 TRP   0.018   0.001   TRP A 277 
 HIS   0.006   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9154)
  covalent geometry    : angle       0.72535 (12368)
  hydrogen bonds       : bond        0.03033 (  261)
  hydrogen bonds       : angle       4.32684 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 113
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8216 (tt0) cc_final: 0.7987 (tp30)
REVERT: B   37 ASP cc_start: 0.8561 (t0) cc_final: 0.8009 (t0)
REVERT: B  171 GLU cc_start: 0.8296 (tp30) cc_final: 0.8054 (tp30)
REVERT: B  253 SER cc_start: 0.9330 (m) cc_final: 0.8551 (t)
REVERT: B  326 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7398 (ptm160)
REVERT: A   29 LYS cc_start: 0.9120 (tmmt) cc_final: 0.8817 (tmmt)
REVERT: A  104 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7739 (ppp80)
REVERT: A  170 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8660 (tt)
REVERT: A  391 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6536 (ptp90)
REVERT: A  586 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7536 (mm110)
REVERT: A  599 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.6944 (pt)
REVERT: A  649 CYS cc_start: 0.7627 (p) cc_final: 0.7366 (p)
REVERT: A  656 SER cc_start: 0.8917 (m) cc_final: 0.8554 (p)
REVERT: A  759 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8184 (m)
REVERT: A  817 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.5472 (p90)
REVERT: A  828 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7964 (mp0)
  outliers start: 46
  outliers final: 27
  residues processed: 147
  average time/residue: 0.0859
  time to fit residues: 18.1245
Evaluate side-chains
  137 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  514 HIS
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  817 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 514 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.129417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.106212 restraints weight = 16345.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.109733 restraints weight = 8675.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.112128 restraints weight = 5553.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.113769 restraints weight = 4053.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.114674 restraints weight = 3231.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9154  Z= 0.143
  Angle     :  0.724  14.539  12368  Z= 0.355
  Chirality :  0.047   0.166   1391
  Planarity :  0.004   0.041   1576
  Dihedral  :  6.486  54.889   1219
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.52 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 15.13 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.26), residues: 1114
  helix: -0.76 (0.25), residues: 446
  sheet: -1.64 (0.48), residues: 132
  loop : -1.39 (0.29), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  82 
 TYR   0.015   0.001   TYR A  27 
 PHE   0.020   0.002   PHE B 139 
 TRP   0.019   0.001   TRP A 277 
 HIS   0.016   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9154)
  covalent geometry    : angle       0.72437 (12368)
  hydrogen bonds       : bond        0.02985 (  261)
  hydrogen bonds       : angle       4.29818 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 112
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8228 (tt0) cc_final: 0.7943 (tp30)
REVERT: B   37 ASP cc_start: 0.8582 (t0) cc_final: 0.8069 (t0)
REVERT: B  253 SER cc_start: 0.9326 (m) cc_final: 0.8556 (t)
REVERT: A   29 LYS cc_start: 0.9115 (tmmt) cc_final: 0.8812 (tmmt)
REVERT: A  104 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7787 (ppp80)
REVERT: A  391 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6478 (ptp90)
REVERT: A  586 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7599 (mm110)
REVERT: A  649 CYS cc_start: 0.7581 (p) cc_final: 0.7293 (p)
REVERT: A  656 SER cc_start: 0.8877 (m) cc_final: 0.8534 (p)
REVERT: A  759 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8262 (m)
REVERT: A  817 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.5382 (p90)
REVERT: A  828 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7959 (mp0)
  outliers start: 44
  outliers final: 29
  residues processed: 144
  average time/residue: 0.0831
  time to fit residues: 17.1316
Evaluate side-chains
  139 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  514 HIS
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  817 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 107 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 514 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.127979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.104391 restraints weight = 16363.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.107949 restraints weight = 8568.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.110410 restraints weight = 5468.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.111982 restraints weight = 3968.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.113168 restraints weight = 3184.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9154  Z= 0.182
  Angle     :  0.776  13.722  12368  Z= 0.380
  Chirality :  0.048   0.170   1391
  Planarity :  0.004   0.042   1576
  Dihedral  :  6.611  55.457   1219
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.61 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 16.42 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.26), residues: 1114
  helix: -0.81 (0.24), residues: 449
  sheet: -1.62 (0.48), residues: 132
  loop : -1.46 (0.29), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  82 
 TYR   0.016   0.002   TYR B  72 
 PHE   0.019   0.002   PHE B 139 
 TRP   0.020   0.001   TRP A 277 
 HIS   0.016   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 9154)
  covalent geometry    : angle       0.77647 (12368)
  hydrogen bonds       : bond        0.03116 (  261)
  hydrogen bonds       : angle       4.40115 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 107
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8220 (tt0) cc_final: 0.7935 (tp30)
REVERT: B   37 ASP cc_start: 0.8588 (t0) cc_final: 0.8124 (t0)
REVERT: B  253 SER cc_start: 0.9339 (m) cc_final: 0.8562 (t)
REVERT: B  326 ARG cc_start: 0.7212 (ptm160) cc_final: 0.6678 (ptm160)
REVERT: A   29 LYS cc_start: 0.9068 (tmmt) cc_final: 0.8765 (tmmt)
REVERT: A  104 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7764 (ppp80)
REVERT: A  391 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6534 (ptp90)
REVERT: A  599 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6967 (pt)
REVERT: A  606 MET cc_start: 0.9168 (ttp) cc_final: 0.8901 (ttm)
REVERT: A  649 CYS cc_start: 0.7605 (p) cc_final: 0.7330 (p)
REVERT: A  656 SER cc_start: 0.8929 (m) cc_final: 0.8570 (p)
REVERT: A  759 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8233 (m)
REVERT: A  817 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.5511 (p90)
REVERT: A  828 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7861 (mp0)
  outliers start: 40
  outliers final: 30
  residues processed: 136
  average time/residue: 0.0805
  time to fit residues: 15.7321
Evaluate side-chains
  136 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  204 ASN
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  514 HIS
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  817 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 1 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.107913 restraints weight = 16111.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111637 restraints weight = 8232.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.114207 restraints weight = 5143.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.115919 restraints weight = 3681.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.117009 restraints weight = 2902.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9154  Z= 0.127
  Angle     :  0.744  13.438  12368  Z= 0.363
  Chirality :  0.046   0.219   1391
  Planarity :  0.004   0.040   1576
  Dihedral  :  6.427  54.890   1219
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.16 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.11 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.26), residues: 1114
  helix: -0.64 (0.25), residues: 449
  sheet: -1.53 (0.49), residues: 132
  loop : -1.36 (0.29), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 695 
 TYR   0.014   0.001   TYR A  27 
 PHE   0.018   0.001   PHE B 139 
 TRP   0.022   0.001   TRP A 277 
 HIS   0.013   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9154)
  covalent geometry    : angle       0.74385 (12368)
  hydrogen bonds       : bond        0.02907 (  261)
  hydrogen bonds       : angle       4.23574 (  729)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8246 (tt0) cc_final: 0.7919 (tp30)
REVERT: B   37 ASP cc_start: 0.8623 (t0) cc_final: 0.8106 (t0)
REVERT: B   39 ASN cc_start: 0.8750 (t0) cc_final: 0.8475 (t0)
REVERT: B  253 SER cc_start: 0.9328 (m) cc_final: 0.8533 (t)
REVERT: B  326 ARG cc_start: 0.7163 (ptm160) cc_final: 0.6629 (ptm160)
REVERT: A   29 LYS cc_start: 0.8995 (tmmt) cc_final: 0.8763 (tmmt)
REVERT: A  104 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7802 (ppp80)
REVERT: A  391 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6908 (ptp-110)
REVERT: A  586 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7650 (mm110)
REVERT: A  599 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6871 (pt)
REVERT: A  606 MET cc_start: 0.9110 (ttp) cc_final: 0.8824 (ttm)
REVERT: A  649 CYS cc_start: 0.7649 (p) cc_final: 0.7365 (p)
REVERT: A  656 SER cc_start: 0.8947 (m) cc_final: 0.8583 (p)
REVERT: A  759 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8109 (m)
REVERT: A  817 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.5242 (p90)
REVERT: A  825 TRP cc_start: 0.8773 (m100) cc_final: 0.8391 (m100)
REVERT: A  828 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7740 (mp0)
  outliers start: 34
  outliers final: 24
  residues processed: 144
  average time/residue: 0.0827
  time to fit residues: 16.9118
Evaluate side-chains
  139 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  204 ASN
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  514 HIS
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  817 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0370
   chunk 0 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    1.1460

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.107818 restraints weight = 15898.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.111435 restraints weight = 8180.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.113966 restraints weight = 5153.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.115666 restraints weight = 3696.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.116845 restraints weight = 2918.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9154  Z= 0.135
  Angle     :  0.757  12.866  12368  Z= 0.370
  Chirality :  0.046   0.186   1391
  Planarity :  0.004   0.041   1576
  Dihedral  :  6.390  55.474   1219
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.69 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.41 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.26), residues: 1114
  helix: -0.61 (0.25), residues: 449
  sheet: -1.58 (0.48), residues: 139
  loop : -1.31 (0.30), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  50 
 TYR   0.014   0.001   TYR A  27 
 PHE   0.027   0.001   PHE A 783 
 TRP   0.021   0.001   TRP A 277 
 HIS   0.013   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9154)
  covalent geometry    : angle       0.75680 (12368)
  hydrogen bonds       : bond        0.02846 (  261)
  hydrogen bonds       : angle       4.22231 (  729)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1420.28 seconds
wall clock time: 25 minutes 13.47 seconds (1513.47 seconds total)