Starting phenix.real_space_refine
on Tue Apr 29 21:27:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6j5w_0683/04_2025/6j5w_0683.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6j5w_0683/04_2025/6j5w_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6j5w_0683/04_2025/6j5w_0683.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6j5w_0683/04_2025/6j5w_0683.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6j5w_0683/04_2025/6j5w_0683.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6j5w_0683/04_2025/6j5w_0683.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.16, per 1000 atoms: 0.57
  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: 2.17
  Conformation dependent library (CDL) restraints added in 978.8 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: 0.93
  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: 2.36

  Time building geometry restraints manager: 2.49 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:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.960
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.750
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.62 (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
 TRP   0.027   0.004   TRP A  96 
 HIS   0.012   0.002   HIS A 597 
 PHE   0.028   0.004   PHE B 120 
 TYR   0.037   0.003   TYR A 109 
 ARG   0.012   0.001   ARG A  66 

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

*********************** 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  : 0.973 
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: 0.8392 (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: 0.8784 (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: 0.8193 (mt-10) cc_final: 0.7716 (mp0)
  outliers start: 9
  outliers final: 1
  residues processed: 210
  average time/residue: 0.2384
  time to fit residues: 67.1427
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  : 1.032 
-------------------------------------------------------------------------------
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 93 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0020
   chunk 46 optimal weight:    0.6980
   chunk 28 optimal weight:    0.2980
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0980
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.3188

-------------------------------------------------------------------------------
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 548 ASN
A 643 ASN
A 742 HIS
A 761 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.135530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.112531 restraints weight = 15820.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.116167 restraints weight = 8182.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.118686 restraints weight = 5158.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9154  Z= 0.122
  Angle     :  0.733  11.945  12368  Z= 0.369
  Chirality :  0.046   0.194   1391
  Planarity :  0.005   0.046   1576
  Dihedral  :  7.624  50.389   1227
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.80 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 10.09 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.67 (0.23), residues: 1114
  helix: -2.55 (0.19), residues: 449
  sheet: -2.72 (0.42), residues: 113
  loop : -2.18 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 825 
 HIS   0.010   0.001   HIS A 597 
 PHE   0.014   0.001   PHE A 748 
 TYR   0.027   0.001   TYR A  27 
 ARG   0.004   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  261)
  hydrogen bonds       : angle       5.14479 (  729)
  covalent geometry    : bond        0.00257 ( 9154)
  covalent geometry    : angle       0.73256 (12368)

*********************** 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
  193 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 162
  time to evaluate  : 0.962 
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: 0.8185 (tt0) cc_final: 0.7858 (tp30)
REVERT: B   37 ASP cc_start: 0.8472 (t0) cc_final: 0.8154 (t0)
REVERT: B  102 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7720 (pttm)
REVERT: B  339 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7677 (mm-30)
REVERT: A   29 LYS cc_start: 0.8717 (tmmt) cc_final: 0.8177 (mmtm)
REVERT: A  169 LYS cc_start: 0.8293 (mptt) cc_final: 0.7769 (mtmt)
REVERT: A  277 TRP cc_start: 0.5980 (t60) cc_final: 0.5739 (t60)
REVERT: A  391 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.7059 (ptp90)
REVERT: A  498 ILE cc_start: 0.9221 (tp) cc_final: 0.8924 (tp)
REVERT: A  612 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8906 (tt)
REVERT: A  622 ASN cc_start: 0.8304 (p0) cc_final: 0.7572 (p0)
REVERT: A  828 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7858 (mp0)
  outliers start: 31
  outliers final: 11
  residues processed: 184
  average time/residue: 0.2296
  time to fit residues: 57.5365
Evaluate side-chains
  137 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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 B residue  339 GLU
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 50 optimal weight:    9.9990
   chunk 106 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 393 ASN
A 450 ASN
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.131236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108443 restraints weight = 16018.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.112037 restraints weight = 8164.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.114526 restraints weight = 5116.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2545

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= 0.139
  Angle     :  0.727  11.332  12368  Z= 0.360
  Chirality :  0.047   0.211   1391
  Planarity :  0.004   0.042   1576
  Dihedral  :  7.018  51.503   1221
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.71 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 11.97 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.24), residues: 1114
  helix: -1.87 (0.22), residues: 448
  sheet: -2.56 (0.41), residues: 130
  loop : -1.85 (0.28), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 162 
 HIS   0.010   0.001   HIS A 597 
 PHE   0.032   0.002   PHE B 139 
 TYR   0.021   0.001   TYR A  27 
 ARG   0.004   0.001   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  261)
  hydrogen bonds       : angle       4.66865 (  729)
  covalent geometry    : bond        0.00322 ( 9154)
  covalent geometry    : angle       0.72720 (12368)

*********************** 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
  175 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 136
  time to evaluate  : 1.102 
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: 0.8097 (tt0) cc_final: 0.7833 (tp30)
REVERT: B   37 ASP cc_start: 0.8473 (t0) cc_final: 0.7989 (t0)
REVERT: B  185 LYS cc_start: 0.8700 (pttp) cc_final: 0.8428 (pttp)
REVERT: B  269 MET cc_start: 0.6312 (ttt) cc_final: 0.5987 (tmm)
REVERT: B  333 MET cc_start: 0.8529 (mmm) cc_final: 0.8239 (tpp)
REVERT: B  339 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7628 (mm-30)
REVERT: A   64 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8261 (t0)
REVERT: A  169 LYS cc_start: 0.8368 (mptt) cc_final: 0.7778 (mtmt)
REVERT: A  498 ILE cc_start: 0.9274 (tp) cc_final: 0.9039 (tp)
REVERT: A  612 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9027 (tt)
REVERT: A  622 ASN cc_start: 0.8287 (p0) cc_final: 0.7557 (p0)
REVERT: A  634 LYS cc_start: 0.7042 (mppt) cc_final: 0.6709 (mmtt)
REVERT: A  817 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.5215 (p90)
REVERT: A  828 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7918 (mp0)
  outliers start: 39
  outliers final: 22
  residues processed: 163
  average time/residue: 0.2155
  time to fit residues: 48.6477
Evaluate side-chains
  144 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
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 43 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0980
   chunk 26 optimal weight:    0.0070
   chunk 93 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 56 optimal weight:    0.7980
   chunk 15 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 99 optimal weight:    0.4980
   chunk 53 optimal weight:    7.9990
   overall best weight:    0.4198

-------------------------------------------------------------------------------
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 414 HIS
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.136145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.113335 restraints weight = 15819.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.117075 restraints weight = 7972.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.119648 restraints weight = 4964.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9154  Z= 0.107
  Angle     :  0.663  11.177  12368  Z= 0.328
  Chirality :  0.044   0.159   1391
  Planarity :  0.003   0.042   1576
  Dihedral  :  6.531  51.434   1221
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.72 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.76 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.25), residues: 1114
  helix: -1.31 (0.23), residues: 444
  sheet: -2.18 (0.46), residues: 113
  loop : -1.54 (0.28), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 162 
 HIS   0.006   0.001   HIS A 597 
 PHE   0.014   0.001   PHE A 748 
 TYR   0.016   0.001   TYR A  27 
 ARG   0.003   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02925 (  261)
  hydrogen bonds       : angle       4.29645 (  729)
  covalent geometry    : bond        0.00228 ( 9154)
  covalent geometry    : angle       0.66252 (12368)

*********************** 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
  181 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8047 (tt0) cc_final: 0.7835 (tp30)
REVERT: B   37 ASP cc_start: 0.8442 (t0) cc_final: 0.7995 (t0)
REVERT: B  106 ASN cc_start: 0.8968 (t0) cc_final: 0.8156 (t0)
REVERT: B  130 PHE cc_start: 0.8439 (m-80) cc_final: 0.8239 (m-80)
REVERT: B  269 MET cc_start: 0.6304 (ttt) cc_final: 0.5445 (ptm)
REVERT: B  333 MET cc_start: 0.8397 (mmm) cc_final: 0.8106 (tpp)
REVERT: B  339 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7614 (mm-30)
REVERT: A   29 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8531 (mmtm)
REVERT: A  169 LYS cc_start: 0.8351 (mptt) cc_final: 0.7787 (mtmt)
REVERT: A  391 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6366 (ptp90)
REVERT: A  498 ILE cc_start: 0.9272 (tp) cc_final: 0.9065 (tp)
REVERT: A  599 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6493 (pt)
REVERT: A  606 MET cc_start: 0.8947 (ttp) cc_final: 0.8649 (ttm)
REVERT: A  622 ASN cc_start: 0.7890 (p0) cc_final: 0.7194 (p0)
REVERT: A  649 CYS cc_start: 0.7571 (p) cc_final: 0.7358 (p)
REVERT: A  817 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.4866 (p90)
REVERT: A  828 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7952 (mp0)
  outliers start: 32
  outliers final: 20
  residues processed: 174
  average time/residue: 0.2138
  time to fit residues: 52.4351
Evaluate side-chains
  142 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 PHE
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   75 ILE
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  394 THR
Chi-restraints excluded: chain A residue  471 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  636 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  706 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 35 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 88 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 342 GLN
A  42 GLN
A 204 ASN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.106423 restraints weight = 16169.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.109932 restraints weight = 8326.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.112209 restraints weight = 5280.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9154  Z= 0.185
  Angle     :  0.727  10.921  12368  Z= 0.363
  Chirality :  0.047   0.167   1391
  Planarity :  0.004   0.041   1576
  Dihedral  :  6.732  55.059   1221
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.34 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 12.86 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.25), residues: 1114
  helix: -1.13 (0.24), residues: 438
  sheet: -2.17 (0.45), residues: 131
  loop : -1.46 (0.29), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 277 
 HIS   0.008   0.001   HIS A 597 
 PHE   0.024   0.002   PHE B 139 
 TYR   0.016   0.002   TYR A  27 
 ARG   0.005   0.000   ARG A 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03169 (  261)
  hydrogen bonds       : angle       4.39954 (  729)
  covalent geometry    : bond        0.00433 ( 9154)
  covalent geometry    : angle       0.72742 (12368)

*********************** 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
  172 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 125
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 ASP cc_start: 0.8540 (t0) cc_final: 0.7982 (t0)
REVERT: B   68 GLN cc_start: 0.8313 (pp30) cc_final: 0.7981 (pp30)
REVERT: B  106 ASN cc_start: 0.8867 (t0) cc_final: 0.8399 (t0)
REVERT: B  333 MET cc_start: 0.8471 (mmm) cc_final: 0.8199 (mmm)
REVERT: B  339 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7588 (mm-30)
REVERT: A   29 LYS cc_start: 0.9114 (tmmt) cc_final: 0.8850 (tmmt)
REVERT: A   40 TYR cc_start: 0.7610 (t80) cc_final: 0.7320 (t80)
REVERT: A  201 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8400 (mm-30)
REVERT: A  391 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6649 (ptp90)
REVERT: A  599 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6637 (pt)
REVERT: A  612 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8890 (tt)
REVERT: A  622 ASN cc_start: 0.8049 (p0) cc_final: 0.7270 (p0)
REVERT: A  649 CYS cc_start: 0.7586 (p) cc_final: 0.7328 (p)
REVERT: A  741 LEU cc_start: 0.8543 (tt) cc_final: 0.8189 (tt)
REVERT: A  817 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.5376 (p90)
REVERT: A  828 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8031 (mp0)
  outliers start: 47
  outliers final: 28
  residues processed: 157
  average time/residue: 0.2091
  time to fit residues: 46.5264
Evaluate side-chains
  145 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
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   14 LEU
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  391 ARG
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  530 HIS
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  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  776 LEU
Chi-restraints excluded: chain A residue  804 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 32 optimal weight:    0.3980
   chunk 71 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0020
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 342 GLN
A 204 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.135508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.112026 restraints weight = 15674.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.115813 restraints weight = 7926.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.118382 restraints weight = 4937.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9154  Z= 0.111
  Angle     :  0.663  10.641  12368  Z= 0.330
  Chirality :  0.044   0.156   1391
  Planarity :  0.004   0.040   1576
  Dihedral  :  6.323  55.174   1221
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.08 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 14.94 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.26), residues: 1114
  helix: -0.82 (0.25), residues: 445
  sheet: -1.96 (0.46), residues: 131
  loop : -1.27 (0.29), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 277 
 HIS   0.005   0.001   HIS A 597 
 PHE   0.014   0.001   PHE A 748 
 TYR   0.014   0.001   TYR A  27 
 ARG   0.002   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02741 (  261)
  hydrogen bonds       : angle       4.17457 (  729)
  covalent geometry    : bond        0.00240 ( 9154)
  covalent geometry    : angle       0.66320 (12368)

*********************** 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
  176 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8110 (tt0) cc_final: 0.7890 (tp30)
REVERT: B   37 ASP cc_start: 0.8507 (t0) cc_final: 0.7987 (t0)
REVERT: B   68 GLN cc_start: 0.8347 (pp30) cc_final: 0.7992 (pp30)
REVERT: B  106 ASN cc_start: 0.8797 (t0) cc_final: 0.8229 (t0)
REVERT: B  339 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7684 (mm-30)
REVERT: A   29 LYS cc_start: 0.9044 (tmmt) cc_final: 0.8525 (mmtm)
REVERT: A   40 TYR cc_start: 0.7445 (t80) cc_final: 0.7169 (t80)
REVERT: A   91 ARG cc_start: 0.7202 (ptt90) cc_final: 0.6919 (ptt-90)
REVERT: A  599 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6902 (pt)
REVERT: A  649 CYS cc_start: 0.7707 (p) cc_final: 0.7445 (p)
REVERT: A  741 LEU cc_start: 0.8247 (tt) cc_final: 0.7757 (tt)
REVERT: A  817 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.4861 (p90)
REVERT: A  825 TRP cc_start: 0.8828 (m100) cc_final: 0.8391 (m100)
REVERT: A  828 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7895 (mp0)
  outliers start: 36
  outliers final: 22
  residues processed: 164
  average time/residue: 0.1836
  time to fit residues: 43.4640
Evaluate side-chains
  146 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
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  394 THR
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  471 ILE
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  612 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  706 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 73 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0070
   chunk 3 optimal weight:    0.9990
   chunk 109 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 79 optimal weight:    0.0020
   chunk 39 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.8010

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.134381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.110858 restraints weight = 16059.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.114645 restraints weight = 8181.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.117247 restraints weight = 5095.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3624

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= 0.113
  Angle     :  0.671  13.128  12368  Z= 0.327
  Chirality :  0.044   0.154   1391
  Planarity :  0.004   0.040   1576
  Dihedral  :  6.266  57.352   1221
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.53 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 14.14 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.26), residues: 1114
  helix: -0.67 (0.25), residues: 446
  sheet: -1.87 (0.47), residues: 131
  loop : -1.18 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 277 
 HIS   0.005   0.001   HIS A 597 
 PHE   0.022   0.001   PHE B 139 
 TYR   0.013   0.001   TYR A  27 
 ARG   0.004   0.000   ARG B 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02697 (  261)
  hydrogen bonds       : angle       4.09836 (  729)
  covalent geometry    : bond        0.00253 ( 9154)
  covalent geometry    : angle       0.67130 (12368)

*********************** 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
  169 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 131
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8054 (tt0) cc_final: 0.7853 (tp30)
REVERT: B   37 ASP cc_start: 0.8500 (t0) cc_final: 0.8028 (t0)
REVERT: B  106 ASN cc_start: 0.8811 (t0) cc_final: 0.8251 (t0)
REVERT: B  201 LYS cc_start: 0.9065 (pmtt) cc_final: 0.8670 (mmmt)
REVERT: B  253 SER cc_start: 0.9319 (m) cc_final: 0.8534 (t)
REVERT: B  333 MET cc_start: 0.7911 (mmm) cc_final: 0.7637 (mpp)
REVERT: B  339 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7546 (mm-30)
REVERT: A   29 LYS cc_start: 0.9051 (tmmt) cc_final: 0.8817 (tmmt)
REVERT: A   40 TYR cc_start: 0.7445 (t80) cc_final: 0.7128 (t80)
REVERT: A   91 ARG cc_start: 0.7062 (ptt90) cc_final: 0.6734 (ptt-90)
REVERT: A  599 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6891 (pt)
REVERT: A  649 CYS cc_start: 0.7666 (p) cc_final: 0.7385 (p)
REVERT: A  656 SER cc_start: 0.8909 (m) cc_final: 0.8535 (p)
REVERT: A  741 LEU cc_start: 0.8290 (tt) cc_final: 0.7940 (tt)
REVERT: A  817 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.5003 (p90)
REVERT: A  825 TRP cc_start: 0.8792 (m100) cc_final: 0.8368 (m100)
REVERT: A  828 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7904 (mp0)
  outliers start: 38
  outliers final: 23
  residues processed: 157
  average time/residue: 0.1873
  time to fit residues: 42.7159
Evaluate side-chains
  146 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
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  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  152 SER
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  394 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  530 HIS
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  657 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  744 LEU
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 61 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0370
   chunk 51 optimal weight:    9.9990
   chunk 14 optimal weight:    0.0470
   chunk 7 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0170
   chunk 23 optimal weight:    9.9990
   chunk 107 optimal weight:    8.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
B 342 GLN
A 204 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 622 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.135893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.112491 restraints weight = 16065.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.116051 restraints weight = 8515.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.118578 restraints weight = 5467.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9154  Z= 0.111
  Angle     :  0.680  13.236  12368  Z= 0.329
  Chirality :  0.044   0.155   1391
  Planarity :  0.003   0.040   1576
  Dihedral  :  6.142  52.645   1221
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.99 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 14.84 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.26), residues: 1114
  helix: -0.57 (0.25), residues: 450
  sheet: -1.72 (0.47), residues: 131
  loop : -1.12 (0.30), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 277 
 HIS   0.007   0.001   HIS A 597 
 PHE   0.012   0.001   PHE A 748 
 TYR   0.013   0.001   TYR A  27 
 ARG   0.003   0.000   ARG B 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02614 (  261)
  hydrogen bonds       : angle       4.04926 (  729)
  covalent geometry    : bond        0.00244 ( 9154)
  covalent geometry    : angle       0.68036 (12368)

*********************** 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
  170 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.985 
Fit side-chains
REVERT: B   37 ASP cc_start: 0.8542 (t0) cc_final: 0.8038 (t0)
REVERT: B  106 ASN cc_start: 0.8844 (t0) cc_final: 0.8254 (t0)
REVERT: B  253 SER cc_start: 0.9315 (m) cc_final: 0.8520 (t)
REVERT: B  333 MET cc_start: 0.7908 (mmm) cc_final: 0.7669 (mpp)
REVERT: B  339 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7559 (mm-30)
REVERT: A   29 LYS cc_start: 0.9118 (tmmt) cc_final: 0.8864 (tmmt)
REVERT: A   40 TYR cc_start: 0.7462 (t80) cc_final: 0.7196 (t80)
REVERT: A   91 ARG cc_start: 0.7068 (ptt90) cc_final: 0.6751 (ptt-90)
REVERT: A  104 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7711 (ppp80)
REVERT: A  209 GLU cc_start: 0.8629 (tt0) cc_final: 0.8395 (tt0)
REVERT: A  599 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6788 (pt)
REVERT: A  649 CYS cc_start: 0.7558 (p) cc_final: 0.7195 (p)
REVERT: A  656 SER cc_start: 0.8836 (m) cc_final: 0.8534 (p)
REVERT: A  741 LEU cc_start: 0.8244 (tt) cc_final: 0.7754 (tt)
REVERT: A  817 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.4969 (p90)
REVERT: A  825 TRP cc_start: 0.8678 (m100) cc_final: 0.8294 (m100)
REVERT: A  828 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7881 (mp0)
  outliers start: 36
  outliers final: 23
  residues processed: 156
  average time/residue: 0.1857
  time to fit residues: 41.6991
Evaluate side-chains
  150 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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  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  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  394 THR
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  471 ILE
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  612 LEU
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  793 ILE
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 38 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 109 optimal weight:    0.8980
   chunk 68 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0770
   chunk 97 optimal weight:    0.6980
   overall best weight:    1.5340

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

Flipped N/Q/H residues before XYZ refinement:
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 ASN
A 228 GLN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 514 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.132805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108761 restraints weight = 16013.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.112413 restraints weight = 8318.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.114927 restraints weight = 5301.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3846

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= 0.141
  Angle     :  0.732  12.552  12368  Z= 0.353
  Chirality :  0.046   0.192   1391
  Planarity :  0.004   0.040   1576
  Dihedral  :  6.214  53.801   1221
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.44 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 16.02 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.26), residues: 1114
  helix: -0.59 (0.24), residues: 451
  sheet: -1.62 (0.48), residues: 131
  loop : -1.23 (0.29), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 277 
 HIS   0.009   0.001   HIS A 597 
 PHE   0.014   0.001   PHE A 633 
 TYR   0.012   0.001   TYR A  27 
 ARG   0.002   0.000   ARG B 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02805 (  261)
  hydrogen bonds       : angle       4.11690 (  729)
  covalent geometry    : bond        0.00329 ( 9154)
  covalent geometry    : angle       0.73185 (12368)

*********************** 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
  160 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 123
  time to evaluate  : 1.126 
Fit side-chains
REVERT: B   37 ASP cc_start: 0.8599 (t0) cc_final: 0.8085 (t0)
REVERT: B  106 ASN cc_start: 0.8647 (t0) cc_final: 0.8340 (t0)
REVERT: B  195 MET cc_start: 0.8765 (mpp) cc_final: 0.8493 (mpp)
REVERT: B  201 LYS cc_start: 0.9114 (pmtt) cc_final: 0.8743 (mmmt)
REVERT: B  253 SER cc_start: 0.9333 (m) cc_final: 0.8550 (t)
REVERT: B  339 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7576 (mm-30)
REVERT: A   29 LYS cc_start: 0.9026 (tmmt) cc_final: 0.8754 (tmmt)
REVERT: A   40 TYR cc_start: 0.7504 (t80) cc_final: 0.7201 (t80)
REVERT: A   91 ARG cc_start: 0.7211 (ptt90) cc_final: 0.6879 (ptt-90)
REVERT: A  104 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7778 (ppp80)
REVERT: A  174 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8490 (tp)
REVERT: A  209 GLU cc_start: 0.8650 (tt0) cc_final: 0.8426 (tt0)
REVERT: A  599 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6871 (pt)
REVERT: A  649 CYS cc_start: 0.7665 (p) cc_final: 0.7367 (p)
REVERT: A  656 SER cc_start: 0.8795 (m) cc_final: 0.8472 (p)
REVERT: A  741 LEU cc_start: 0.8386 (tt) cc_final: 0.8100 (tt)
REVERT: A  817 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.5238 (p90)
REVERT: A  825 TRP cc_start: 0.8795 (m100) cc_final: 0.8403 (m100)
REVERT: A  828 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7844 (mp0)
  outliers start: 37
  outliers final: 27
  residues processed: 148
  average time/residue: 0.1937
  time to fit residues: 41.4334
Evaluate side-chains
  149 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
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  258 LEU
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  152 SER
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  394 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  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  612 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  793 ILE
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 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  42 GLN
A 228 GLN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 514 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.131077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.106842 restraints weight = 16231.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110409 restraints weight = 8496.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.112902 restraints weight = 5439.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9154  Z= 0.159
  Angle     :  0.752  12.982  12368  Z= 0.364
  Chirality :  0.047   0.192   1391
  Planarity :  0.004   0.039   1576
  Dihedral  :  6.255  53.029   1221
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.89 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.26), residues: 1114
  helix: -0.65 (0.24), residues: 453
  sheet: -1.49 (0.48), residues: 133
  loop : -1.23 (0.30), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 277 
 HIS   0.009   0.001   HIS A 597 
 PHE   0.019   0.002   PHE A 783 
 TYR   0.013   0.001   TYR A  27 
 ARG   0.002   0.000   ARG B 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02980 (  261)
  hydrogen bonds       : angle       4.21688 (  729)
  covalent geometry    : bond        0.00374 ( 9154)
  covalent geometry    : angle       0.75237 (12368)

********************** 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
  153 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 GLU cc_start: 0.8157 (tt0) cc_final: 0.7850 (tp30)
REVERT: B   37 ASP cc_start: 0.8604 (t0) cc_final: 0.8033 (t0)
REVERT: B  106 ASN cc_start: 0.8806 (t0) cc_final: 0.8195 (t0)
REVERT: B  145 MET cc_start: 0.7364 (ttt) cc_final: 0.7063 (ttt)
REVERT: B  253 SER cc_start: 0.9333 (m) cc_final: 0.8560 (t)
REVERT: B  339 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7605 (mm-30)
REVERT: A   29 LYS cc_start: 0.9053 (tmmt) cc_final: 0.8764 (tmmt)
REVERT: A   40 TYR cc_start: 0.7356 (t80) cc_final: 0.7032 (t80)
REVERT: A   91 ARG cc_start: 0.7104 (ptt90) cc_final: 0.6844 (ptt-90)
REVERT: A  104 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7811 (ppp80)
REVERT: A  174 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8465 (tp)
REVERT: A  209 GLU cc_start: 0.8713 (tt0) cc_final: 0.8447 (tt0)
REVERT: A  599 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.6900 (pt)
REVERT: A  649 CYS cc_start: 0.7665 (p) cc_final: 0.7381 (p)
REVERT: A  656 SER cc_start: 0.8880 (m) cc_final: 0.8520 (p)
REVERT: A  741 LEU cc_start: 0.8488 (tt) cc_final: 0.8246 (tt)
REVERT: A  817 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.5443 (p90)
REVERT: A  825 TRP cc_start: 0.8871 (m100) cc_final: 0.8468 (m100)
REVERT: A  828 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7839 (mp0)
  outliers start: 32
  outliers final: 27
  residues processed: 142
  average time/residue: 0.2011
  time to fit residues: 41.3367
Evaluate side-chains
  143 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
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  258 LEU
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  152 SER
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  394 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  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  612 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  793 ILE
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 24 optimal weight:    0.0670
   chunk 95 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0370
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 87 optimal weight:    0.4980
   chunk 57 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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**
** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 GLN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.131611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.107554 restraints weight = 16080.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111213 restraints weight = 8331.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.113719 restraints weight = 5277.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   9154  Z= 0.220
  Angle     :  1.049  57.299  12368  Z= 0.635
  Chirality :  0.049   0.570   1391
  Planarity :  0.004   0.059   1576
  Dihedral  :  6.211  53.067   1219
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.98 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.42 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.26), residues: 1114
  helix: -0.62 (0.24), residues: 453
  sheet: -1.52 (0.48), residues: 133
  loop : -1.22 (0.30), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 277 
 HIS   0.084   0.003   HIS A 514 
 PHE   0.014   0.002   PHE A 633 
 TYR   0.012   0.001   TYR A  27 
 ARG   0.017   0.000   ARG B 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02984 (  261)
  hydrogen bonds       : angle       4.21522 (  729)
  covalent geometry    : bond        0.00428 ( 9154)
  covalent geometry    : angle       1.04864 (12368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2916.09 seconds
wall clock time: 51 minutes 46.65 seconds (3106.65 seconds total)