Starting phenix.real_space_refine
on Wed Feb  4 22:05:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kmr_62442/02_2026/9kmr_62442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kmr_62442/02_2026/9kmr_62442.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kmr_62442/02_2026/9kmr_62442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kmr_62442/02_2026/9kmr_62442.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kmr_62442/02_2026/9kmr_62442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kmr_62442/02_2026/9kmr_62442.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.030
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       4      5.49       5
     S      65      5.16       5
     C    8264      2.51       5
     N    2211      2.21       5
     O    2485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13029
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5168
          Classifications: {'peptide': 635}
          Link IDs: {'PTRANS': 15, 'TRANS': 619}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5168
          Classifications: {'peptide': 635}
          Link IDs: {'PTRANS': 15, 'TRANS': 619}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2639
          Classifications: {'peptide': 343}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 321}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.90, per 1000 atoms: 0.22
  Number of scatterers: 13029
  At special positions: 0
  Unit cell: (92.1882, 128.716, 134.804, 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      65     16.00
     P       4     15.00
     O    2485      8.00
     N    2211      7.00
     C    8264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 907.4 milliseconds
  

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3068

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 10 sheets defined
      45.8% alpha, 11.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 36
    Processing helix  chain 'A' and resid 42 through 66
      removed outlier: 4.498A  pdb=" N   ARG A  46 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A  64 " --> pdb=" O   ARG A  60 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR A  65 " --> pdb=" O   TYR A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 71
    Processing helix  chain 'A' and resid 99 through 109
      removed outlier: 3.520A  pdb=" N   THR A 109 " --> pdb=" O   ASN A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 122
    Processing helix  chain 'A' and resid 137 through 143
    Processing helix  chain 'A' and resid 192 through 198
      removed outlier: 3.564A  pdb=" N   THR A 195 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   GLU A 196 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 210
      removed outlier: 3.972A  pdb=" N   ILE A 203 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 296
      removed outlier: 3.604A  pdb=" N   THR A 295 " --> pdb=" O   PRO A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 314
      removed outlier: 3.523A  pdb=" N   GLU A 308 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 375
    Processing helix  chain 'A' and resid 376 through 380
    Processing helix  chain 'A' and resid 403 through 425
      removed outlier: 3.783A  pdb=" N   LYS A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A 408 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 449
      removed outlier: 6.449A  pdb=" N   LYS A 440 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ASN A 441 " --> pdb=" O   GLN A 437 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 458
      removed outlier: 4.320A  pdb=" N   GLU A 458 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 481
    Processing helix  chain 'A' and resid 495 through 501
    Processing helix  chain 'A' and resid 504 through 512
      removed outlier: 4.715A  pdb=" N   LEU A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.620A  pdb=" N   CYS A 526 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 575
      removed outlier: 3.634A  pdb=" N   LYS A 555 " --> pdb=" O   ASP A 551 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   ASN A 567 " --> pdb=" O   THR A 563 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   LEU A 568 " --> pdb=" O   LYS A 564 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LYS A 570 " --> pdb=" O   GLU A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 614
    Processing helix  chain 'A' and resid 618 through 625
    Processing helix  chain 'A' and resid 637 through 650
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 677 through 694
      removed outlier: 4.053A  pdb=" N   HIS A 681 " --> pdb=" O   ASP A 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 36
    Processing helix  chain 'B' and resid 42 through 66
      removed outlier: 4.498A  pdb=" N   ARG B  46 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU B  64 " --> pdb=" O   ARG B  60 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR B  65 " --> pdb=" O   TYR B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 71
    Processing helix  chain 'B' and resid 99 through 109
      removed outlier: 3.520A  pdb=" N   THR B 109 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 122
    Processing helix  chain 'B' and resid 137 through 145
    Processing helix  chain 'B' and resid 191 through 198
      removed outlier: 3.564A  pdb=" N   THR B 195 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   GLU B 196 " --> pdb=" O   ASP B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 210
      removed outlier: 3.973A  pdb=" N   ILE B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 296
      removed outlier: 3.603A  pdb=" N   THR B 295 " --> pdb=" O   PRO B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 314
      removed outlier: 3.522A  pdb=" N   GLU B 308 " --> pdb=" O   GLU B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 375
    Processing helix  chain 'B' and resid 376 through 380
    Processing helix  chain 'B' and resid 403 through 425
      removed outlier: 3.783A  pdb=" N   LYS B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL B 408 " --> pdb=" O   LYS B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 449
      removed outlier: 6.449A  pdb=" N   LYS B 440 " --> pdb=" O   GLU B 436 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASN B 441 " --> pdb=" O   GLN B 437 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 458
      removed outlier: 4.327A  pdb=" N   GLU B 458 " --> pdb=" O   LYS B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 481
    Processing helix  chain 'B' and resid 495 through 501
    Processing helix  chain 'B' and resid 504 through 512
      removed outlier: 4.715A  pdb=" N   LEU B 508 " --> pdb=" O   PHE B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 528
      removed outlier: 3.620A  pdb=" N   CYS B 526 " --> pdb=" O   ILE B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 575
      removed outlier: 3.634A  pdb=" N   LYS B 555 " --> pdb=" O   ASP B 551 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ASN B 567 " --> pdb=" O   THR B 563 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   LEU B 568 " --> pdb=" O   LYS B 564 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LYS B 570 " --> pdb=" O   GLU B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 614
    Processing helix  chain 'B' and resid 618 through 625
    Processing helix  chain 'B' and resid 637 through 650
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 677 through 694
      removed outlier: 4.052A  pdb=" N   HIS B 681 " --> pdb=" O   ASP B 677 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 240
    Processing helix  chain 'C' and resid 257 through 262
    Processing helix  chain 'C' and resid 325 through 332
    Processing helix  chain 'C' and resid 335 through 355
    Processing helix  chain 'C' and resid 433 through 447
      removed outlier: 3.564A  pdb=" N   PHE C 447 " --> pdb=" O   ALA C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 451 through 456
    Processing helix  chain 'C' and resid 479 through 490
      removed outlier: 3.845A  pdb=" N   LEU C 490 " --> pdb=" O   VAL C 486 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 499 through 512
    Processing helix  chain 'C' and resid 519 through 523
      removed outlier: 4.265A  pdb=" N   LEU C 522 " --> pdb=" O   LEU C 519 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 527 through 539
      removed outlier: 3.918A  pdb=" N   LEU C 539 " --> pdb=" O   SER C 535 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 539 through 545
      removed outlier: 4.112A  pdb=" N   LEU C 544 " --> pdb=" O   LEU C 540 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 548 through 559
      removed outlier: 3.580A  pdb=" N   THR C 552 " --> pdb=" O   CYS C 548 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 563 through 579
      removed outlier: 4.489A  pdb=" N   CYS C 575 " --> pdb=" O   ALA C 571 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ARG C 578 " --> pdb=" O   LEU C 574 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19
      removed outlier: 3.916A  pdb=" N   GLU A  18 " --> pdb=" O   VAL B 172 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL B 172 " --> pdb=" O   GLU A  18 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LYS B 147 " --> pdb=" O   HIS B 189 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ILE B  78 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU B 285 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 286
      removed outlier: 3.660A  pdb=" N   GLU A 285 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE A  78 " --> pdb=" O   THR A 219 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LYS A 147 " --> pdb=" O   HIS A 189 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 329
      removed outlier: 3.814A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLY A 384 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ILE A 358 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
      removed outlier: 5.483A  pdb=" N   ASP A 369 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   LEU A 360 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 473
      removed outlier: 4.046A  pdb=" N   TYR A 463 " --> pdb=" O   TYR A 517 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   ILE A 488 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 583 through 585
    Processing sheet with id=AA6, first strand: chain 'B' and resid 322 through 329
      removed outlier: 3.814A  pdb=" N   ALA B 322 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLY B 384 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   ILE B 358 " --> pdb=" O   ASP B 369 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   ASP B 369 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   LEU B 360 " --> pdb=" O   ILE B 367 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 472 through 473
      removed outlier: 4.046A  pdb=" N   TYR B 463 " --> pdb=" O   TYR B 517 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   ILE B 488 " --> pdb=" O   VAL B 539 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 583 through 585
    Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 164
      removed outlier: 3.648A  pdb=" N   ILE C 162 " --> pdb=" O   VAL C 170 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL C 170 " --> pdb=" O   ILE C 162 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LYS C 164 " --> pdb=" O   ALA C 168 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA C 168 " --> pdb=" O   LYS C 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 323 through 324
      removed outlier: 4.220A  pdb=" N   CYS C 323 " --> pdb=" O   VAL C 370 " (cutoff:3.500A)

    580 hydrogen bonds defined for protein.
    1605 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: 2.27

  Time building geometry restraints manager: 1.26 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: 3592
        1.33 -     1.45: 2027
        1.45 -     1.57: 7523
        1.57 -     1.69: 6
        1.69 -     1.81: 106
  Bond restraints: 13254
  Sorted by residual:
  bond pdb=" CA  TYR A 435 "
       pdb=" C   TYR A 435 "
    ideal  model  delta    sigma   weight residual
    1.524  1.469  0.055 1.26e-02 6.30e+03 1.91e+01
  bond pdb=" CA  TYR B 431 "
       pdb=" C   TYR B 431 "
    ideal  model  delta    sigma   weight residual
    1.523  1.482  0.041 1.30e-02 5.92e+03 9.90e+00
  bond pdb=" CA  TYR A 431 "
       pdb=" C   TYR A 431 "
    ideal  model  delta    sigma   weight residual
    1.523  1.486  0.037 1.30e-02 5.92e+03 8.30e+00
  bond pdb=" CA  ASP B 427 "
       pdb=" C   ASP B 427 "
    ideal  model  delta    sigma   weight residual
    1.525  1.491  0.034 1.28e-02 6.10e+03 7.05e+00
  bond pdb=" CA  ALA B 141 "
       pdb=" C   ALA B 141 "
    ideal  model  delta    sigma   weight residual
    1.522  1.485  0.037 1.41e-02 5.03e+03 7.02e+00
  ... (remaining 13249 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 17489
        1.94 -     3.87: 304
        3.87 -     5.81: 51
        5.81 -     7.75: 14
        7.75 -     9.68: 1
  Bond angle restraints: 17859
  Sorted by residual:
  angle pdb=" N   TYR A 435 "
        pdb=" CA  TYR A 435 "
        pdb=" C   TYR A 435 "
      ideal   model   delta    sigma   weight residual
     111.14  106.00    5.14 1.08e+00 8.57e-01 2.26e+01
  angle pdb=" N   LEU B 456 "
        pdb=" CA  LEU B 456 "
        pdb=" C   LEU B 456 "
      ideal   model   delta    sigma   weight residual
     113.23  107.62    5.61 1.24e+00 6.50e-01 2.05e+01
  angle pdb=" N   LEU B 460 "
        pdb=" CA  LEU B 460 "
        pdb=" C   LEU B 460 "
      ideal   model   delta    sigma   weight residual
     110.23  116.10   -5.87 1.45e+00 4.76e-01 1.64e+01
  angle pdb=" N   LEU A 460 "
        pdb=" CA  LEU A 460 "
        pdb=" C   LEU A 460 "
      ideal   model   delta    sigma   weight residual
     110.23  115.64   -5.41 1.45e+00 4.76e-01 1.39e+01
  angle pdb=" CA  GLN B  23 "
        pdb=" CB  GLN B  23 "
        pdb=" CG  GLN B  23 "
      ideal   model   delta    sigma   weight residual
     114.10  121.54   -7.44 2.00e+00 2.50e-01 1.38e+01
  ... (remaining 17854 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 6977
       17.69 -    35.38: 829
       35.38 -    53.07: 230
       53.07 -    70.76: 87
       70.76 -    88.45: 42
  Dihedral angle restraints: 8165
    sinusoidal: 3430
      harmonic: 4735
  Sorted by residual:
  dihedral pdb=" C5' ADP B 801 "
           pdb=" O5' ADP B 801 "
           pdb=" PA  ADP B 801 "
           pdb=" O2A ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   23.95  -83.95     1      2.00e+01 2.50e-03 2.15e+01
  dihedral pdb=" C5' ADP A 801 "
           pdb=" O5' ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" O2A ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   23.93  -83.93     1      2.00e+01 2.50e-03 2.15e+01
  dihedral pdb=" CA  CYS B 371 "
           pdb=" C   CYS B 371 "
           pdb=" N   GLU B 372 "
           pdb=" CA  GLU B 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.53  -20.47     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 8162 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1669
       0.057 -    0.113: 302
       0.113 -    0.170: 32
       0.170 -    0.226: 1
       0.226 -    0.283: 1
  Chirality restraints: 2005
  Sorted by residual:
  chirality pdb=" CA  TYR B 142 "
            pdb=" N   TYR B 142 "
            pdb=" C   TYR B 142 "
            pdb=" CB  TYR B 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  TYR A 142 "
            pdb=" N   TYR A 142 "
            pdb=" C   TYR A 142 "
            pdb=" CB  TYR A 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.63e-01
  chirality pdb=" CA  PHE A 170 "
            pdb=" N   PHE A 170 "
            pdb=" C   PHE A 170 "
            pdb=" CB  PHE A 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.31e-01
  ... (remaining 2002 not shown)

  Planarity restraints: 2268
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 139 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.78e+00
        pdb=" C   TYR B 139 "    0.034 2.00e-02 2.50e+03
        pdb=" O   TYR B 139 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER B 140 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 373 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.74e+00
        pdb=" N   PRO C 374 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO C 374 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 374 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 160 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.84e+00
        pdb=" C   TYR B 160 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   TYR B 160 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA B 161 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2265 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2333
        2.76 -     3.29: 13500
        3.29 -     3.83: 21433
        3.83 -     4.36: 24972
        4.36 -     4.90: 41935
  Nonbonded interactions: 104173
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 105 "
            pdb=" OG1 THR A 109 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   ASN B 105 "
            pdb=" OG1 THR B 109 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   THR C 174 "
            pdb=" OG1 THR C 174 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   ALA C 541 "
            pdb=" OG1 THR C 545 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   ARG A  60 "
            pdb=" OG  SER A  63 "
     model   vdw
     2.245 3.040
  ... (remaining 104168 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.650
  Find NCS groups from input model:        0.140
  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:8.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
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      :  0.004   0.055  13254  Z= 0.226
  Angle     :  0.660   9.683  17859  Z= 0.379
  Chirality :  0.043   0.283   2005
  Planarity :  0.003   0.048   2268
  Dihedral  : 18.442  88.450   5097
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  8.64 %
    Allowed  : 24.88 %
    Favored  : 66.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.19), residues: 1599
  helix: -0.85 (0.19), residues: 640
  sheet: -1.25 (0.32), residues: 250
  loop : -2.41 (0.21), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 383 
 TYR   0.019   0.001   TYR B 142 
 PHE   0.024   0.001   PHE A 170 
 TRP   0.019   0.001   TRP B 162 
 HIS   0.003   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (13254)
  covalent geometry    : angle       0.65954 (17859)
  hydrogen bonds       : bond        0.18056 (  580)
  hydrogen bonds       : angle       7.24444 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 124
    poor density    : 73
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8120 (tm-30)
REVERT: A  205 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8633 (pp20)
REVERT: A  377 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8514 (tm-30)
REVERT: B   25 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8305 (tm-30)
REVERT: B  102 ASP cc_start: 0.9158 (t0) cc_final: 0.8927 (t0)
REVERT: B  356 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.7050 (p0)
REVERT: B  467 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8729 (p)
REVERT: B  607 MET cc_start: 0.9212 (tpt) cc_final: 0.8929 (tpt)
REVERT: B  608 GLU cc_start: 0.9348 (tm-30) cc_final: 0.8764 (tm-30)
REVERT: C  266 LYS cc_start: 0.7140 (mttt) cc_final: 0.6848 (mmmm)
REVERT: C  318 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6770 (tmm)
REVERT: C  514 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7470 (mp0)
  outliers start: 124
  outliers final: 44
  residues processed: 188
  average time/residue: 0.4331
  time to fit residues: 90.0423
Evaluate side-chains
  107 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 57
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  165 SER
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  193 ASP
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  356 ASN
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  450 SER
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  467 SER
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  495 THR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  604 THR
Chi-restraints excluded: chain B residue  619 ASN
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  318 MET
Chi-restraints excluded: chain C residue  370 VAL
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  435 ASP
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  514 GLU
Chi-restraints excluded: chain C residue  576 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A 159 GLN
A 212 GLN
A 297 ASN
** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 ASN
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN
A 441 ASN
A 485 GLN
A 614 GLN
A 645 GLN
A 683 ASN
B  35 ASN
B 159 GLN
B 212 GLN
** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 441 ASN
B 485 GLN
B 614 GLN
B 645 GLN
B 683 ASN
C 332 ASN
C 345 GLN
C 456 GLN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.057579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.045720 restraints weight = 49946.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.2563 rms_B_bonded: 3.42
r_work: 0.2435 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13254  Z= 0.225
  Angle     :  0.661   8.297  17859  Z= 0.337
  Chirality :  0.044   0.164   2005
  Planarity :  0.004   0.041   2268
  Dihedral  :  8.716  97.900   1832
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 26.27 %
    Favored  : 67.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.21), residues: 1599
  helix: -0.07 (0.20), residues: 651
  sheet: -0.50 (0.34), residues: 250
  loop : -1.94 (0.22), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 352 
 TYR   0.017   0.001   TYR B 431 
 PHE   0.014   0.001   PHE B 339 
 TRP   0.030   0.002   TRP A 162 
 HIS   0.006   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (13254)
  covalent geometry    : angle       0.66122 (17859)
  hydrogen bonds       : bond        0.04835 (  580)
  hydrogen bonds       : angle       5.34668 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 56
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8141 (tm-30)
REVERT: A  119 MET cc_start: 0.9534 (tpp) cc_final: 0.9236 (tpt)
REVERT: A  205 GLU cc_start: 0.9343 (tm-30) cc_final: 0.9009 (tm-30)
REVERT: A  377 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8759 (tm-30)
REVERT: A  607 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9278 (tpt)
REVERT: A  611 MET cc_start: 0.9252 (mtm) cc_final: 0.9034 (mtm)
REVERT: B   25 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8251 (tm-30)
REVERT: B  102 ASP cc_start: 0.9384 (t0) cc_final: 0.9121 (t0)
REVERT: B  220 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8265 (tt)
REVERT: B  368 MET cc_start: 0.9508 (ttp) cc_final: 0.9303 (ptm)
REVERT: B  470 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8400 (pp20)
REVERT: B  471 MET cc_start: 0.9444 (mtt) cc_final: 0.9029 (mtt)
REVERT: B  528 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8712 (pt0)
REVERT: B  608 GLU cc_start: 0.9516 (tm-30) cc_final: 0.9031 (tm-30)
REVERT: C  266 LYS cc_start: 0.7003 (mttt) cc_final: 0.6736 (mmmm)
REVERT: C  318 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7330 (tmm)
REVERT: C  514 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7256 (pm20)
  outliers start: 91
  outliers final: 49
  residues processed: 143
  average time/residue: 0.4095
  time to fit residues: 65.6324
Evaluate side-chains
  114 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 57
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  470 GLU
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  528 GLN
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  619 ASN
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  294 ASP
Chi-restraints excluded: chain C residue  318 MET
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  435 ASP
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  514 GLU
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  549 CYS
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 137 optimal weight:   10.0000
   chunk 94 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 129 optimal weight:    6.9990
   chunk 149 optimal weight:    5.9990
   chunk 148 optimal weight:    6.9990
   chunk 117 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 320 HIS
** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 ASN
** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.057588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.045665 restraints weight = 50572.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.2559 rms_B_bonded: 3.44
r_work: 0.2433 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  13254  Z= 0.212
  Angle     :  0.631  10.689  17859  Z= 0.318
  Chirality :  0.043   0.195   2005
  Planarity :  0.004   0.048   2268
  Dihedral  :  8.058  96.650   1809
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 26.48 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.21), residues: 1599
  helix:  0.30 (0.21), residues: 647
  sheet: -0.21 (0.35), residues: 250
  loop : -1.75 (0.22), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 343 
 TYR   0.017   0.001   TYR B 431 
 PHE   0.011   0.001   PHE B 339 
 TRP   0.025   0.002   TRP A 162 
 HIS   0.004   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (13254)
  covalent geometry    : angle       0.63101 (17859)
  hydrogen bonds       : bond        0.04468 (  580)
  hydrogen bonds       : angle       5.09282 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 59
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7957 (tm-30)
REVERT: A  119 MET cc_start: 0.9573 (tpp) cc_final: 0.9289 (tpt)
REVERT: A  205 GLU cc_start: 0.9342 (tm-30) cc_final: 0.9039 (tm-30)
REVERT: A  377 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8722 (tm-30)
REVERT: A  607 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.9163 (tpp)
REVERT: B   25 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8472 (tm-30)
REVERT: B   84 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.8968 (mtpp)
REVERT: B  102 ASP cc_start: 0.9388 (t0) cc_final: 0.9108 (t0)
REVERT: B  220 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8379 (tt)
REVERT: B  352 ARG cc_start: 0.9217 (mmp80) cc_final: 0.8995 (mmp80)
REVERT: B  423 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8720 (mp0)
REVERT: B  470 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8371 (pp20)
REVERT: B  528 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8876 (pt0)
REVERT: B  608 GLU cc_start: 0.9544 (tm-30) cc_final: 0.8986 (tm-30)
REVERT: C  266 LYS cc_start: 0.7062 (mttt) cc_final: 0.6766 (mmmm)
REVERT: C  318 MET cc_start: 0.7511 (ttp) cc_final: 0.7294 (tmm)
REVERT: C  456 GLN cc_start: 0.5588 (OUTLIER) cc_final: 0.4701 (pp30)
REVERT: C  514 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7200 (pm20)
  outliers start: 91
  outliers final: 48
  residues processed: 146
  average time/residue: 0.4486
  time to fit residues: 73.2792
Evaluate side-chains
  114 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 57
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   84 LYS
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  470 GLU
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  528 GLN
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  595 CYS
Chi-restraints excluded: chain B residue  610 ILE
Chi-restraints excluded: chain B residue  619 ASN
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  220 MET
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  456 GLN
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  514 GLU
Chi-restraints excluded: chain C residue  549 CYS
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 134 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 120 optimal weight:    0.9980
   chunk 156 optimal weight:    0.9990
   chunk 153 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 140 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 138 optimal weight:    7.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.057945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.046025 restraints weight = 49989.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.2564 rms_B_bonded: 3.42
r_work: 0.2440 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13254  Z= 0.187
  Angle     :  0.603   8.983  17859  Z= 0.303
  Chirality :  0.042   0.171   2005
  Planarity :  0.003   0.039   2268
  Dihedral  :  7.573  97.377   1799
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 25.92 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.21), residues: 1599
  helix:  0.50 (0.21), residues: 648
  sheet: -0.04 (0.35), residues: 250
  loop : -1.64 (0.23), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 343 
 TYR   0.016   0.001   TYR B 431 
 PHE   0.011   0.001   PHE A 339 
 TRP   0.023   0.002   TRP A 162 
 HIS   0.004   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (13254)
  covalent geometry    : angle       0.60318 (17859)
  hydrogen bonds       : bond        0.04090 (  580)
  hydrogen bonds       : angle       4.88815 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 58
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8051 (tm-30)
REVERT: A  119 MET cc_start: 0.9587 (tpp) cc_final: 0.9217 (tpt)
REVERT: A  205 GLU cc_start: 0.9328 (tm-30) cc_final: 0.9025 (tm-30)
REVERT: A  377 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8703 (tm-30)
REVERT: A  607 MET cc_start: 0.9585 (tpt) cc_final: 0.9361 (tpt)
REVERT: B   23 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.9015 (mp10)
REVERT: B   84 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.8979 (mtpp)
REVERT: B  102 ASP cc_start: 0.9344 (t0) cc_final: 0.9137 (t0)
REVERT: B  220 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8371 (tt)
REVERT: B  368 MET cc_start: 0.9551 (ttp) cc_final: 0.9349 (ptm)
REVERT: B  423 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8703 (mp0)
REVERT: B  467 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.8779 (p)
REVERT: B  608 GLU cc_start: 0.9527 (tm-30) cc_final: 0.9003 (tm-30)
REVERT: C  266 LYS cc_start: 0.7068 (mttt) cc_final: 0.6778 (mmmm)
REVERT: C  456 GLN cc_start: 0.5529 (OUTLIER) cc_final: 0.4673 (pp30)
REVERT: C  514 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7347 (pm20)
  outliers start: 98
  outliers final: 52
  residues processed: 152
  average time/residue: 0.4097
  time to fit residues: 69.5592
Evaluate side-chains
  117 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 58
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   84 LYS
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  467 SER
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  619 ASN
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  456 GLN
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  514 GLU
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  549 CYS
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 150 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 125 optimal weight:    0.6980
   chunk 123 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 91 optimal weight:    0.3980
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
B  79 ASN
B 297 ASN
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.059033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.046991 restraints weight = 49390.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2598 rms_B_bonded: 3.42
r_work: 0.2475 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  13254  Z= 0.125
  Angle     :  0.586   8.087  17859  Z= 0.292
  Chirality :  0.041   0.178   2005
  Planarity :  0.003   0.038   2268
  Dihedral  :  7.044  93.213   1792
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 28.01 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.22), residues: 1599
  helix:  0.66 (0.21), residues: 649
  sheet:  0.00 (0.36), residues: 250
  loop : -1.53 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 343 
 TYR   0.014   0.001   TYR B 431 
 PHE   0.011   0.001   PHE A 339 
 TRP   0.020   0.001   TRP A 162 
 HIS   0.003   0.001   HIS B 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13254)
  covalent geometry    : angle       0.58625 (17859)
  hydrogen bonds       : bond        0.03761 (  580)
  hydrogen bonds       : angle       4.69706 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 59
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.9590 (tpp) cc_final: 0.9304 (tpt)
REVERT: A  205 GLU cc_start: 0.9320 (tm-30) cc_final: 0.9009 (tm-30)
REVERT: A  377 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8773 (tm-30)
REVERT: A  607 MET cc_start: 0.9568 (OUTLIER) cc_final: 0.8976 (tpp)
REVERT: B   23 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.9016 (mp10)
REVERT: B   84 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.9003 (mtpp)
REVERT: B  102 ASP cc_start: 0.9367 (t0) cc_final: 0.9149 (t0)
REVERT: B  368 MET cc_start: 0.9546 (ttp) cc_final: 0.9322 (ptm)
REVERT: B  423 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8652 (mp0)
REVERT: B  467 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.8788 (p)
REVERT: B  608 GLU cc_start: 0.9469 (tm-30) cc_final: 0.8963 (tm-30)
REVERT: B  624 TYR cc_start: 0.8746 (m-10) cc_final: 0.8468 (m-80)
REVERT: C  266 LYS cc_start: 0.7130 (mttt) cc_final: 0.6854 (mmmm)
REVERT: C  456 GLN cc_start: 0.5462 (OUTLIER) cc_final: 0.4582 (pp30)
  outliers start: 69
  outliers final: 43
  residues processed: 124
  average time/residue: 0.4295
  time to fit residues: 59.1537
Evaluate side-chains
  106 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 58
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   84 LYS
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  467 SER
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  619 ASN
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  456 GLN
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 136 optimal weight:    0.0370
   chunk 69 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 123 optimal weight:    0.6980
   chunk 152 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9980
   chunk 159 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 120 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.059918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.047750 restraints weight = 49322.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.2610 rms_B_bonded: 3.43
r_work: 0.2496 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13254  Z= 0.102
  Angle     :  0.577   9.626  17859  Z= 0.286
  Chirality :  0.041   0.174   2005
  Planarity :  0.003   0.039   2268
  Dihedral  :  6.635  90.383   1786
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 28.99 %
    Favored  : 66.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.22), residues: 1599
  helix:  0.70 (0.21), residues: 649
  sheet:  0.04 (0.36), residues: 250
  loop : -1.46 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 343 
 TYR   0.012   0.001   TYR B 431 
 PHE   0.012   0.001   PHE A 339 
 TRP   0.012   0.001   TRP C 437 
 HIS   0.003   0.001   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (13254)
  covalent geometry    : angle       0.57658 (17859)
  hydrogen bonds       : bond        0.03517 (  580)
  hydrogen bonds       : angle       4.54093 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 61
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.9599 (tpp) cc_final: 0.9336 (tpt)
REVERT: A  205 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9012 (tm-30)
REVERT: A  377 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8814 (tm-30)
REVERT: A  607 MET cc_start: 0.9544 (OUTLIER) cc_final: 0.9191 (tpp)
REVERT: B   23 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.9042 (mp10)
REVERT: B   84 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.8995 (mtpp)
REVERT: B  123 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7871 (pp30)
REVERT: B  205 GLU cc_start: 0.9391 (tm-30) cc_final: 0.9169 (tm-30)
REVERT: B  368 MET cc_start: 0.9529 (ttp) cc_final: 0.9296 (ptm)
REVERT: B  423 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8662 (mp0)
REVERT: B  608 GLU cc_start: 0.9465 (tm-30) cc_final: 0.8913 (tm-30)
REVERT: C  266 LYS cc_start: 0.7253 (mttt) cc_final: 0.6984 (mmmm)
  outliers start: 59
  outliers final: 39
  residues processed: 115
  average time/residue: 0.4752
  time to fit residues: 60.3939
Evaluate side-chains
  101 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 58
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   84 LYS
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  123 GLN
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  619 ASN
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 85 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 126 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 61 optimal weight:    7.9990
   chunk 81 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 121 optimal weight:    3.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.058657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.046571 restraints weight = 50308.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2572 rms_B_bonded: 3.39
r_work: 0.2460 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13254  Z= 0.186
  Angle     :  0.602   7.564  17859  Z= 0.301
  Chirality :  0.042   0.159   2005
  Planarity :  0.003   0.037   2268
  Dihedral  :  6.620  92.856   1785
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 28.01 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.22), residues: 1599
  helix:  0.73 (0.21), residues: 649
  sheet: -0.08 (0.35), residues: 260
  loop : -1.43 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 352 
 TYR   0.036   0.001   TYR B 624 
 PHE   0.011   0.001   PHE A 339 
 TRP   0.012   0.001   TRP B 603 
 HIS   0.003   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (13254)
  covalent geometry    : angle       0.60176 (17859)
  hydrogen bonds       : bond        0.03755 (  580)
  hydrogen bonds       : angle       4.64265 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 57
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.9596 (tpp) cc_final: 0.9344 (tpt)
REVERT: A  205 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8994 (tm-30)
REVERT: A  228 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7828 (pttp)
REVERT: A  377 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8836 (tm-30)
REVERT: A  520 GLU cc_start: 0.9064 (mp0) cc_final: 0.8734 (mp0)
REVERT: B   23 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9059 (mp10)
REVERT: B   84 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9009 (mtpp)
REVERT: B  123 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7760 (pp30)
REVERT: B  352 ARG cc_start: 0.9172 (mmm160) cc_final: 0.8841 (mmp80)
REVERT: B  368 MET cc_start: 0.9521 (ttp) cc_final: 0.9272 (ptm)
REVERT: B  608 GLU cc_start: 0.9483 (tm-30) cc_final: 0.8918 (tm-30)
REVERT: C  266 LYS cc_start: 0.7217 (mttt) cc_final: 0.6912 (mmmm)
REVERT: C  456 GLN cc_start: 0.5456 (OUTLIER) cc_final: 0.4615 (pp30)
REVERT: C  514 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7399 (pm20)
  outliers start: 80
  outliers final: 57
  residues processed: 134
  average time/residue: 0.4953
  time to fit residues: 73.4156
Evaluate side-chains
  121 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 58
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   84 LYS
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  123 GLN
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  446 ILE
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  456 GLN
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  514 GLU
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  549 CYS
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.058086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.046072 restraints weight = 49977.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.2553 rms_B_bonded: 3.36
r_work: 0.2441 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13254  Z= 0.220
  Angle     :  0.631  11.215  17859  Z= 0.317
  Chirality :  0.042   0.182   2005
  Planarity :  0.003   0.037   2268
  Dihedral  :  6.639  94.862   1783
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 28.71 %
    Favored  : 65.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.22), residues: 1599
  helix:  0.68 (0.21), residues: 651
  sheet: -0.06 (0.35), residues: 260
  loop : -1.48 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 352 
 TYR   0.017   0.001   TYR B 431 
 PHE   0.010   0.001   PHE B 339 
 TRP   0.011   0.001   TRP C 437 
 HIS   0.004   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (13254)
  covalent geometry    : angle       0.63117 (17859)
  hydrogen bonds       : bond        0.03942 (  580)
  hydrogen bonds       : angle       4.74503 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 57
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.9598 (tpp) cc_final: 0.9345 (tpt)
REVERT: A  205 GLU cc_start: 0.9310 (tm-30) cc_final: 0.9006 (tm-30)
REVERT: A  228 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7783 (pttp)
REVERT: A  377 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8795 (tm-30)
REVERT: A  520 GLU cc_start: 0.9070 (mp0) cc_final: 0.8749 (mp0)
REVERT: B   23 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.9053 (mp10)
REVERT: B   84 LYS cc_start: 0.9493 (OUTLIER) cc_final: 0.8996 (mtpp)
REVERT: B  123 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8178 (pp30)
REVERT: B  368 MET cc_start: 0.9504 (ttp) cc_final: 0.9290 (ptm)
REVERT: B  607 MET cc_start: 0.9122 (tpt) cc_final: 0.8769 (tpp)
REVERT: C  318 MET cc_start: 0.6518 (ttp) cc_final: 0.4996 (ttm)
REVERT: C  456 GLN cc_start: 0.5520 (OUTLIER) cc_final: 0.4672 (pp30)
REVERT: C  514 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7405 (pm20)
  outliers start: 76
  outliers final: 59
  residues processed: 130
  average time/residue: 0.4499
  time to fit residues: 64.9138
Evaluate side-chains
  122 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 57
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   68 SER
Chi-restraints excluded: chain B residue   84 LYS
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  123 GLN
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  446 ILE
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  456 GLN
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  514 GLU
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  549 CYS
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   chunk 123 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 138 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.059122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.047082 restraints weight = 49813.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.2587 rms_B_bonded: 3.37
r_work: 0.2476 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13254  Z= 0.134
  Angle     :  0.597  11.265  17859  Z= 0.298
  Chirality :  0.041   0.163   2005
  Planarity :  0.003   0.038   2268
  Dihedral  :  6.540  93.896   1783
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 29.27 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.22), residues: 1599
  helix:  0.72 (0.21), residues: 651
  sheet: -0.03 (0.35), residues: 260
  loop : -1.38 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 609 
 TYR   0.014   0.001   TYR B 431 
 PHE   0.010   0.001   PHE A 339 
 TRP   0.014   0.001   TRP B 603 
 HIS   0.003   0.001   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (13254)
  covalent geometry    : angle       0.59667 (17859)
  hydrogen bonds       : bond        0.03691 (  580)
  hydrogen bonds       : angle       4.61281 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 59
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.9601 (tpp) cc_final: 0.9302 (tpt)
REVERT: A  205 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8986 (tm-30)
REVERT: A  520 GLU cc_start: 0.9077 (mp0) cc_final: 0.8777 (mp0)
REVERT: A  607 MET cc_start: 0.9347 (tpt) cc_final: 0.9120 (tpp)
REVERT: B   23 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.9056 (mp10)
REVERT: B   84 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.8999 (mtpp)
REVERT: B  123 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8232 (pp30)
REVERT: B  368 MET cc_start: 0.9508 (ttp) cc_final: 0.9299 (ptm)
  outliers start: 67
  outliers final: 54
  residues processed: 122
  average time/residue: 0.4502
  time to fit residues: 60.8784
Evaluate side-chains
  114 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 57
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   68 SER
Chi-restraints excluded: chain B residue   84 LYS
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  123 GLN
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 114 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 139 optimal weight:    6.9990
   chunk 124 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 528 GLN
C 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.058803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.046726 restraints weight = 50463.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.2578 rms_B_bonded: 3.40
r_work: 0.2465 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13254  Z= 0.163
  Angle     :  0.613  10.095  17859  Z= 0.307
  Chirality :  0.041   0.178   2005
  Planarity :  0.004   0.098   2268
  Dihedral  :  6.512  94.444   1783
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 29.48 %
    Favored  : 65.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.22), residues: 1599
  helix:  0.73 (0.21), residues: 650
  sheet: -0.01 (0.35), residues: 260
  loop : -1.40 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.000   ARG B 352 
 TYR   0.016   0.001   TYR B 431 
 PHE   0.011   0.001   PHE B 339 
 TRP   0.011   0.001   TRP C 437 
 HIS   0.004   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (13254)
  covalent geometry    : angle       0.61337 (17859)
  hydrogen bonds       : bond        0.03715 (  580)
  hydrogen bonds       : angle       4.61159 ( 1605)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 57
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.9566 (tpp) cc_final: 0.9285 (tpt)
REVERT: A  205 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8998 (tm-30)
REVERT: A  228 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7815 (pttp)
REVERT: A  520 GLU cc_start: 0.9085 (mp0) cc_final: 0.8788 (mp0)
REVERT: B   23 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.9055 (mp10)
REVERT: B   84 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9006 (mtpp)
REVERT: B  123 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8271 (pp30)
REVERT: B  352 ARG cc_start: 0.9454 (mmm160) cc_final: 0.9170 (mmp80)
REVERT: C  514 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7419 (pm20)
  outliers start: 65
  outliers final: 55
  residues processed: 120
  average time/residue: 0.5399
  time to fit residues: 71.7881
Evaluate side-chains
  117 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 57
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  619 ASN
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   68 SER
Chi-restraints excluded: chain B residue   84 LYS
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  123 GLN
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  464 THR
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  158 ILE
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  471 LEU
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  514 GLU
Chi-restraints excluded: chain C residue  564 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 49 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 132 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 85 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.058691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.046658 restraints weight = 50165.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.2582 rms_B_bonded: 3.44
r_work: 0.2473 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13254  Z= 0.170
  Angle     :  0.618  10.477  17859  Z= 0.309
  Chirality :  0.042   0.171   2005
  Planarity :  0.004   0.081   2268
  Dihedral  :  6.487  94.516   1783
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 29.48 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.22), residues: 1599
  helix:  0.72 (0.21), residues: 650
  sheet:  0.03 (0.35), residues: 260
  loop : -1.40 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.000   ARG B 352 
 TYR   0.016   0.001   TYR B 431 
 PHE   0.010   0.001   PHE B 339 
 TRP   0.011   0.001   TRP C 437 
 HIS   0.005   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (13254)
  covalent geometry    : angle       0.61769 (17859)
  hydrogen bonds       : bond        0.03760 (  580)
  hydrogen bonds       : angle       4.61773 ( 1605)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3188.29 seconds
wall clock time: 55 minutes 32.55 seconds (3332.55 seconds total)