Starting phenix.real_space_refine
on Fri Jun 13 23:22:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z8x_39850/06_2025/8z8x_39850.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z8x_39850/06_2025/8z8x_39850.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z8x_39850/06_2025/8z8x_39850.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z8x_39850/06_2025/8z8x_39850.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z8x_39850/06_2025/8z8x_39850.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z8x_39850/06_2025/8z8x_39850.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic.
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      36      5.49       5
     S      82      5.16       5
     C    9238      2.51       5
     N    2559      2.21       5
     O    2853      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14768
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 620, 5014
          Classifications: {'peptide': 620}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 31, 'TRANS': 588}
    Chain: "B"
      Number of atoms: 5710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 710, 5710
          Classifications: {'peptide': 710}
          Link IDs: {'PTRANS': 39, 'TRANS': 670}
    Chain: "C"
      Number of atoms: 3273
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 400, 3253
          Classifications: {'peptide': 400}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 372}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 400, 3253
          Classifications: {'peptide': 400}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 372}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3317
    Chain: "D"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 388
          Classifications: {'RNA': 18}
          Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 3, 'rna3p': 14}
    Chain: "E"
      Number of atoms: 351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 351
          Classifications: {'RNA': 17}
          Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 7, 'rna3p': 9}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'G2P': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AILE C 330 " occ=0.68
      ... (14 atoms not shown)
      pdb=" CD1BILE C 330 " occ=0.32
    residue:
      pdb=" N  ASER C 336 " occ=0.72
      ... (10 atoms not shown)
      pdb=" OG BSER C 336 " occ=0.28
    residue:
      pdb=" N  ASER C 384 " occ=0.56
      ... (10 atoms not shown)
      pdb=" OG BSER C 384 " occ=0.44
  Time building chain proxies: 10.06, per 1000 atoms: 0.68
  Number of scatterers: 14768
  At special positions: 0
  Unit cell: (108.714, 105.12, 138.363, 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      82     16.00
     P      36     15.00
     O    2853      8.00
     N    2559      7.00
     C    9238      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: 3.49
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3308

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 21 sheets defined
      46.5% alpha, 11.8% beta
      8 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 5.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 17
    Processing helix  chain 'A' and resid 27 through 45
    Processing helix  chain 'A' and resid 64 through 75
    Processing helix  chain 'A' and resid 126 through 132
    Processing helix  chain 'A' and resid 134 through 155
      removed outlier: 3.529A  pdb=" N   TRP A 151 " --> pdb=" O   ARG A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 167
      removed outlier: 3.830A  pdb=" N   VAL A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 184
      removed outlier: 3.515A  pdb=" N   LEU A 182 " --> pdb=" O   THR A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 187
      No H-bonds generated for 'chain 'A' and resid 185 through 187'
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.722A  pdb=" N   TRP A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 287
      removed outlier: 3.542A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 304 through 316
      removed outlier: 3.693A  pdb=" N   GLU A 308 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 344
      removed outlier: 4.354A  pdb=" N   GLU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 4.368A  pdb=" N   ARG A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 400
      removed outlier: 3.686A  pdb=" N   THR A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 493
      removed outlier: 3.651A  pdb=" N   ASN A 493 " --> pdb=" O   TYR A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 497
    Processing helix  chain 'A' and resid 498 through 517
    Processing helix  chain 'A' and resid 540 through 557
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 4.465A  pdb=" N   ARG A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   LEU A 572 " --> pdb=" O   ASN A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
      removed outlier: 3.502A  pdb=" N   GLU A 599 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 616
    Processing helix  chain 'B' and resid 11 through 20
      removed outlier: 4.310A  pdb=" N   GLU B  17 " --> pdb=" O   THR B  14 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TYR B  20 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 47
      Proline residue:  B  44  - end of helix
    Processing helix  chain 'B' and resid 53 through 58
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 94
    Processing helix  chain 'B' and resid 95 through 109
    Processing helix  chain 'B' and resid 110 through 113
    Processing helix  chain 'B' and resid 114 through 121
      removed outlier: 3.552A  pdb=" N   GLY B 121 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 151
    Processing helix  chain 'B' and resid 157 through 169
      removed outlier: 3.737A  pdb=" N   MET B 169 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 250 through 266
    Processing helix  chain 'B' and resid 274 through 278
      removed outlier: 3.873A  pdb=" N   GLU B 278 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 287
      removed outlier: 3.933A  pdb=" N   LYS B 283 " --> pdb=" O   GLU B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 326
      removed outlier: 3.920A  pdb=" N   MET B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 336
      removed outlier: 3.682A  pdb=" N   MET B 332 " --> pdb=" O   PRO B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 344
    Processing helix  chain 'B' and resid 374 through 378
      removed outlier: 3.701A  pdb=" N   VAL B 377 " --> pdb=" O   ASP B 374 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ARG B 378 " --> pdb=" O   ASP B 375 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 374 through 378'
    Processing helix  chain 'B' and resid 397 through 409
    Processing helix  chain 'B' and resid 432 through 450
      removed outlier: 3.568A  pdb=" N   VAL B 450 " --> pdb=" O   THR B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 459
      removed outlier: 3.904A  pdb=" N   CYS B 459 " --> pdb=" O   PRO B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 490
      Proline residue:  B 488  - end of helix
    Processing helix  chain 'B' and resid 496 through 514
    Processing helix  chain 'B' and resid 518 through 537
    Processing helix  chain 'B' and resid 543 through 551
    Processing helix  chain 'B' and resid 558 through 562
    Processing helix  chain 'B' and resid 568 through 572
      removed outlier: 4.005A  pdb=" N   MET B 572 " --> pdb=" O   PHE B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 583
    Processing helix  chain 'B' and resid 587 through 595
      removed outlier: 3.599A  pdb=" N   ARG B 593 " --> pdb=" O   GLU B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 643 through 645
      No H-bonds generated for 'chain 'B' and resid 643 through 645'
    Processing helix  chain 'B' and resid 646 through 662
      removed outlier: 4.205A  pdb=" N   ASN B 650 " --> pdb=" O   LYS B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 695
    Processing helix  chain 'B' and resid 698 through 709
    Processing helix  chain 'C' and resid 11 through 27
    Processing helix  chain 'C' and resid 27 through 32
    Processing helix  chain 'C' and resid 33 through 36
      removed outlier: 6.284A  pdb=" N   THR C  36 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 33 through 36'
    Processing helix  chain 'C' and resid 37 through 42
    Processing helix  chain 'C' and resid 52 through 55
      removed outlier: 3.840A  pdb=" N   MET C  55 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 52 through 55'
    Processing helix  chain 'C' and resid 56 through 61
    Processing helix  chain 'C' and resid 102 through 110
      removed outlier: 3.871A  pdb=" N   LYS C 109 " --> pdb=" O   ASP C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 123
    Processing helix  chain 'C' and resid 123 through 134
    Processing helix  chain 'C' and resid 166 through 176
    Processing helix  chain 'C' and resid 181 through 187
    Processing helix  chain 'C' and resid 192 through 201
    Processing helix  chain 'C' and resid 202 through 204
      No H-bonds generated for 'chain 'C' and resid 202 through 204'
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.932A  pdb=" N   HIS C 214 " --> pdb=" O   GLU C 210 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE C 215 " --> pdb=" O   SER C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 245
      removed outlier: 3.755A  pdb=" N   CYS C 245 " --> pdb=" O   ALA C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 413
      removed outlier: 3.591A  pdb=" N   LEU C 407 " --> pdb=" O   LEU C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 431 through 446
    Processing helix  chain 'C' and resid 447 through 455
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59
    Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100
      removed outlier: 3.670A  pdb=" N   PHE A 119 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211
    Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242
      removed outlier: 7.674A  pdb=" N   TRP A 426 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU A 475 " --> pdb=" O   MET A 451 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 242
      removed outlier: 5.566A  pdb=" N   PHE A 425 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   THR A 416 " --> pdb=" O   PHE A 425 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY A 427 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323
      removed outlier: 3.954A  pdb=" N   LEU B 360 " --> pdb=" O   LYS B 357 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 530
    Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 125
    Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 175
    Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 180
    Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 191
      removed outlier: 4.894A  pdb=" N   GLN B 188 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 242 through 246
      removed outlier: 7.450A  pdb=" N   LEU B 226 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 467 through 470
      removed outlier: 4.418A  pdb=" N   PHE B 474 " --> pdb=" O   VAL B 480 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 608 through 611
      removed outlier: 3.701A  pdb=" N   MET B 609 " --> pdb=" O   MET B 621 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 67 through 69
      removed outlier: 5.041A  pdb=" N   ARG C  98 " --> pdb=" O   ASP C  86 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AB9, first strand: chain 'C' and resid 141 through 143
    Processing sheet with id=AC1, first strand: chain 'C' and resid 149 through 154
    Processing sheet with id=AC2, first strand: chain 'C' and resid 339 through 340
      removed outlier: 3.539A  pdb=" N   ASN C 339 " --> pdb=" O   LYS C 371 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS C 394 " --> pdb=" O   TYR C 382 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   GLU C 392 " --> pdb=" O  ASER C 384 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   THR C 386 " --> pdb=" O   ILE C 390 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   ILE C 390 " --> pdb=" O   THR C 386 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   THR C 482 " --> pdb=" O   ASP C 391 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ILE C 393 " --> pdb=" O   THR C 482 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 345 through 352

    625 hydrogen bonds defined for protein.
    1723 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      21 hydrogen bonds
      42 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 5.11

  Time building geometry restraints manager: 4.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4723
        1.34 -     1.47: 3681
        1.47 -     1.60: 6603
        1.60 -     1.72: 36
        1.72 -     1.85: 135
  Bond restraints: 15178
  Sorted by residual:
  bond pdb=" N   GLY C 455 "
       pdb=" CA  GLY C 455 "
    ideal  model  delta    sigma   weight residual
    1.449  1.471 -0.021 1.45e-02 4.76e+03 2.20e+00
  bond pdb=" C3'   A E   2 "
       pdb=" O3'   A E   2 "
    ideal  model  delta    sigma   weight residual
    1.427  1.444 -0.017 1.50e-02 4.44e+03 1.34e+00
  bond pdb=" CG1 ILE A 393 "
       pdb=" CD1 ILE A 393 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.27e+00
  bond pdb=" CB  PRO B 644 "
       pdb=" CG  PRO B 644 "
    ideal  model  delta    sigma   weight residual
    1.492  1.545 -0.053 5.00e-02 4.00e+02 1.12e+00
  bond pdb=" CB  GLU B 263 "
       pdb=" CG  GLU B 263 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.10e+00
  ... (remaining 15173 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 20288
        1.88 -     3.75: 386
        3.75 -     5.63: 38
        5.63 -     7.51: 8
        7.51 -     9.38: 2
  Bond angle restraints: 20722
  Sorted by residual:
  angle pdb=" C   ARG C  62 "
        pdb=" N   LYS C  63 "
        pdb=" CA  LYS C  63 "
      ideal   model   delta    sigma   weight residual
     120.49  129.87   -9.38 1.42e+00 4.96e-01 4.37e+01
  angle pdb=" N   VAL C 230 "
        pdb=" CA  VAL C 230 "
        pdb=" C   VAL C 230 "
      ideal   model   delta    sigma   weight residual
     113.53  107.59    5.94 9.80e-01 1.04e+00 3.68e+01
  angle pdb=" C   VAL C 102 "
        pdb=" N   VAL C 103 "
        pdb=" CA  VAL C 103 "
      ideal   model   delta    sigma   weight residual
     120.24  122.76   -2.52 6.30e-01 2.52e+00 1.60e+01
  angle pdb=" C3'   A E   2 "
        pdb=" O3'   A E   2 "
        pdb=" P     C E   3 "
      ideal   model   delta    sigma   weight residual
     120.20  125.12   -4.92 1.50e+00 4.44e-01 1.07e+01
  angle pdb=" N   VAL A 597 "
        pdb=" CA  VAL A 597 "
        pdb=" C   VAL A 597 "
      ideal   model   delta    sigma   weight residual
     111.81  109.14    2.67 8.60e-01 1.35e+00 9.67e+00
  ... (remaining 20717 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.81: 9066
       33.81 -    67.61: 229
       67.61 -   101.42: 26
      101.42 -   135.22: 1
      135.22 -   169.03: 2
  Dihedral angle restraints: 9324
    sinusoidal: 4228
      harmonic: 5096
  Sorted by residual:
  dihedral pdb=" CA  GLU A 456 "
           pdb=" C   GLU A 456 "
           pdb=" N   GLU A 457 "
           pdb=" CA  GLU A 457 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.83   21.17     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" C4'   A E   2 "
           pdb=" C3'   A E   2 "
           pdb=" O3'   A E   2 "
           pdb=" P     C E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   59.03 -169.03     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'   C E   7 "
           pdb=" C3'   C E   7 "
           pdb=" O3'   C E   7 "
           pdb=" P     U E   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   69.54  150.46     1      3.50e+01 8.16e-04 1.47e+01
  ... (remaining 9321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1611
       0.037 -    0.074: 496
       0.074 -    0.111: 167
       0.111 -    0.148: 37
       0.148 -    0.185: 2
  Chirality restraints: 2313
  Sorted by residual:
  chirality pdb=" C3'   A E   2 "
            pdb=" C4'   A E   2 "
            pdb=" O3'   A E   2 "
            pdb=" C2'   A E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.56   -0.18 2.00e-01 2.50e+01 8.55e-01
  chirality pdb=" CA  GLU B 263 "
            pdb=" N   GLU B 263 "
            pdb=" C   GLU B 263 "
            pdb=" CB  GLU B 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.49e-01
  chirality pdb=" CA  ILE C 395 "
            pdb=" N   ILE C 395 "
            pdb=" C   ILE C 395 "
            pdb=" CB  ILE C 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.31e-01
  ... (remaining 2310 not shown)

  Planarity restraints: 2532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 643 "    0.055 5.00e-02 4.00e+02   8.28e-02 1.10e+01
        pdb=" N   PRO B 644 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO B 644 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 644 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 463 "   -0.048 5.00e-02 4.00e+02   7.32e-02 8.57e+00
        pdb=" N   PRO B 464 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 464 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 464 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 354 "   -0.040 5.00e-02 4.00e+02   6.10e-02 5.94e+00
        pdb=" N   PRO C 355 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 355 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 355 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 2529 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 427
        2.70 -     3.25: 14967
        3.25 -     3.80: 23895
        3.80 -     4.35: 32670
        4.35 -     4.90: 52933
  Nonbonded interactions: 124892
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 126 "
            pdb=" OG  SER A 128 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" OG1 THR C 229 "
            pdb=" O   VAL C 231 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OD2 ASP B 500 "
            pdb=" OH  TYR B 537 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OE1 GLU C  10 "
            pdb=" OG1 THR C  12 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OD1 ASN B 132 "
            pdb=" ND2 ASN B 227 "
     model   vdw
     2.264 3.120
  ... (remaining 124887 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.28 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:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     40.010
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
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      :  0.003   0.053  15178  Z= 0.124
  Angle     :  0.610   9.385  20722  Z= 0.328
  Chirality :  0.041   0.185   2313
  Planarity :  0.006   0.083   2532
  Dihedral  : 14.960 169.029   6016
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.20), residues: 1729
  helix:  0.66 (0.20), residues: 715
  sheet: -0.83 (0.37), residues: 207
  loop : -1.33 (0.21), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 185 
 HIS   0.003   0.001   HIS C 242 
 PHE   0.024   0.002   PHE C 335 
 TYR   0.010   0.001   TYR B 533 
 ARG   0.008   0.001   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18644 (  642)
  hydrogen bonds       : angle       7.08157 ( 1765)
  covalent geometry    : bond        0.00268 (15178)
  covalent geometry    : angle       0.61026 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 ASP cc_start: 0.8841 (m-30) cc_final: 0.8636 (m-30)
REVERT: A  150 GLU cc_start: 0.8924 (mp0) cc_final: 0.8692 (pm20)
REVERT: B  259 ASP cc_start: 0.8364 (m-30) cc_final: 0.8147 (m-30)
REVERT: C  380 GLN cc_start: 0.8244 (pm20) cc_final: 0.7997 (pm20)
REVERT: C  383 PHE cc_start: 0.8549 (p90) cc_final: 0.8223 (p90)
REVERT: C  410 ILE cc_start: 0.8952 (mt) cc_final: 0.8511 (mt)
REVERT: C  421 PHE cc_start: 0.7675 (m-80) cc_final: 0.7413 (m-80)
REVERT: C  433 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7538 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.3103
  time to fit residues: 106.1165
Evaluate side-chains
  199 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 132 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9980
   chunk 137 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9980
   chunk 158 optimal weight:    9.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
A 257 GLN
B 123 GLN
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 233 HIS
C 376 ASN
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.118568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.083572 restraints weight = 61911.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 3.59
r_work: 0.2806 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2815
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2815
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  15178  Z= 0.207
  Angle     :  0.637   6.627  20722  Z= 0.330
  Chirality :  0.045   0.180   2313
  Planarity :  0.005   0.062   2532
  Dihedral  : 13.499 164.876   2463
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.69 %
    Favored  : 91.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.20), residues: 1729
  helix:  0.86 (0.20), residues: 718
  sheet: -1.05 (0.34), residues: 226
  loop : -1.30 (0.21), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.011   0.001   HIS C 233 
 PHE   0.028   0.002   PHE C  41 
 TYR   0.034   0.002   TYR C 382 
 ARG   0.006   0.001   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  642)
  hydrogen bonds       : angle       5.12211 ( 1765)
  covalent geometry    : bond        0.00486 (15178)
  covalent geometry    : angle       0.63692 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 2.626 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.8695 (ttm170) cc_final: 0.8416 (mtp180)
REVERT: B  259 ASP cc_start: 0.8870 (m-30) cc_final: 0.8604 (m-30)
REVERT: B  393 MET cc_start: 0.8284 (ppp) cc_final: 0.8038 (ptm)
REVERT: B  479 PHE cc_start: 0.8325 (m-80) cc_final: 0.8124 (m-80)
REVERT: C  110 TYR cc_start: 0.8491 (m-80) cc_final: 0.8227 (m-80)
REVERT: C  346 GLU cc_start: 0.9101 (tt0) cc_final: 0.8370 (tm-30)
REVERT: C  380 GLN cc_start: 0.8500 (pm20) cc_final: 0.8212 (pm20)
REVERT: C  383 PHE cc_start: 0.8381 (p90) cc_final: 0.8067 (p90)
REVERT: C  410 ILE cc_start: 0.8818 (mt) cc_final: 0.8536 (mt)
REVERT: C  416 PHE cc_start: 0.8402 (m-80) cc_final: 0.8077 (m-10)
REVERT: C  433 ARG cc_start: 0.8088 (tpp-160) cc_final: 0.7632 (tpp80)
  outliers start: 17
  outliers final: 10
  residues processed: 214
  average time/residue: 0.3583
  time to fit residues: 107.8742
Evaluate side-chains
  196 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 186
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  257 GLN
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain C residue  183 ASP
Chi-restraints excluded: chain C residue  335 PHE
Chi-restraints excluded: chain C residue  376 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 166 optimal weight:   20.0000
   chunk 148 optimal weight:    0.0570
   chunk 126 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 134 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.1502

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

Flipped N/Q/H residues before XYZ refinement:
A 257 GLN
B 148 GLN
C 233 HIS
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 375 GLN
C 376 ASN
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.120991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.087851 restraints weight = 69298.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 4.24
r_work: 0.2785 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15178  Z= 0.122
  Angle     :  0.561   6.943  20722  Z= 0.287
  Chirality :  0.041   0.172   2313
  Planarity :  0.005   0.053   2532
  Dihedral  : 13.366 163.889   2463
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 10.19 %
    Favored  : 88.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.20), residues: 1729
  helix:  1.08 (0.20), residues: 713
  sheet: -0.96 (0.34), residues: 225
  loop : -1.22 (0.21), residues: 791

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.006   0.001   HIS C 443 
 PHE   0.026   0.002   PHE C  41 
 TYR   0.020   0.001   TYR C 373 
 ARG   0.005   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  642)
  hydrogen bonds       : angle       4.79001 ( 1765)
  covalent geometry    : bond        0.00276 (15178)
  covalent geometry    : angle       0.56083 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 1.534 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 GLN cc_start: 0.9003 (tp40) cc_final: 0.8700 (tp-100)
REVERT: B  186 ASP cc_start: 0.8862 (t70) cc_final: 0.8529 (t0)
REVERT: B  259 ASP cc_start: 0.8921 (m-30) cc_final: 0.8618 (m-30)
REVERT: B  473 LYS cc_start: 0.8321 (mmmt) cc_final: 0.7806 (mtmm)
REVERT: B  479 PHE cc_start: 0.8385 (m-80) cc_final: 0.8181 (m-80)
REVERT: C  110 TYR cc_start: 0.8525 (m-80) cc_final: 0.8268 (m-80)
REVERT: C  346 GLU cc_start: 0.9111 (tt0) cc_final: 0.8368 (tm-30)
REVERT: C  349 LYS cc_start: 0.7516 (tptp) cc_final: 0.7293 (tptt)
REVERT: C  380 GLN cc_start: 0.8490 (pm20) cc_final: 0.8189 (pm20)
REVERT: C  423 GLN cc_start: 0.8125 (pm20) cc_final: 0.7840 (pm20)
REVERT: C  433 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7613 (tpp80)
  outliers start: 16
  outliers final: 9
  residues processed: 208
  average time/residue: 0.3290
  time to fit residues: 96.6051
Evaluate side-chains
  197 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 188
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain C residue  183 ASP
Chi-restraints excluded: chain C residue  335 PHE
Chi-restraints excluded: chain C residue  376 ASN
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 128 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 173 optimal weight:    7.9990
   chunk 123 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 164 optimal weight:    8.9990
   chunk 102 optimal weight:    0.6980
   chunk 149 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 110 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
C 233 HIS
** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 ASN
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.084995 restraints weight = 50639.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 3.38
r_work: 0.2828 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15178  Z= 0.144
  Angle     :  0.563   6.673  20722  Z= 0.288
  Chirality :  0.042   0.172   2313
  Planarity :  0.005   0.054   2532
  Dihedral  : 13.314 163.526   2463
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.58 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.20), residues: 1729
  helix:  1.06 (0.20), residues: 723
  sheet: -0.97 (0.34), residues: 226
  loop : -1.25 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 253 
 HIS   0.010   0.001   HIS C 233 
 PHE   0.025   0.002   PHE C  41 
 TYR   0.023   0.001   TYR C 382 
 ARG   0.006   0.000   ARG B 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03660 (  642)
  hydrogen bonds       : angle       4.64004 ( 1765)
  covalent geometry    : bond        0.00331 (15178)
  covalent geometry    : angle       0.56333 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 191
  time to evaluate  : 1.562 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 GLN cc_start: 0.8972 (tp40) cc_final: 0.8631 (tp-100)
REVERT: B  186 ASP cc_start: 0.8858 (t70) cc_final: 0.8509 (t0)
REVERT: B  259 ASP cc_start: 0.8826 (m-30) cc_final: 0.8532 (m-30)
REVERT: B  473 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7811 (mtmm)
REVERT: B  479 PHE cc_start: 0.8418 (m-80) cc_final: 0.8172 (m-80)
REVERT: C  110 TYR cc_start: 0.8487 (m-80) cc_final: 0.8264 (m-80)
REVERT: C  346 GLU cc_start: 0.9104 (tt0) cc_final: 0.8412 (tm-30)
REVERT: C  374 PHE cc_start: 0.8669 (p90) cc_final: 0.8276 (p90)
REVERT: C  380 GLN cc_start: 0.8501 (pm20) cc_final: 0.8157 (pm20)
REVERT: C  433 ARG cc_start: 0.8077 (tpp-160) cc_final: 0.7604 (tpp80)
  outliers start: 22
  outliers final: 17
  residues processed: 203
  average time/residue: 0.3019
  time to fit residues: 87.2201
Evaluate side-chains
  202 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain C residue   24 CYS
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  335 PHE
Chi-restraints excluded: chain C residue  376 ASN
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 119 optimal weight:    6.9990
   chunk 154 optimal weight:    3.9990
   chunk 125 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 167 optimal weight:    8.9990
   chunk 107 optimal weight:    0.6980
   chunk 118 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
C  39 ASN
C 233 HIS
C 254 ASN
C 376 ASN
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.118975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.082908 restraints weight = 67497.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 3.82
r_work: 0.2802 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15178  Z= 0.156
  Angle     :  0.562   7.148  20722  Z= 0.288
  Chirality :  0.042   0.179   2313
  Planarity :  0.005   0.054   2532
  Dihedral  : 13.292 163.399   2463
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.96 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.20), residues: 1729
  helix:  1.10 (0.20), residues: 725
  sheet: -0.93 (0.34), residues: 228
  loop : -1.19 (0.21), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 253 
 HIS   0.009   0.001   HIS C 233 
 PHE   0.026   0.002   PHE C  41 
 TYR   0.015   0.001   TYR B 533 
 ARG   0.006   0.000   ARG B 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  642)
  hydrogen bonds       : angle       4.57486 ( 1765)
  covalent geometry    : bond        0.00365 (15178)
  covalent geometry    : angle       0.56219 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 192
  time to evaluate  : 1.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 GLN cc_start: 0.8985 (tp40) cc_final: 0.8646 (tp-100)
REVERT: A  569 MET cc_start: 0.9136 (tpp) cc_final: 0.8915 (tpt)
REVERT: B  259 ASP cc_start: 0.8812 (m-30) cc_final: 0.8608 (m-30)
REVERT: B  435 GLU cc_start: 0.8823 (tp30) cc_final: 0.8621 (tp30)
REVERT: B  473 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7908 (mtmm)
REVERT: B  479 PHE cc_start: 0.8438 (m-80) cc_final: 0.8187 (m-80)
REVERT: C  110 TYR cc_start: 0.8509 (m-80) cc_final: 0.8300 (m-80)
REVERT: C  160 GLU cc_start: 0.8225 (tp30) cc_final: 0.8011 (tp30)
REVERT: C  346 GLU cc_start: 0.9081 (tt0) cc_final: 0.8467 (tm-30)
REVERT: C  374 PHE cc_start: 0.8517 (p90) cc_final: 0.8119 (p90)
REVERT: C  380 GLN cc_start: 0.8516 (pm20) cc_final: 0.8146 (pm20)
REVERT: C  423 GLN cc_start: 0.8449 (pm20) cc_final: 0.8117 (pm20)
REVERT: C  437 ASP cc_start: 0.8814 (m-30) cc_final: 0.8543 (m-30)
  outliers start: 27
  outliers final: 18
  residues processed: 208
  average time/residue: 0.3130
  time to fit residues: 92.8360
Evaluate side-chains
  201 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain C residue   24 CYS
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  251 VAL
Chi-restraints excluded: chain C residue  335 PHE
Chi-restraints excluded: chain C residue  376 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 155 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 64 optimal weight:    0.1980
   chunk 60 optimal weight:    0.9990
   chunk 119 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 132 optimal weight:    9.9990
   chunk 170 optimal weight:    9.9990
   chunk 136 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 161 optimal weight:   40.0000
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
C 254 ASN
C 376 ASN
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.119792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.086098 restraints weight = 51995.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 3.25
r_work: 0.2837 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15178  Z= 0.145
  Angle     :  0.560   7.043  20722  Z= 0.286
  Chirality :  0.042   0.178   2313
  Planarity :  0.005   0.055   2532
  Dihedral  : 13.268 163.244   2463
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.22 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.20), residues: 1729
  helix:  1.15 (0.20), residues: 724
  sheet: -0.87 (0.34), residues: 228
  loop : -1.19 (0.21), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 253 
 HIS   0.007   0.001   HIS C 233 
 PHE   0.025   0.002   PHE C  41 
 TYR   0.016   0.001   TYR B 533 
 ARG   0.006   0.000   ARG B 708 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03583 (  642)
  hydrogen bonds       : angle       4.51877 ( 1765)
  covalent geometry    : bond        0.00338 (15178)
  covalent geometry    : angle       0.56027 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 194
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 GLN cc_start: 0.8976 (tp40) cc_final: 0.8632 (tp-100)
REVERT: B  186 ASP cc_start: 0.8869 (t70) cc_final: 0.8485 (t0)
REVERT: B  259 ASP cc_start: 0.8810 (m-30) cc_final: 0.8580 (m-30)
REVERT: B  473 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7858 (mtmm)
REVERT: B  479 PHE cc_start: 0.8452 (m-80) cc_final: 0.8176 (m-80)
REVERT: C   29 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8913 (ttpp)
REVERT: C  110 TYR cc_start: 0.8481 (m-80) cc_final: 0.8280 (m-80)
REVERT: C  160 GLU cc_start: 0.8207 (tp30) cc_final: 0.7992 (tp30)
REVERT: C  346 GLU cc_start: 0.9039 (tt0) cc_final: 0.8475 (tm-30)
REVERT: C  349 LYS cc_start: 0.7603 (tptt) cc_final: 0.7358 (tptp)
REVERT: C  374 PHE cc_start: 0.8463 (p90) cc_final: 0.8089 (p90)
REVERT: C  380 GLN cc_start: 0.8514 (pm20) cc_final: 0.8123 (pm20)
REVERT: C  423 GLN cc_start: 0.8420 (pm20) cc_final: 0.8116 (pm20)
REVERT: C  437 ASP cc_start: 0.8798 (m-30) cc_final: 0.8566 (m-30)
  outliers start: 28
  outliers final: 20
  residues processed: 211
  average time/residue: 0.3224
  time to fit residues: 96.5558
Evaluate side-chains
  205 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 1.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  210 TYR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain C residue   24 CYS
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  251 VAL
Chi-restraints excluded: chain C residue  335 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 150 optimal weight:    6.9990
   chunk 152 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 135 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
C 254 ASN
C 376 ASN
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.120393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.084416 restraints weight = 64751.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 3.77
r_work: 0.2832 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15178  Z= 0.118
  Angle     :  0.558   7.662  20722  Z= 0.284
  Chirality :  0.041   0.177   2313
  Planarity :  0.005   0.055   2532
  Dihedral  : 13.229 162.757   2463
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.18 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.20), residues: 1729
  helix:  1.26 (0.20), residues: 715
  sheet: -0.79 (0.34), residues: 226
  loop : -1.13 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 253 
 HIS   0.006   0.001   HIS C 233 
 PHE   0.025   0.001   PHE C  41 
 TYR   0.016   0.001   TYR B 533 
 ARG   0.006   0.000   ARG B 708 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03360 (  642)
  hydrogen bonds       : angle       4.42853 ( 1765)
  covalent geometry    : bond        0.00271 (15178)
  covalent geometry    : angle       0.55789 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 1.754 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 GLN cc_start: 0.8965 (tp40) cc_final: 0.8633 (tp-100)
REVERT: B  120 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8873 (mtmt)
REVERT: B  259 ASP cc_start: 0.8848 (m-30) cc_final: 0.8594 (m-30)
REVERT: B  473 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7927 (mtmm)
REVERT: B  479 PHE cc_start: 0.8425 (m-80) cc_final: 0.8157 (m-80)
REVERT: B  701 ARG cc_start: 0.9231 (mtp85) cc_final: 0.9015 (mtp85)
REVERT: C   29 LYS cc_start: 0.9212 (mtmt) cc_final: 0.8927 (ttpp)
REVERT: C   95 LYS cc_start: 0.8471 (mtmm) cc_final: 0.7975 (ptmm)
REVERT: C  110 TYR cc_start: 0.8501 (m-80) cc_final: 0.8279 (m-80)
REVERT: C  160 GLU cc_start: 0.8213 (tp30) cc_final: 0.7993 (tp30)
REVERT: C  346 GLU cc_start: 0.9053 (tt0) cc_final: 0.8503 (tm-30)
REVERT: C  374 PHE cc_start: 0.8469 (p90) cc_final: 0.8128 (p90)
REVERT: C  380 GLN cc_start: 0.8522 (pm20) cc_final: 0.8142 (pm20)
  outliers start: 23
  outliers final: 20
  residues processed: 210
  average time/residue: 0.3194
  time to fit residues: 98.0697
Evaluate side-chains
  207 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 1.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  210 TYR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain C residue   24 CYS
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  335 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 80 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   chunk 2 optimal weight:    8.9990
   chunk 47 optimal weight:    0.7980
   chunk 173 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 163 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 257 GLN
C 233 HIS
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.119771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.083700 restraints weight = 67294.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 3.83
r_work: 0.2820 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15178  Z= 0.133
  Angle     :  0.564   7.311  20722  Z= 0.287
  Chirality :  0.041   0.176   2313
  Planarity :  0.005   0.056   2532
  Dihedral  : 13.228 162.845   2463
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.24 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.20), residues: 1729
  helix:  1.30 (0.20), residues: 711
  sheet: -0.73 (0.34), residues: 226
  loop : -1.13 (0.21), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 185 
 HIS   0.009   0.001   HIS C 233 
 PHE   0.024   0.001   PHE C  41 
 TYR   0.015   0.001   TYR B 533 
 ARG   0.007   0.000   ARG B 708 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 (  642)
  hydrogen bonds       : angle       4.40579 ( 1765)
  covalent geometry    : bond        0.00309 (15178)
  covalent geometry    : angle       0.56362 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 191
  time to evaluate  : 2.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 ASN cc_start: 0.8658 (p0) cc_final: 0.8370 (p0)
REVERT: A  159 GLN cc_start: 0.8978 (tp40) cc_final: 0.8644 (tp-100)
REVERT: B  120 LYS cc_start: 0.9176 (mtmt) cc_final: 0.8873 (mtmt)
REVERT: B  186 ASP cc_start: 0.8877 (t70) cc_final: 0.8528 (t0)
REVERT: B  259 ASP cc_start: 0.8860 (m-30) cc_final: 0.8633 (m-30)
REVERT: B  473 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7937 (mtmm)
REVERT: B  701 ARG cc_start: 0.9234 (mtp85) cc_final: 0.9021 (mtp85)
REVERT: C   29 LYS cc_start: 0.9204 (mtmt) cc_final: 0.8924 (ttpp)
REVERT: C   95 LYS cc_start: 0.8478 (mtmm) cc_final: 0.7980 (ptmm)
REVERT: C  110 TYR cc_start: 0.8520 (m-80) cc_final: 0.8300 (m-80)
REVERT: C  160 GLU cc_start: 0.8229 (tp30) cc_final: 0.7983 (tp30)
REVERT: C  346 GLU cc_start: 0.9062 (tt0) cc_final: 0.8499 (tm-30)
REVERT: C  349 LYS cc_start: 0.7365 (tptt) cc_final: 0.7097 (tptp)
REVERT: C  374 PHE cc_start: 0.8465 (p90) cc_final: 0.8140 (p90)
REVERT: C  380 GLN cc_start: 0.8526 (pm20) cc_final: 0.8145 (pm20)
  outliers start: 29
  outliers final: 21
  residues processed: 209
  average time/residue: 0.3790
  time to fit residues: 112.8017
Evaluate side-chains
  206 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 2.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  210 TYR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain C residue   24 CYS
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  251 VAL
Chi-restraints excluded: chain C residue  335 PHE
Chi-restraints excluded: chain C residue  408 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 111 optimal weight:    1.9990
   chunk 115 optimal weight:    0.7980
   chunk 104 optimal weight:    5.9990
   chunk 147 optimal weight:   10.0000
   chunk 154 optimal weight:    0.0970
   chunk 162 optimal weight:    8.9990
   chunk 142 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 257 GLN
C 233 HIS
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.085011 restraints weight = 58880.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 3.87
r_work: 0.2795 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15178  Z= 0.134
  Angle     :  0.570   7.384  20722  Z= 0.289
  Chirality :  0.042   0.261   2313
  Planarity :  0.005   0.055   2532
  Dihedral  : 13.225 162.829   2463
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.56 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.20), residues: 1729
  helix:  1.25 (0.20), residues: 717
  sheet: -0.71 (0.34), residues: 228
  loop : -1.14 (0.21), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 185 
 HIS   0.005   0.001   HIS C 233 
 PHE   0.024   0.001   PHE C  41 
 TYR   0.015   0.001   TYR B 533 
 ARG   0.007   0.000   ARG B 477 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  642)
  hydrogen bonds       : angle       4.40411 ( 1765)
  covalent geometry    : bond        0.00312 (15178)
  covalent geometry    : angle       0.56963 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 192
  time to evaluate  : 1.794 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 ASN cc_start: 0.8630 (p0) cc_final: 0.8348 (p0)
REVERT: A  159 GLN cc_start: 0.9031 (tp40) cc_final: 0.8683 (tp-100)
REVERT: B  120 LYS cc_start: 0.9176 (mtmt) cc_final: 0.8885 (mtmt)
REVERT: B  186 ASP cc_start: 0.8864 (t70) cc_final: 0.8517 (t0)
REVERT: B  259 ASP cc_start: 0.8940 (m-30) cc_final: 0.8660 (m-30)
REVERT: B  473 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7792 (mtmm)
REVERT: C   29 LYS cc_start: 0.9185 (mtmt) cc_final: 0.8876 (ttpp)
REVERT: C   95 LYS cc_start: 0.8499 (mtmm) cc_final: 0.7890 (ptmm)
REVERT: C  110 TYR cc_start: 0.8575 (m-80) cc_final: 0.8320 (m-80)
REVERT: C  160 GLU cc_start: 0.8270 (tp30) cc_final: 0.7995 (tp30)
REVERT: C  346 GLU cc_start: 0.9065 (tt0) cc_final: 0.8457 (tm-30)
REVERT: C  349 LYS cc_start: 0.7403 (tptt) cc_final: 0.7111 (tptp)
REVERT: C  374 PHE cc_start: 0.8469 (p90) cc_final: 0.8186 (p90)
REVERT: C  380 GLN cc_start: 0.8525 (pm20) cc_final: 0.8152 (pm20)
  outliers start: 22
  outliers final: 22
  residues processed: 205
  average time/residue: 0.3400
  time to fit residues: 98.5721
Evaluate side-chains
  209 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 187
  time to evaluate  : 1.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  584 GLN
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  210 TYR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain C residue   24 CYS
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  251 VAL
Chi-restraints excluded: chain C residue  335 PHE
Chi-restraints excluded: chain C residue  408 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 136 optimal weight:    3.9990
   chunk 133 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 151 optimal weight:    0.7980
   chunk 105 optimal weight:    3.9990
   chunk 148 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0870
   chunk 70 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 144 optimal weight:    0.2980
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
C 233 HIS
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.121147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.085846 restraints weight = 64611.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 4.00
r_work: 0.2836 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  15178  Z= 0.105
  Angle     :  0.559   7.809  20722  Z= 0.283
  Chirality :  0.041   0.194   2313
  Planarity :  0.005   0.056   2532
  Dihedral  : 13.163 162.161   2463
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.69 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.20), residues: 1729
  helix:  1.35 (0.20), residues: 716
  sheet: -0.68 (0.34), residues: 223
  loop : -1.10 (0.21), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 185 
 HIS   0.011   0.001   HIS C 233 
 PHE   0.028   0.001   PHE C 383 
 TYR   0.015   0.001   TYR B 533 
 ARG   0.008   0.000   ARG B 477 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  642)
  hydrogen bonds       : angle       4.32350 ( 1765)
  covalent geometry    : bond        0.00236 (15178)
  covalent geometry    : angle       0.55949 (20722)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 1.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ASN cc_start: 0.8556 (p0) cc_final: 0.8210 (p0)
REVERT: A  159 GLN cc_start: 0.8977 (tp40) cc_final: 0.8497 (tp-100)
REVERT: B  120 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8896 (mtmt)
REVERT: B  186 ASP cc_start: 0.8835 (t70) cc_final: 0.8515 (t0)
REVERT: B  259 ASP cc_start: 0.8937 (m-30) cc_final: 0.8680 (m-30)
REVERT: B  473 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7860 (mtmm)
REVERT: C   29 LYS cc_start: 0.9193 (mtmt) cc_final: 0.8901 (ttpp)
REVERT: C   95 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7882 (ptmm)
REVERT: C  110 TYR cc_start: 0.8536 (m-80) cc_final: 0.8286 (m-80)
REVERT: C  160 GLU cc_start: 0.8251 (tp30) cc_final: 0.7992 (tp30)
REVERT: C  346 GLU cc_start: 0.9074 (tt0) cc_final: 0.8440 (tm-30)
REVERT: C  349 LYS cc_start: 0.7415 (tptt) cc_final: 0.7001 (tptp)
REVERT: C  374 PHE cc_start: 0.8266 (p90) cc_final: 0.7989 (p90)
REVERT: C  380 GLN cc_start: 0.8534 (pm20) cc_final: 0.8161 (pm20)
  outliers start: 21
  outliers final: 17
  residues processed: 213
  average time/residue: 0.3184
  time to fit residues: 96.3673
Evaluate side-chains
  208 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 191
  time to evaluate  : 1.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  210 TYR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  551 GLU
Chi-restraints excluded: chain B residue  706 LEU
Chi-restraints excluded: chain C residue   24 CYS
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  251 VAL
Chi-restraints excluded: chain C residue  335 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 130 optimal weight:    8.9990
   chunk 163 optimal weight:   10.0000
   chunk 167 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9990
   chunk 162 optimal weight:    8.9990
   chunk 11 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 123 optimal weight:    3.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
C 233 HIS
** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.119139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.084996 restraints weight = 52329.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 3.50
r_work: 0.2823 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15178  Z= 0.144
  Angle     :  0.583   8.727  20722  Z= 0.295
  Chirality :  0.042   0.175   2313
  Planarity :  0.005   0.055   2532
  Dihedral  : 13.204 162.754   2463
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.76 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.20), residues: 1729
  helix:  1.32 (0.20), residues: 717
  sheet: -0.63 (0.34), residues: 223
  loop : -1.12 (0.21), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 185 
 HIS   0.012   0.001   HIS C 233 
 PHE   0.028   0.002   PHE C 383 
 TYR   0.021   0.001   TYR B 632 
 ARG   0.007   0.000   ARG B 477 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03444 (  642)
  hydrogen bonds       : angle       4.38696 ( 1765)
  covalent geometry    : bond        0.00338 (15178)
  covalent geometry    : angle       0.58254 (20722)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8205.75 seconds
wall clock time: 143 minutes 24.31 seconds (8604.31 seconds total)