Starting phenix.real_space_refine
on Thu Feb 13 11:14:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zd5_14636/02_2025/7zd5_14636_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zd5_14636/02_2025/7zd5_14636.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zd5_14636/02_2025/7zd5_14636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zd5_14636/02_2025/7zd5_14636.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zd5_14636/02_2025/7zd5_14636_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zd5_14636/02_2025/7zd5_14636_neut.cif"
  }
  resolution = 3.17
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    5750      2.51       5
     N    1575      2.21       5
     O    1613      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8967
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 4383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4383
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 18, 'TRANS': 551}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "D"
      Number of atoms: 4584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4584
          Classifications: {'peptide': 587}
          Link IDs: {'PTRANS': 27, 'TRANS': 559}
  Time building chain proxies: 5.53, per 1000 atoms: 0.62
  Number of scatterers: 8967
  At special positions: 0
  Unit cell: (115.506, 95.418, 112.995, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1613      8.00
     N    1575      7.00
     C    5750      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 5 sheets defined
      67.9% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 10 through 13
      removed outlier: 3.854A  pdb=" N   ARG C  13 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 10 through 13'
    Processing helix  chain 'C' and resid 14 through 50
      removed outlier: 3.657A  pdb=" N   ALA C  25 " --> pdb=" O   GLY C  21 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU C  36 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 54
    Processing helix  chain 'C' and resid 61 through 103
      removed outlier: 3.759A  pdb=" N   ARG C  67 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   THR C  74 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG C  77 " --> pdb=" O   ARG C  73 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   HIS C  94 " --> pdb=" O   ARG C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 118
      removed outlier: 3.979A  pdb=" N   GLN C 116 " --> pdb=" O   ARG C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 131
    Processing helix  chain 'C' and resid 131 through 137
      removed outlier: 4.518A  pdb=" N   LEU C 135 " --> pdb=" O   ASP C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 157
      removed outlier: 3.854A  pdb=" N   PHE C 157 " --> pdb=" O   ILE C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 176
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 185 through 208
      removed outlier: 3.600A  pdb=" N   GLY C 189 " --> pdb=" O   GLY C 185 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU C 195 " --> pdb=" O   ASN C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'C' and resid 220 through 267
      removed outlier: 3.664A  pdb=" N   THR C 224 " --> pdb=" O   ASP C 220 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   THR C 244 " --> pdb=" O   GLN C 240 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL C 259 " --> pdb=" O   GLY C 255 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 290
      removed outlier: 3.548A  pdb=" N   LEU C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 293
      No H-bonds generated for 'chain 'C' and resid 291 through 293'
    Processing helix  chain 'C' and resid 296 through 318
      removed outlier: 3.754A  pdb=" N   GLY C 305 " --> pdb=" O   PHE C 301 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLN C 306 " --> pdb=" O   GLN C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 387
    Processing helix  chain 'C' and resid 405 through 407
      No H-bonds generated for 'chain 'C' and resid 405 through 407'
    Processing helix  chain 'C' and resid 408 through 415
      removed outlier: 3.903A  pdb=" N   GLN C 414 " --> pdb=" O   ALA C 410 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 430 through 436
    Processing helix  chain 'C' and resid 442 through 453
    Processing helix  chain 'C' and resid 476 through 492
    Processing helix  chain 'C' and resid 506 through 521
      removed outlier: 3.959A  pdb=" N   GLN C 512 " --> pdb=" O   THR C 508 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU C 514 " --> pdb=" O   GLU C 510 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 535 through 539
    Processing helix  chain 'C' and resid 555 through 562
      removed outlier: 3.645A  pdb=" N   ARG C 562 " --> pdb=" O   GLU C 558 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 564 through 571
      removed outlier: 3.640A  pdb=" N   GLN C 571 " --> pdb=" O   TYR C 567 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 16
    Processing helix  chain 'D' and resid 21 through 54
      removed outlier: 3.613A  pdb=" N   ARG D  28 " --> pdb=" O   LEU D  24 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE D  39 " --> pdb=" O   GLY D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 61
    Processing helix  chain 'D' and resid 62 through 109
      removed outlier: 3.589A  pdb=" N   ILE D  94 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 115
    Processing helix  chain 'D' and resid 118 through 127
    Processing helix  chain 'D' and resid 130 through 132
      No H-bonds generated for 'chain 'D' and resid 130 through 132'
    Processing helix  chain 'D' and resid 133 through 139
      removed outlier: 3.588A  pdb=" N   TYR D 137 " --> pdb=" O   MET D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 162
      removed outlier: 3.667A  pdb=" N   ALA D 145 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL D 148 " --> pdb=" O   MET D 144 " (cutoff:3.500A)
      Proline residue:  D 151  - end of helix
      Proline residue:  D 160  - end of helix
    Processing helix  chain 'D' and resid 164 through 183
      removed outlier: 3.627A  pdb=" N   LEU D 169 " --> pdb=" O   ALA D 165 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA D 173 " --> pdb=" O   LEU D 169 " (cutoff:3.500A)
      Proline residue:  D 174  - end of helix
      Proline residue:  D 177  - end of helix
    Processing helix  chain 'D' and resid 183 through 194
      removed outlier: 3.618A  pdb=" N   ASN D 191 " --> pdb=" O   ALA D 187 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ARG D 192 " --> pdb=" O   ALA D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 202
    Processing helix  chain 'D' and resid 203 through 211
    Processing helix  chain 'D' and resid 211 through 218
      removed outlier: 3.564A  pdb=" N   PHE D 218 " --> pdb=" O   THR D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 273
      removed outlier: 4.069A  pdb=" N   GLU D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER D 227 " --> pdb=" O   ALA D 223 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL D 242 " --> pdb=" O   ARG D 238 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER D 249 " --> pdb=" O   LEU D 245 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 310
      Proline residue:  D 298  - end of helix
      removed outlier: 3.921A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 311 through 328
      removed outlier: 3.822A  pdb=" N   THR D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE D 327 " --> pdb=" O   SER D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 398
      removed outlier: 3.955A  pdb=" N   LEU D 393 " --> pdb=" O   LYS D 389 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 412 through 416
    Processing helix  chain 'D' and resid 417 through 422
    Processing helix  chain 'D' and resid 438 through 445
      removed outlier: 3.519A  pdb=" N   VAL D 443 " --> pdb=" O   LEU D 439 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 451 through 462
    Processing helix  chain 'D' and resid 473 through 477
      removed outlier: 3.823A  pdb=" N   ASP D 476 " --> pdb=" O   GLN D 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 500
      removed outlier: 3.731A  pdb=" N   ARG D 493 " --> pdb=" O   GLY D 489 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL D 494 " --> pdb=" O   GLN D 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 517 through 535
      removed outlier: 3.870A  pdb=" N   GLN D 522 " --> pdb=" O   ALA D 518 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA D 530 " --> pdb=" O   GLU D 526 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU D 533 " --> pdb=" O   ASN D 529 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ARG D 534 " --> pdb=" O   ALA D 530 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLN D 535 " --> pdb=" O   ALA D 531 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 546 through 550
      removed outlier: 4.168A  pdb=" N   ASP D 549 " --> pdb=" O   ASP D 546 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 566 through 572
      removed outlier: 3.989A  pdb=" N   VAL D 572 " --> pdb=" O   ALA D 568 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 575 through 587
      removed outlier: 3.541A  pdb=" N   GLU D 587 " --> pdb=" O   HIS D 583 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 339 through 342
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.462A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   THR C 530 " --> pdb=" O   ILE C 369 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   ILE C 371 " --> pdb=" O   THR C 530 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE C 542 " --> pdb=" O   GLN C 553 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLN C 553 " --> pdb=" O   ILE C 542 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   VAL C 544 " --> pdb=" O   ILE C 551 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 428 through 429
    Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.462A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   GLY D 367 " --> pdb=" O   LEU D 355 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLU D 353 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   PHE D 371 " --> pdb=" O   GLU D 351 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   GLU D 351 " --> pdb=" O   PHE D 371 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 429
      removed outlier: 6.932A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 508 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   ASP D 510 " --> pdb=" O   SER D 426 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   VAL D 428 " --> pdb=" O   ASP D 510 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU D 509 " --> pdb=" O   VAL D 540 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   MET D 539 " --> pdb=" O   ALA D 379 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   GLY D 383 " --> pdb=" O   THR D 541 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   TRP D 554 " --> pdb=" O   ARG D 378 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)

    521 hydrogen bonds defined for protein.
    1521 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.80

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1866
        1.33 -     1.45: 2024
        1.45 -     1.57: 5198
        1.57 -     1.70: 0
        1.70 -     1.82: 55
  Bond restraints: 9143
  Sorted by residual:
  bond pdb=" N   ASN D 431 "
       pdb=" CA  ASN D 431 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.032 9.10e-03 1.21e+04 1.22e+01
  bond pdb=" N   LEU C 533 "
       pdb=" CA  LEU C 533 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.08e-02 8.57e+03 9.17e+00
  bond pdb=" N   GLN D 430 "
       pdb=" CA  GLN D 430 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.038 1.34e-02 5.57e+03 7.91e+00
  bond pdb=" N   GLN D 302 "
       pdb=" CA  GLN D 302 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.04e-02 9.25e+03 7.39e+00
  bond pdb=" C   ALA D  90 "
       pdb=" O   ALA D  90 "
    ideal  model  delta    sigma   weight residual
    1.236  1.205  0.031 1.16e-02 7.43e+03 7.21e+00
  ... (remaining 9138 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 12065
        1.90 -     3.81: 297
        3.81 -     5.71: 49
        5.71 -     7.61: 7
        7.61 -     9.51: 3
  Bond angle restraints: 12421
  Sorted by residual:
  angle pdb=" C   GLU C 118 "
        pdb=" N   LEU C 119 "
        pdb=" CA  LEU C 119 "
      ideal   model   delta    sigma   weight residual
     120.44  129.95   -9.51 1.36e+00 5.41e-01 4.89e+01
  angle pdb=" N   GLU C 118 "
        pdb=" CA  GLU C 118 "
        pdb=" C   GLU C 118 "
      ideal   model   delta    sigma   weight residual
     113.17  104.45    8.72 1.26e+00 6.30e-01 4.79e+01
  angle pdb=" N   ILE D  19 "
        pdb=" CA  ILE D  19 "
        pdb=" C   ILE D  19 "
      ideal   model   delta    sigma   weight residual
     109.30  102.95    6.35 1.25e+00 6.40e-01 2.58e+01
  angle pdb=" CA  GLU C 118 "
        pdb=" C   GLU C 118 "
        pdb=" N   LEU C 119 "
      ideal   model   delta    sigma   weight residual
     118.27  112.69    5.58 1.31e+00 5.83e-01 1.82e+01
  angle pdb=" C   ASN D 431 "
        pdb=" CA  ASN D 431 "
        pdb=" CB  ASN D 431 "
      ideal   model   delta    sigma   weight residual
     110.71  114.59   -3.88 9.40e-01 1.13e+00 1.71e+01
  ... (remaining 12416 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 4853
       16.91 -    33.82: 484
       33.82 -    50.73: 106
       50.73 -    67.64: 10
       67.64 -    84.55: 6
  Dihedral angle restraints: 5459
    sinusoidal: 2142
      harmonic: 3317
  Sorted by residual:
  dihedral pdb=" CA  THR D 541 "
           pdb=" C   THR D 541 "
           pdb=" N   HIS D 542 "
           pdb=" CA  HIS D 542 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.77   19.23     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  PRO C 296 "
           pdb=" C   PRO C 296 "
           pdb=" N   VAL C 297 "
           pdb=" CA  VAL C 297 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.62  -17.38     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" C   HIS D  93 "
           pdb=" N   HIS D  93 "
           pdb=" CA  HIS D  93 "
           pdb=" CB  HIS D  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.27    8.67     0      2.50e+00 1.60e-01 1.20e+01
  ... (remaining 5456 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1216
       0.058 -    0.116: 203
       0.116 -    0.174: 22
       0.174 -    0.232: 6
       0.232 -    0.289: 2
  Chirality restraints: 1449
  Sorted by residual:
  chirality pdb=" CA  ILE D  19 "
            pdb=" N   ILE D  19 "
            pdb=" C   ILE D  19 "
            pdb=" CB  ILE D  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CA  HIS D  93 "
            pdb=" N   HIS D  93 "
            pdb=" C   HIS D  93 "
            pdb=" CB  HIS D  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ARG C   2 "
            pdb=" N   ARG C   2 "
            pdb=" C   ARG C   2 "
            pdb=" CB  ARG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1446 not shown)

  Planarity restraints: 1590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D  90 "   -0.017 2.00e-02 2.50e+03   3.40e-02 1.15e+01
        pdb=" C   ALA D  90 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ALA D  90 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLY D  91 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D 557 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   GLN D 557 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLN D 557 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP D 558 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D  89 "    0.010 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" C   HIS D  89 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   HIS D  89 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA D  90 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1587 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1421
        2.76 -     3.29: 8859
        3.29 -     3.83: 14276
        3.83 -     4.36: 17801
        4.36 -     4.90: 30676
  Nonbonded interactions: 73033
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG D 105 "
            pdb=" O   THR D 330 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" ND2 ASN D 162 "
            pdb=" OH  TYR D 267 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" NE2 GLN C 421 "
            pdb=" OE1 GLU C 500 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   ALA C 365 "
            pdb=" OG1 THR C 525 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   SER C 315 "
            pdb=" CB  ASP C 319 "
     model   vdw
     2.262 3.440
  ... (remaining 73028 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.140
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
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      :  0.006   0.055   9143  Z= 0.371
  Angle     :  0.725   9.515  12421  Z= 0.449
  Chirality :  0.047   0.289   1449
  Planarity :  0.004   0.041   1590
  Dihedral  : 13.880  84.554   3319
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.60 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.23), residues: 1151
  helix: -1.55 (0.18), residues: 683
  sheet: -0.66 (0.75), residues: 49
  loop : -0.40 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 427 
 HIS   0.004   0.001   HIS D  93 
 PHE   0.012   0.001   PHE C 216 
 TYR   0.011   0.001   TYR D  88 
 ARG   0.006   0.001   ARG C 452 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8534 (tttt) cc_final: 0.8149 (mmtm)
REVERT: C  262 MET cc_start: 0.8726 (mmp) cc_final: 0.8499 (mmp)
REVERT: C  520 MET cc_start: 0.7007 (mtm) cc_final: 0.6756 (mtm)
REVERT: D   19 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7694 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 89
  average time/residue: 0.3020
  time to fit residues: 35.1056
Evaluate side-chains
  72 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   19 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C 208 GLN
C 571 GLN
D  41 GLN
D  92 GLN
D  93 HIS
D 129 GLN
D 377 GLN
D 431 ASN
D 490 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.126261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.089609 restraints weight = 11219.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 1.76
r_work: 0.2863 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9143  Z= 0.268
  Angle     :  0.624   6.086  12421  Z= 0.320
  Chirality :  0.042   0.146   1449
  Planarity :  0.005   0.037   1590
  Dihedral  :  4.424  18.149   1259
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.49 %
    Favored  : 91.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.24), residues: 1151
  helix:  0.14 (0.19), residues: 691
  sheet: -0.31 (0.79), residues: 49
  loop : -0.53 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 427 
 HIS   0.004   0.001   HIS C  85 
 PHE   0.014   0.002   PHE C 216 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.003   0.000   ARG C 522 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.938 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8768 (tttt) cc_final: 0.7918 (mmtm)
REVERT: C  183 ARG cc_start: 0.8557 (ttp80) cc_final: 0.7842 (mtm110)
REVERT: C  319 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8147 (m-30)
REVERT: C  515 GLU cc_start: 0.8349 (mp0) cc_final: 0.7815 (mp0)
REVERT: D   71 LEU cc_start: 0.8685 (tp) cc_final: 0.8409 (mt)
REVERT: D   94 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8823 (mp)
REVERT: D  154 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8027 (mp)
REVERT: D  325 LYS cc_start: 0.8538 (tttm) cc_final: 0.8300 (tttm)
  outliers start: 8
  outliers final: 3
  residues processed: 97
  average time/residue: 0.2575
  time to fit residues: 33.9302
Evaluate side-chains
  85 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  319 ASP
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  546 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 81 optimal weight:    0.0970
   chunk 99 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.6978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.128559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.091894 restraints weight = 11309.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.78
r_work: 0.2916 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9143  Z= 0.196
  Angle     :  0.540   6.748  12421  Z= 0.274
  Chirality :  0.039   0.138   1449
  Planarity :  0.004   0.037   1590
  Dihedral  :  4.130  17.037   1257
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.80 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1151
  helix:  1.03 (0.20), residues: 694
  sheet: -0.11 (0.77), residues: 49
  loop : -0.43 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.011   0.001   PHE C 164 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 384 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 1.223 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8741 (tttt) cc_final: 0.7941 (mmtm)
REVERT: C  183 ARG cc_start: 0.8568 (ttp80) cc_final: 0.7855 (mtm110)
REVERT: D   71 LEU cc_start: 0.8686 (tp) cc_final: 0.8409 (mt)
REVERT: D  154 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8184 (mp)
REVERT: D  441 ASP cc_start: 0.8371 (t0) cc_final: 0.8117 (t0)
REVERT: D  525 MET cc_start: 0.8376 (mmt) cc_final: 0.7831 (mmt)
  outliers start: 12
  outliers final: 6
  residues processed: 107
  average time/residue: 0.2901
  time to fit residues: 41.5664
Evaluate side-chains
  89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  343 ASP
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  546 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0270
   chunk 111 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0070
   overall best weight:    0.5856

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

Flipped N/Q/H residues before XYZ refinement:
C 385 GLN
C 571 GLN
D  41 GLN
** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.129784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.093097 restraints weight = 11194.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.79
r_work: 0.2916 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9143  Z= 0.178
  Angle     :  0.536  13.196  12421  Z= 0.266
  Chirality :  0.039   0.143   1449
  Planarity :  0.003   0.037   1590
  Dihedral  :  3.962  17.317   1257
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.55 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.25), residues: 1151
  helix:  1.45 (0.20), residues: 696
  sheet:  0.03 (0.76), residues: 49
  loop : -0.39 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.009   0.001   PHE C 216 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 100 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 1.001 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8697 (tttt) cc_final: 0.7923 (mmtm)
REVERT: C  183 ARG cc_start: 0.8539 (ttp80) cc_final: 0.7836 (mtm110)
REVERT: D   71 LEU cc_start: 0.8653 (tp) cc_final: 0.8393 (mt)
REVERT: D  154 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8182 (mp)
REVERT: D  441 ASP cc_start: 0.8378 (t0) cc_final: 0.8082 (t0)
REVERT: D  525 MET cc_start: 0.8344 (mmt) cc_final: 0.7809 (mmt)
REVERT: D  570 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7435 (tt)
  outliers start: 13
  outliers final: 8
  residues processed: 102
  average time/residue: 0.2587
  time to fit residues: 35.3585
Evaluate side-chains
  92 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  343 ASP
Chi-restraints excluded: chain C residue  401 ASP
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  299 GLU
Chi-restraints excluded: chain D residue  546 ASP
Chi-restraints excluded: chain D residue  570 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
C 385 GLN
** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.125557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.088731 restraints weight = 11283.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 1.77
r_work: 0.2764 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2620 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9143  Z= 0.330
  Angle     :  0.593  11.336  12421  Z= 0.294
  Chirality :  0.043   0.135   1449
  Planarity :  0.004   0.040   1590
  Dihedral  :  4.099  17.642   1257
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.58 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1151
  helix:  1.33 (0.20), residues: 701
  sheet: -0.15 (0.75), residues: 49
  loop : -0.39 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C  85 
 PHE   0.017   0.002   PHE C 216 
 TYR   0.017   0.002   TYR D  88 
 ARG   0.004   0.000   ARG C 452 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.947 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8722 (tttt) cc_final: 0.7889 (mmtm)
REVERT: C  183 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7755 (mtm110)
REVERT: C  520 MET cc_start: 0.8343 (mmm) cc_final: 0.7854 (mmm)
REVERT: D   71 LEU cc_start: 0.8553 (tp) cc_final: 0.8291 (mt)
REVERT: D  154 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8036 (mp)
REVERT: D  441 ASP cc_start: 0.8431 (t0) cc_final: 0.8080 (t0)
REVERT: D  525 MET cc_start: 0.8262 (mmt) cc_final: 0.7815 (mmt)
REVERT: D  570 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7329 (tt)
REVERT: D  588 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7362 (pt)
  outliers start: 17
  outliers final: 10
  residues processed: 101
  average time/residue: 0.2785
  time to fit residues: 37.5803
Evaluate side-chains
  95 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  343 ASP
Chi-restraints excluded: chain C residue  401 ASP
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  528 MET
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  546 ASP
Chi-restraints excluded: chain D residue  570 LEU
Chi-restraints excluded: chain D residue  588 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0370
   chunk 101 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0040
   chunk 55 optimal weight:    0.0570
   chunk 106 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
D 492 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.129200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.092645 restraints weight = 11178.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.76
r_work: 0.2824 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9143  Z= 0.155
  Angle     :  0.530  10.137  12421  Z= 0.262
  Chirality :  0.038   0.128   1449
  Planarity :  0.003   0.038   1590
  Dihedral  :  3.902  17.605   1257
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.33 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.25), residues: 1151
  helix:  1.70 (0.20), residues: 703
  sheet:  0.05 (0.78), residues: 49
  loop : -0.30 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.009   0.001   PHE C 216 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 100 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 1.041 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8643 (tttt) cc_final: 0.7830 (mmtm)
REVERT: C  183 ARG cc_start: 0.8496 (ttp80) cc_final: 0.7772 (mtm110)
REVERT: C  367 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8043 (mt-10)
REVERT: D   71 LEU cc_start: 0.8536 (tp) cc_final: 0.8301 (mt)
REVERT: D  154 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8095 (mp)
REVERT: D  441 ASP cc_start: 0.8425 (t0) cc_final: 0.8074 (t0)
REVERT: D  525 MET cc_start: 0.8170 (mmt) cc_final: 0.7714 (mmt)
REVERT: D  570 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7282 (tt)
REVERT: D  588 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7230 (pt)
  outliers start: 12
  outliers final: 6
  residues processed: 98
  average time/residue: 0.2693
  time to fit residues: 35.6864
Evaluate side-chains
  95 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  343 ASP
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  570 LEU
Chi-restraints excluded: chain D residue  588 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 104 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 112 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
C 385 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.126817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.090029 restraints weight = 11342.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.77
r_work: 0.2879 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9143  Z= 0.268
  Angle     :  0.563   9.669  12421  Z= 0.279
  Chirality :  0.041   0.134   1449
  Planarity :  0.004   0.036   1590
  Dihedral  :  3.953  17.823   1257
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.76 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1151
  helix:  1.61 (0.20), residues: 704
  sheet: -0.09 (0.77), residues: 49
  loop : -0.29 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C  85 
 PHE   0.014   0.001   PHE C 216 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 100 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.944 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8723 (tttt) cc_final: 0.7938 (mmtm)
REVERT: C  183 ARG cc_start: 0.8514 (ttp80) cc_final: 0.7792 (mtm110)
REVERT: C  367 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8068 (mt-10)
REVERT: D   71 LEU cc_start: 0.8604 (tp) cc_final: 0.8357 (mt)
REVERT: D  154 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8156 (mp)
REVERT: D  201 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8442 (mp)
REVERT: D  441 ASP cc_start: 0.8450 (t70) cc_final: 0.8087 (t0)
REVERT: D  525 MET cc_start: 0.8271 (mmt) cc_final: 0.7840 (mmt)
REVERT: D  570 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7346 (tt)
REVERT: D  588 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7378 (pt)
  outliers start: 19
  outliers final: 9
  residues processed: 104
  average time/residue: 0.2591
  time to fit residues: 36.9709
Evaluate side-chains
  100 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  343 ASP
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  201 LEU
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  570 LEU
Chi-restraints excluded: chain D residue  588 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 385 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.128602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.091788 restraints weight = 11356.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.80
r_work: 0.2915 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9143  Z= 0.196
  Angle     :  0.539   9.116  12421  Z= 0.267
  Chirality :  0.039   0.148   1449
  Planarity :  0.003   0.037   1590
  Dihedral  :  3.864  17.661   1257
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.08 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1151
  helix:  1.75 (0.20), residues: 704
  sheet: -0.07 (0.78), residues: 49
  loop : -0.24 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.012   0.001   PHE C 216 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 100 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 1.006 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8706 (tttt) cc_final: 0.7958 (mmtm)
REVERT: C  183 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7816 (mtm110)
REVERT: C  367 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8078 (mt-10)
REVERT: C  515 GLU cc_start: 0.7881 (pp20) cc_final: 0.7596 (mp0)
REVERT: D   71 LEU cc_start: 0.8618 (tp) cc_final: 0.8387 (mt)
REVERT: D  154 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8225 (mp)
REVERT: D  201 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8506 (mp)
REVERT: D  441 ASP cc_start: 0.8451 (t70) cc_final: 0.8081 (t0)
REVERT: D  525 MET cc_start: 0.8283 (mmt) cc_final: 0.7828 (mmt)
REVERT: D  570 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7344 (tt)
REVERT: D  588 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7364 (pt)
  outliers start: 16
  outliers final: 10
  residues processed: 100
  average time/residue: 0.2603
  time to fit residues: 35.2684
Evaluate side-chains
  98 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  170 MET
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  343 ASP
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  201 LEU
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  408 ILE
Chi-restraints excluded: chain D residue  570 LEU
Chi-restraints excluded: chain D residue  588 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.129806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.093201 restraints weight = 11093.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 1.78
r_work: 0.2916 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9143  Z= 0.207
  Angle     :  0.546   8.959  12421  Z= 0.269
  Chirality :  0.040   0.132   1449
  Planarity :  0.004   0.041   1590
  Dihedral  :  3.864  17.721   1257
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.40 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.25), residues: 1151
  helix:  1.81 (0.20), residues: 702
  sheet: -0.08 (0.77), residues: 49
  loop : -0.25 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.012   0.001   PHE C 216 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 100 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 1.063 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8715 (tttt) cc_final: 0.7963 (mmtm)
REVERT: C  183 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7810 (mtm110)
REVERT: C  367 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8057 (mt-10)
REVERT: C  515 GLU cc_start: 0.7911 (pp20) cc_final: 0.7702 (pp20)
REVERT: D   71 LEU cc_start: 0.8614 (tp) cc_final: 0.8381 (mt)
REVERT: D  154 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8220 (mp)
REVERT: D  201 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8509 (mp)
REVERT: D  441 ASP cc_start: 0.8455 (t70) cc_final: 0.8080 (t0)
REVERT: D  525 MET cc_start: 0.8276 (mmt) cc_final: 0.7819 (mmt)
REVERT: D  570 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7360 (tt)
REVERT: D  588 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7339 (pt)
  outliers start: 14
  outliers final: 9
  residues processed: 101
  average time/residue: 0.2545
  time to fit residues: 35.0530
Evaluate side-chains
  99 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  343 ASP
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  201 LEU
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  570 LEU
Chi-restraints excluded: chain D residue  588 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.129990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.093320 restraints weight = 11257.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.79
r_work: 0.2831 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9143  Z= 0.190
  Angle     :  0.541   8.835  12421  Z= 0.267
  Chirality :  0.039   0.130   1449
  Planarity :  0.004   0.048   1590
  Dihedral  :  3.834  17.708   1257
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 15.72 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.25), residues: 1151
  helix:  1.87 (0.20), residues: 703
  sheet: -0.06 (0.78), residues: 49
  loop : -0.21 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.011   0.001   PHE C 216 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.009   0.000   ARG C 452 

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 1.041 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8665 (tttt) cc_final: 0.7872 (mmtm)
REVERT: C  183 ARG cc_start: 0.8461 (ttp80) cc_final: 0.7765 (mtm110)
REVERT: C  367 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8078 (mt-10)
REVERT: D   71 LEU cc_start: 0.8537 (tp) cc_final: 0.8300 (mt)
REVERT: D  154 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8113 (mp)
REVERT: D  201 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8406 (mp)
REVERT: D  525 MET cc_start: 0.8185 (mmt) cc_final: 0.7741 (mmt)
REVERT: D  570 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7279 (tt)
REVERT: D  588 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7191 (pt)
  outliers start: 13
  outliers final: 8
  residues processed: 99
  average time/residue: 0.2542
  time to fit residues: 34.1754
Evaluate side-chains
  98 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  343 ASP
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  201 LEU
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  570 LEU
Chi-restraints excluded: chain D residue  588 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 99 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 97 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0670
   chunk 74 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.5318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.130359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.093899 restraints weight = 11272.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 1.76
r_work: 0.2839 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9143  Z= 0.167
  Angle     :  0.549  15.091  12421  Z= 0.267
  Chirality :  0.039   0.146   1449
  Planarity :  0.003   0.051   1590
  Dihedral  :  3.762  17.540   1257
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.94 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.25), residues: 1151
  helix:  1.96 (0.20), residues: 709
  sheet: -0.01 (0.78), residues: 49
  loop : -0.16 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D  81 
 HIS   0.003   0.000   HIS C  85 
 PHE   0.009   0.001   PHE C 216 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.003   0.000   ARG C 522 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4753.73 seconds
wall clock time: 84 minutes 51.72 seconds (5091.72 seconds total)