Starting phenix.real_space_refine
on Thu Mar 13 13:47:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zd5_14636/03_2025/7zd5_14636_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zd5_14636/03_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_14636/03_2025/7zd5_14636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zd5_14636/03_2025/7zd5_14636.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zd5_14636/03_2025/7zd5_14636_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zd5_14636/03_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-5624/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: 5.90, per 1000 atoms: 0.66
  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: 2.24
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.01
  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: 2.58

  Time building geometry restraints manager: 2.66 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:                  0.010
  Normalize map: mean=0, sd=1:             13.110
  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:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.750
  Find NCS groups from input model:        0.120
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.440
-------------------------------------------------------------------------------
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  : 1.045 
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: 0.2879
  time to fit residues: 33.8218
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  : 0.931 
-------------------------------------------------------------------------------
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 = 0.126260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.089603 restraints weight = 11219.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 1.76
r_work: 0.2902 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
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   6.087  12421  Z= 0.321
  Chirality :  0.042   0.146   1449
  Planarity :  0.005   0.037   1590
  Dihedral  :  4.424  18.149   1259
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.84
  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  : 0.969 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8780 (tttt) cc_final: 0.7954 (mmtm)
REVERT: C  183 ARG cc_start: 0.8562 (ttp80) cc_final: 0.7860 (mtm110)
REVERT: C  319 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8138 (m-30)
REVERT: C  515 GLU cc_start: 0.8345 (mp0) cc_final: 0.7823 (mp0)
REVERT: D   71 LEU cc_start: 0.8712 (tp) cc_final: 0.8439 (mt)
REVERT: D   94 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8854 (mp)
REVERT: D  154 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8071 (mp)
REVERT: D  325 LYS cc_start: 0.8566 (tttm) cc_final: 0.8332 (tttm)
  outliers start: 8
  outliers final: 3
  residues processed: 97
  average time/residue: 0.2550
  time to fit residues: 33.5163
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  : 1.046 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.129240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.094449 restraints weight = 11254.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.72
r_work: 0.2915 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9143  Z= 0.220
  Angle     :  0.551   6.240  12421  Z= 0.280
  Chirality :  0.040   0.139   1449
  Planarity :  0.004   0.036   1590
  Dihedral  :  4.166  17.174   1257
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.02 %
    Favored  : 87.81 %
  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:  0.57 (0.25), residues: 1151
  helix:  0.97 (0.20), residues: 694
  sheet: -0.17 (0.76), residues: 49
  loop : -0.44 (0.30), residues: 408

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   0.010   0.001   PHE C 346 
 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
  104 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 1.000 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8734 (tttt) cc_final: 0.7925 (mmtm)
REVERT: C  183 ARG cc_start: 0.8562 (ttp80) cc_final: 0.7857 (mtm110)
REVERT: D   71 LEU cc_start: 0.8656 (tp) cc_final: 0.8403 (mt)
REVERT: D  154 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8181 (mp)
REVERT: D  325 LYS cc_start: 0.8528 (tttm) cc_final: 0.8294 (tttp)
REVERT: D  441 ASP cc_start: 0.8367 (t0) cc_final: 0.8108 (t0)
REVERT: D  525 MET cc_start: 0.8356 (mmt) cc_final: 0.7916 (mmt)
  outliers start: 11
  outliers final: 6
  residues processed: 101
  average time/residue: 0.2500
  time to fit residues: 34.0245
Evaluate side-chains
  87 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0870
   overall best weight:    0.7362

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.127992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.091388 restraints weight = 11257.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 1.76
r_work: 0.2917 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.1859

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= 0.198
  Angle     :  0.539  12.251  12421  Z= 0.268
  Chirality :  0.039   0.132   1449
  Planarity :  0.003   0.037   1590
  Dihedral  :  4.021  17.478   1257
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.09 %
    Favored  : 86.52 %
  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:  0.96 (0.25), residues: 1151
  helix:  1.34 (0.20), residues: 695
  sheet: -0.06 (0.75), residues: 49
  loop : -0.40 (0.30), residues: 407

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   0.011   0.001   PHE C 216 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.002   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
  102 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.911 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8722 (tttt) cc_final: 0.7960 (mmtm)
REVERT: C  183 ARG cc_start: 0.8535 (ttp80) cc_final: 0.7840 (mtm110)
REVERT: C  212 GLU cc_start: 0.7845 (mp0) cc_final: 0.7639 (mp0)
REVERT: D   71 LEU cc_start: 0.8645 (tp) cc_final: 0.8409 (mt)
REVERT: D  154 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8219 (mp)
REVERT: D  325 LYS cc_start: 0.8517 (tttm) cc_final: 0.8301 (tttp)
REVERT: D  427 TRP cc_start: 0.7231 (p-90) cc_final: 0.6975 (p-90)
REVERT: D  441 ASP cc_start: 0.8366 (t0) cc_final: 0.8064 (t0)
REVERT: D  525 MET cc_start: 0.8375 (mmt) cc_final: 0.7846 (mmt)
REVERT: D  570 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7465 (tt)
  outliers start: 13
  outliers final: 8
  residues processed: 98
  average time/residue: 0.2488
  time to fit residues: 32.8629
Evaluate side-chains
  95 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0870
   chunk 75 optimal weight:    0.3980
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
C 385 GLN
C 421 GLN
C 571 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 = 0.3453 r_free = 0.3453 target = 0.129241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.092627 restraints weight = 11173.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.78
r_work: 0.2894 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2038

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= 0.174
  Angle     :  0.524  11.404  12421  Z= 0.261
  Chirality :  0.039   0.131   1449
  Planarity :  0.003   0.038   1590
  Dihedral  :  3.905  17.325   1257
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.37 %
    Favored  : 85.13 %
  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:  1.25 (0.25), residues: 1151
  helix:  1.57 (0.20), residues: 702
  sheet:  0.06 (0.77), residues: 49
  loop : -0.34 (0.30), residues: 400

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   0.005   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
  108 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.926 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8673 (tttt) cc_final: 0.7888 (mmtm)
REVERT: C  183 ARG cc_start: 0.8519 (ttp80) cc_final: 0.7779 (mtm110)
REVERT: C  367 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: C  520 MET cc_start: 0.8272 (mmm) cc_final: 0.7877 (mmm)
REVERT: D   71 LEU cc_start: 0.8587 (tp) cc_final: 0.8356 (mt)
REVERT: D  154 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8164 (mp)
REVERT: D  325 LYS cc_start: 0.8445 (tttm) cc_final: 0.8230 (tttp)
REVERT: D  427 TRP cc_start: 0.7346 (p-90) cc_final: 0.7117 (p-90)
REVERT: D  441 ASP cc_start: 0.8405 (t0) cc_final: 0.8073 (t0)
REVERT: D  525 MET cc_start: 0.8320 (mmt) cc_final: 0.7815 (mmt)
REVERT: D  570 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7357 (tt)
  outliers start: 14
  outliers final: 8
  residues processed: 105
  average time/residue: 0.2471
  time to fit residues: 34.8605
Evaluate side-chains
  94 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
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  526 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   52 MET
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  546 ASP
Chi-restraints excluded: chain D residue  570 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0980
   chunk 55 optimal weight:    4.9990
   chunk 106 optimal weight:    0.5980
   chunk 111 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.090337 restraints weight = 11211.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.76
r_work: 0.2886 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9143  Z= 0.252
  Angle     :  0.557  10.330  12421  Z= 0.276
  Chirality :  0.040   0.133   1449
  Planarity :  0.004   0.037   1590
  Dihedral  :  3.952  17.773   1257
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.01 %
    Favored  : 84.17 %
  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:  1.24 (0.25), residues: 1151
  helix:  1.55 (0.20), residues: 703
  sheet:  0.04 (0.77), residues: 49
  loop : -0.31 (0.31), residues: 399

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   0.002   0.000   ARG D 210 

*********************** 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
  107 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.937 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8713 (tttt) cc_final: 0.7935 (mmtm)
REVERT: C  183 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7787 (mtm110)
REVERT: C  367 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8049 (mt-10)
REVERT: D   71 LEU cc_start: 0.8607 (tp) cc_final: 0.8363 (mt)
REVERT: D  154 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8172 (mp)
REVERT: D  441 ASP cc_start: 0.8424 (t70) cc_final: 0.8070 (t0)
REVERT: D  525 MET cc_start: 0.8289 (mmt) cc_final: 0.7809 (mmt)
REVERT: D  570 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7341 (tt)
  outliers start: 17
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2525
  time to fit residues: 34.6632
Evaluate side-chains
  97 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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  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:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 112 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.127271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.090513 restraints weight = 11324.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 1.77
r_work: 0.2792 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2646 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9143  Z= 0.238
  Angle     :  0.550   9.771  12421  Z= 0.273
  Chirality :  0.040   0.131   1449
  Planarity :  0.004   0.037   1590
  Dihedral  :  3.945  18.074   1257
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.97 %
    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:  1.31 (0.25), residues: 1151
  helix:  1.62 (0.20), residues: 703
  sheet:  0.08 (0.78), residues: 49
  loop : -0.30 (0.31), residues: 399

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   0.013   0.001   PHE C 216 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.004   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
  107 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 1.078 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8688 (tttt) cc_final: 0.7865 (mmtm)
REVERT: C  183 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7762 (mtm110)
REVERT: C  367 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8054 (mt-10)
REVERT: D   71 LEU cc_start: 0.8549 (tp) cc_final: 0.8304 (mt)
REVERT: D  154 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8081 (mp)
REVERT: D  441 ASP cc_start: 0.8456 (t70) cc_final: 0.8092 (t0)
REVERT: D  525 MET cc_start: 0.8188 (mmt) cc_final: 0.7764 (mmt)
REVERT: D  570 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7268 (tt)
  outliers start: 18
  outliers final: 11
  residues processed: 104
  average time/residue: 0.2671
  time to fit residues: 38.8514
Evaluate side-chains
  98 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
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  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  530 THR
Chi-restraints excluded: chain D residue  154 ILE
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:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0370
   chunk 5 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 99 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 76 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5258

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.129640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.094305 restraints weight = 11324.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 1.66
r_work: 0.2857 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2280

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= 0.164
  Angle     :  0.521   9.121  12421  Z= 0.260
  Chirality :  0.039   0.130   1449
  Planarity :  0.003   0.038   1590
  Dihedral  :  3.823  17.847   1257
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 15.51 %
    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:  1.58 (0.25), residues: 1151
  helix:  1.87 (0.20), residues: 701
  sheet:  0.16 (0.79), residues: 49
  loop : -0.25 (0.30), residues: 401

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   0.010   0.001   PHE C 216 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.004   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
  105 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.086 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.8649 (tttt) cc_final: 0.7859 (mmtm)
REVERT: C  183 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7768 (mtm110)
REVERT: C  367 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8069 (mt-10)
REVERT: D   71 LEU cc_start: 0.8551 (tp) cc_final: 0.8311 (mt)
REVERT: D  154 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8147 (mp)
REVERT: D  201 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: D  441 ASP cc_start: 0.8452 (t70) cc_final: 0.8084 (t0)
REVERT: D  525 MET cc_start: 0.8185 (mmt) cc_final: 0.7764 (mmt)
REVERT: D  570 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7275 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2516
  time to fit residues: 35.4000
Evaluate side-chains
  100 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
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  570 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0270
   chunk 53 optimal weight:    0.7980
   chunk 93 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.130299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.093848 restraints weight = 11119.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.75
r_work: 0.2841 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9143  Z= 0.161
  Angle     :  0.528   9.202  12421  Z= 0.259
  Chirality :  0.039   0.131   1449
  Planarity :  0.003   0.044   1590
  Dihedral  :  3.762  17.835   1257
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.51 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.70 (0.25), residues: 1151
  helix:  1.97 (0.20), residues: 703
  sheet:  0.06 (0.77), 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   0.000   HIS C  85 
 PHE   0.010   0.001   PHE C 181 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.008   0.000   ARG D 193 

*********************** 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
  106 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8622 (tttt) cc_final: 0.7812 (mmtm)
REVERT: C  183 ARG cc_start: 0.8438 (ttp80) cc_final: 0.7740 (mtm110)
REVERT: C  367 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8037 (mt-10)
REVERT: D   71 LEU cc_start: 0.8494 (tp) cc_final: 0.8263 (mt)
REVERT: D  154 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8093 (mp)
REVERT: D  193 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7709 (mtm-85)
REVERT: D  201 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8357 (mp)
REVERT: D  441 ASP cc_start: 0.8465 (t70) cc_final: 0.8090 (t0)
REVERT: D  525 MET cc_start: 0.8153 (mmt) cc_final: 0.7729 (mmt)
REVERT: D  570 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7265 (tt)
  outliers start: 14
  outliers final: 7
  residues processed: 103
  average time/residue: 0.2362
  time to fit residues: 33.4611
Evaluate side-chains
  98 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
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  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  570 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 97 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3490 r_free = 0.3490 target = 0.131963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.095513 restraints weight = 11199.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.78
r_work: 0.2934 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.2394

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= 0.188
  Angle     :  0.545  14.514  12421  Z= 0.264
  Chirality :  0.039   0.136   1449
  Planarity :  0.004   0.048   1590
  Dihedral  :  3.756  17.750   1257
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 16.36 %
    Favored  : 82.57 %
  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:  1.71 (0.25), residues: 1151
  helix:  1.97 (0.20), residues: 702
  sheet:  0.18 (0.75), residues: 54
  loop : -0.21 (0.31), residues: 395

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   0.011   0.001   PHE C 216 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.007   0.000   ARG D 193 

********************** 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
  102 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8675 (tttt) cc_final: 0.7924 (mmtm)
REVERT: C  183 ARG cc_start: 0.8451 (ttp80) cc_final: 0.7813 (mtm110)
REVERT: C  367 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8070 (mt-10)
REVERT: D   71 LEU cc_start: 0.8594 (tp) cc_final: 0.8371 (mt)
REVERT: D  154 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8230 (mp)
REVERT: D  201 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8482 (mp)
REVERT: D  525 MET cc_start: 0.8285 (mmt) cc_final: 0.7847 (mmt)
REVERT: D  570 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7394 (tt)
  outliers start: 10
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2587
  time to fit residues: 34.8518
Evaluate side-chains
  100 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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  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  570 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.130909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.096198 restraints weight = 11221.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.68
r_work: 0.2916 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9143  Z= 0.213
  Angle     :  0.553  14.354  12421  Z= 0.268
  Chirality :  0.040   0.134   1449
  Planarity :  0.004   0.050   1590
  Dihedral  :  3.796  17.976   1257
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 16.47 %
    Favored  : 82.46 %
  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:  1.66 (0.25), residues: 1151
  helix:  1.92 (0.20), residues: 703
  sheet:  0.16 (0.74), residues: 54
  loop : -0.20 (0.31), residues: 394

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   0.013   0.001   PHE C 216 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 100 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4970.47 seconds
wall clock time: 86 minutes 47.48 seconds (5207.48 seconds total)