Starting phenix.real_space_refine
on Tue Mar  3 22:54:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zdr_14667/03_2026/7zdr_14667_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zdr_14667/03_2026/7zdr_14667.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zdr_14667/03_2026/7zdr_14667.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zdr_14667/03_2026/7zdr_14667.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zdr_14667/03_2026/7zdr_14667_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zdr_14667/03_2026/7zdr_14667_neut.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      29      5.16       5
     C    5770      2.51       5
     N    1584      2.21       5
     O    1627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9014
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 4415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4415
          Classifications: {'peptide': 573}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 18, 'TRANS': 554}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "D"
      Number of atoms: 4567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4567
          Classifications: {'peptide': 585}
          Link IDs: {'PTRANS': 27, 'TRANS': 557}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.24, per 1000 atoms: 0.25
  Number of scatterers: 9014
  At special positions: 0
  Unit cell: (120.528, 77.841, 112.995, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      29     16.00
     P       3     15.00
     Mg      1     11.99
     O    1627      8.00
     N    1584      7.00
     C    5770      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 384.6 milliseconds
  

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2142

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      66.8% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1 through 3
      No H-bonds generated for 'chain 'C' and resid 1 through 3'
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 10 through 13
      removed outlier: 3.844A  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: 3.523A  pdb=" N   ILE C  22 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA C  25 " --> pdb=" O   GLY C  21 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE C  33 " --> pdb=" O   LEU C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 54
    Processing helix  chain 'C' and resid 59 through 104
      removed outlier: 3.579A  pdb=" N   TYR C  78 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE C  89 " --> pdb=" O   ALA C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 132
      removed outlier: 3.684A  pdb=" N   ASN C 121 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA C 125 " --> pdb=" O   ASN C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 137 through 156
    Processing helix  chain 'C' and resid 159 through 176
      removed outlier: 3.760A  pdb=" N   THR C 165 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 185 through 209
    Processing helix  chain 'C' and resid 209 through 216
      removed outlier: 3.510A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 267
      removed outlier: 3.608A  pdb=" N   MET C 251 " --> pdb=" O   SER C 247 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET C 262 " --> pdb=" O   ALA C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 290
      removed outlier: 4.338A  pdb=" N   ALA C 281 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE C 283 " --> pdb=" O   LEU C 279 " (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 319
      removed outlier: 3.840A  pdb=" N   GLY C 305 " --> pdb=" O   PHE C 301 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLN C 306 " --> pdb=" O   GLN C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 387
      removed outlier: 3.516A  pdb=" N   GLN C 385 " --> pdb=" O   THR C 381 " (cutoff:3.500A)
    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: 3.741A  pdb=" N   GLN C 414 " --> pdb=" O   ALA C 410 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 454
      removed outlier: 3.532A  pdb=" N   SER C 447 " --> pdb=" O   ASP C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 455 through 459
      removed outlier: 3.528A  pdb=" N   LEU C 458 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 492
    Processing helix  chain 'C' and resid 506 through 520
      removed outlier: 3.686A  pdb=" N   GLN C 512 " --> pdb=" O   THR C 508 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 562
      removed outlier: 3.598A  pdb=" N   ARG C 562 " --> pdb=" O   GLU C 558 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 564 through 572
    Processing helix  chain 'D' and resid 5 through 16
    Processing helix  chain 'D' and resid 17 through 19
      No H-bonds generated for 'chain 'D' and resid 17 through 19'
    Processing helix  chain 'D' and resid 20 through 54
      removed outlier: 3.608A  pdb=" N   LEU D  24 " --> pdb=" O   SER D  20 " (cutoff:3.500A)
      removed outlier: 3.605A  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: 3.520A  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 128
      removed outlier: 3.577A  pdb=" N   THR D 124 " --> pdb=" O   GLY D 120 " (cutoff:3.500A)
    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: 3.616A  pdb=" N   TYR D 137 " --> pdb=" O   MET D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 159
      removed outlier: 3.702A  pdb=" N   VAL D 148 " --> pdb=" O   MET D 144 " (cutoff:3.500A)
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 162 through 185
      removed outlier: 3.623A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 3.733A  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 187 through 194
      removed outlier: 3.656A  pdb=" N   ASN D 191 " --> pdb=" O   ALA D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 203
      removed outlier: 4.172A  pdb=" N   GLY D 203 " --> pdb=" O   ALA D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 211
    Processing helix  chain 'D' and resid 211 through 219
    Processing helix  chain 'D' and resid 220 through 273
      removed outlier: 4.085A  pdb=" N   GLU D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER D 227 " --> pdb=" O   ALA D 223 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLU D 241 " --> pdb=" O   GLN D 237 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL D 242 " --> pdb=" O   ARG D 238 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER D 249 " --> pdb=" O   LEU D 245 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 310
      removed outlier: 3.514A  pdb=" N   GLY D 290 " --> pdb=" O   THR D 286 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 3.931A  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 310 through 330
      removed outlier: 3.558A  pdb=" N   LYS D 314 " --> pdb=" O   PHE D 310 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER D 323 " --> pdb=" O   GLY D 319 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   THR D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 398
      removed outlier: 3.667A  pdb=" N   LEU D 392 " --> pdb=" O   GLY D 388 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU D 393 " --> pdb=" O   LYS D 389 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 417 through 422
    Processing helix  chain 'D' and resid 438 through 444
    Processing helix  chain 'D' and resid 451 through 462
    Processing helix  chain 'D' and resid 473 through 477
      removed outlier: 4.015A  pdb=" N   ASP D 476 " --> pdb=" O   GLN D 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 500
    Processing helix  chain 'D' and resid 517 through 530
    Processing helix  chain 'D' and resid 566 through 572
      removed outlier: 3.792A  pdb=" N   VAL D 572 " --> pdb=" O   ALA D 568 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 575 through 587
      removed outlier: 3.502A  pdb=" N   ARG D 584 " --> pdb=" O   LEU D 580 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 359 through 362
      removed outlier: 7.388A  pdb=" N   LEU C 361 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   ARG C 342 " --> pdb=" O   LEU C 361 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.375A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   THR C 530 " --> pdb=" O   ILE C 369 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   ILE C 371 " --> pdb=" O   THR C 530 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ALA C 370 " --> pdb=" O   ILE C 543 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   MET C 545 " --> pdb=" O   ALA C 370 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LEU C 372 " --> pdb=" O   MET C 545 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ILE C 542 " --> pdb=" O   GLN C 553 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLN C 553 " --> pdb=" O   ILE C 542 " (cutoff:3.500A)
      removed outlier: 7.115A  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 371 through 373
      removed outlier: 3.526A  pdb=" N   PHE D 371 " --> pdb=" O   ALA D 352 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 366
      removed outlier: 6.582A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 425 through 429
      removed outlier: 7.115A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 508 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ASP D 510 " --> pdb=" O   SER D 426 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL D 428 " --> pdb=" O   ASP D 510 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU D 509 " --> pdb=" O   VAL D 540 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE D 553 " --> pdb=" O   GLN D 564 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLN D 564 " --> pdb=" O   ILE D 553 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN D 557 " --> pdb=" O   ARG D 560 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG D 560 " --> pdb=" O   GLN D 557 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1569 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: 1.42

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2897
        1.33 -     1.45: 1107
        1.45 -     1.57: 5127
        1.57 -     1.69: 5
        1.69 -     1.81: 56
  Bond restraints: 9192
  Sorted by residual:
  bond pdb=" O3A ANP D 602 "
       pdb=" PB  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.23e+01
  bond pdb=" N3B ANP D 602 "
       pdb=" PG  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.795  1.691  0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" O5' ANP D 602 "
       pdb=" PA  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.655  1.580  0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" N   GLN D 377 "
       pdb=" CA  GLN D 377 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.23e-02 6.61e+03 7.10e+00
  bond pdb=" N   GLU C 350 "
       pdb=" CA  GLU C 350 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.31e-02 5.83e+03 6.88e+00
  ... (remaining 9187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.45: 12423
        3.45 -     6.89: 66
        6.89 -    10.34: 5
       10.34 -    13.78: 1
       13.78 -    17.23: 1
  Bond angle restraints: 12496
  Sorted by residual:
  angle pdb=" PB  ANP D 602 "
        pdb=" N3B ANP D 602 "
        pdb=" PG  ANP D 602 "
      ideal   model   delta    sigma   weight residual
     126.95  109.72   17.23 3.00e+00 1.11e-01 3.30e+01
  angle pdb=" N   ASN C 121 "
        pdb=" CA  ASN C 121 "
        pdb=" C   ASN C 121 "
      ideal   model   delta    sigma   weight residual
     112.89  108.02    4.87 1.24e+00 6.50e-01 1.54e+01
  angle pdb=" O1B ANP D 602 "
        pdb=" PB  ANP D 602 "
        pdb=" O2B ANP D 602 "
      ideal   model   delta    sigma   weight residual
     120.08  109.62   10.46 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" N   GLN C 248 "
        pdb=" CA  GLN C 248 "
        pdb=" C   GLN C 248 "
      ideal   model   delta    sigma   weight residual
     113.41  109.30    4.11 1.22e+00 6.72e-01 1.14e+01
  angle pdb=" CA  GLU C 350 "
        pdb=" C   GLU C 350 "
        pdb=" O   GLU C 350 "
      ideal   model   delta    sigma   weight residual
     121.81  118.07    3.74 1.18e+00 7.18e-01 1.01e+01
  ... (remaining 12491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.64: 4989
       19.64 -    39.29: 433
       39.29 -    58.93: 51
       58.93 -    78.58: 24
       78.58 -    98.22: 5
  Dihedral angle restraints: 5502
    sinusoidal: 2180
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CA  LYS C  12 "
           pdb=" C   LYS C  12 "
           pdb=" N   ARG C  13 "
           pdb=" CA  ARG C  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  MET D 556 "
           pdb=" C   MET D 556 "
           pdb=" N   GLN D 557 "
           pdb=" CA  GLN D 557 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.43   17.57     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" O1B ANP D 602 "
           pdb=" N3B ANP D 602 "
           pdb=" PB  ANP D 602 "
           pdb=" PG  ANP D 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15  -63.07   98.22     1      3.00e+01 1.11e-03 1.22e+01
  ... (remaining 5499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1177
       0.054 -    0.108: 247
       0.108 -    0.162: 26
       0.162 -    0.215: 3
       0.215 -    0.269: 1
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" C3' ANP D 602 "
            pdb=" C2' ANP D 602 "
            pdb=" C4' ANP D 602 "
            pdb=" O3' ANP D 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  TYR C 348 "
            pdb=" N   TYR C 348 "
            pdb=" C   TYR C 348 "
            pdb=" CB  TYR C 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  GLN C 232 "
            pdb=" N   GLN C 232 "
            pdb=" C   GLN C 232 "
            pdb=" CB  GLN C 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.61e-01
  ... (remaining 1451 not shown)

  Planarity restraints: 1595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 347 "    0.016 2.00e-02 2.50e+03   3.16e-02 9.96e+00
        pdb=" C   THR C 347 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR C 347 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR C 348 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 178 "    0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO C 179 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C 179 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 179 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 552 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.82e+00
        pdb=" C   GLU C 552 "    0.023 2.00e-02 2.50e+03
        pdb=" O   GLU C 552 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLN C 553 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1592 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 61
        2.61 -     3.18: 7681
        3.18 -     3.75: 13885
        3.75 -     4.33: 19631
        4.33 -     4.90: 32804
  Nonbonded interactions: 74062
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 390 "
            pdb="MG    MG D 601 "
     model   vdw
     2.031 2.170
  nonbonded pdb="MG    MG D 601 "
            pdb=" O1G ANP D 602 "
     model   vdw
     2.056 2.170
  nonbonded pdb=" OE1 GLN D 129 "
            pdb=" OG  SER D 323 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" NH2 ARG D   5 "
            pdb=" OD1 ASP D 322 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OG  SER C 438 "
            pdb=" OG  SER C 441 "
     model   vdw
     2.213 3.040
  ... (remaining 74057 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:             2.030
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.970
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
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   0.145   9192  Z= 0.275
  Angle     :  0.708  17.228  12496  Z= 0.378
  Chirality :  0.044   0.269   1454
  Planarity :  0.004   0.039   1595
  Dihedral  : 15.073  98.223   3360
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.22), residues: 1154
  helix: -1.59 (0.18), residues: 687
  sheet:  0.34 (0.70), residues: 52
  loop : -1.17 (0.26), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG D 560 
 TYR   0.015   0.001   TYR D 311 
 PHE   0.010   0.001   PHE D  73 
 TRP   0.014   0.001   TRP D 427 
 HIS   0.005   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 9192)
  covalent geometry    : angle       0.70824 (12496)
  hydrogen bonds       : bond        0.26029 (  536)
  hydrogen bonds       : angle       9.17640 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.301 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.7857 (t0) cc_final: 0.7495 (t0)
REVERT: C  541 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7819 (tp40)
REVERT: D  311 TYR cc_start: 0.7620 (t80) cc_final: 0.7407 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1160
  time to fit residues: 16.9108
Evaluate side-chains
  92 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
C 248 GLN
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 424 HIS
C 553 GLN
C 563 GLN
D  15 GLN
D 394 ASN
D 433 GLN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 461 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.138044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.103449 restraints weight = 10645.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.70
r_work: 0.2983 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9192  Z= 0.162
  Angle     :  0.620   8.294  12496  Z= 0.316
  Chirality :  0.041   0.146   1454
  Planarity :  0.005   0.042   1595
  Dihedral  :  7.576  90.001   1294
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  6.84 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.23), residues: 1154
  helix:  0.14 (0.19), residues: 717
  sheet:  0.19 (0.74), residues: 47
  loop : -1.12 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 560 
 TYR   0.019   0.002   TYR D  88 
 PHE   0.014   0.001   PHE C 346 
 TRP   0.014   0.001   TRP D  81 
 HIS   0.005   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 9192)
  covalent geometry    : angle       0.62023 (12496)
  hydrogen bonds       : bond        0.05549 (  536)
  hydrogen bonds       : angle       4.78882 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.349 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8269 (t0) cc_final: 0.7823 (t0)
REVERT: C  506 ASP cc_start: 0.7452 (p0) cc_final: 0.6810 (t0)
REVERT: C  541 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7849 (tp-100)
REVERT: D   94 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8917 (mp)
REVERT: D  154 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8112 (mp)
REVERT: D  311 TYR cc_start: 0.7897 (t80) cc_final: 0.7641 (t80)
REVERT: D  587 GLU cc_start: 0.7448 (tt0) cc_final: 0.7241 (tt0)
  outliers start: 7
  outliers final: 3
  residues processed: 110
  average time/residue: 0.1204
  time to fit residues: 17.7043
Evaluate side-chains
  98 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 111 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 105 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 237 GLN
C 394 GLN
C 549 GLN
D 143 GLN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.139811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.105333 restraints weight = 10553.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.68
r_work: 0.3005 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9192  Z= 0.140
  Angle     :  0.549   7.948  12496  Z= 0.277
  Chirality :  0.040   0.136   1454
  Planarity :  0.004   0.042   1595
  Dihedral  :  6.241  88.317   1294
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.48 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.24), residues: 1154
  helix:  0.99 (0.19), residues: 709
  sheet:  0.39 (0.74), residues: 47
  loop : -0.96 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 139 
 TYR   0.020   0.002   TYR D  88 
 PHE   0.016   0.001   PHE C 346 
 TRP   0.014   0.001   TRP D  81 
 HIS   0.005   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9192)
  covalent geometry    : angle       0.54880 (12496)
  hydrogen bonds       : bond        0.04625 (  536)
  hydrogen bonds       : angle       4.25535 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.338 
Fit side-chains
REVERT: C  118 GLU cc_start: 0.7498 (pt0) cc_final: 0.7244 (pp20)
REVERT: C  343 ASP cc_start: 0.8336 (t0) cc_final: 0.7830 (t0)
REVERT: C  394 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7925 (pt0)
REVERT: D   94 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8945 (mp)
REVERT: D  154 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8444 (mt)
REVERT: D  234 ASP cc_start: 0.8324 (t0) cc_final: 0.8098 (t0)
REVERT: D  311 TYR cc_start: 0.7908 (t80) cc_final: 0.7687 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1048
  time to fit residues: 16.2029
Evaluate side-chains
  105 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  394 GLN
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  167 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 113 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 557 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.140057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.105409 restraints weight = 10636.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 1.69
r_work: 0.2951 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9192  Z= 0.139
  Angle     :  0.536   7.799  12496  Z= 0.271
  Chirality :  0.040   0.136   1454
  Planarity :  0.004   0.043   1595
  Dihedral  :  5.898  86.635   1294
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.55 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.24), residues: 1154
  helix:  1.31 (0.19), residues: 714
  sheet:  0.30 (0.75), residues: 47
  loop : -0.97 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 139 
 TYR   0.020   0.002   TYR D  88 
 PHE   0.019   0.001   PHE C 346 
 TRP   0.014   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9192)
  covalent geometry    : angle       0.53605 (12496)
  hydrogen bonds       : bond        0.04354 (  536)
  hydrogen bonds       : angle       4.11955 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.353 
Fit side-chains
REVERT: C  118 GLU cc_start: 0.7417 (pt0) cc_final: 0.7157 (pp20)
REVERT: C  343 ASP cc_start: 0.8353 (t0) cc_final: 0.7775 (t0)
REVERT: C  506 ASP cc_start: 0.7221 (p0) cc_final: 0.6438 (t0)
REVERT: C  541 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7602 (tp-100)
REVERT: D   94 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8923 (mp)
REVERT: D  154 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8421 (mt)
REVERT: D  233 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7887 (mt-10)
REVERT: D  234 ASP cc_start: 0.8244 (t0) cc_final: 0.7993 (t0)
REVERT: D  311 TYR cc_start: 0.7840 (t80) cc_final: 0.7600 (t80)
REVERT: D  460 ASP cc_start: 0.8236 (m-30) cc_final: 0.8011 (m-30)
REVERT: D  529 ASN cc_start: 0.8318 (t0) cc_final: 0.7999 (m-40)
  outliers start: 20
  outliers final: 9
  residues processed: 118
  average time/residue: 0.1142
  time to fit residues: 18.1373
Evaluate side-chains
  113 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  167 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 7 optimal weight:    0.0970
   chunk 50 optimal weight:    0.0970
   chunk 20 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 110 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 101 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0470
   overall best weight:    0.2874

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
C 421 GLN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.143579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.109222 restraints weight = 10522.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.70
r_work: 0.3008 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9192  Z= 0.103
  Angle     :  0.486   6.527  12496  Z= 0.248
  Chirality :  0.038   0.212   1454
  Planarity :  0.004   0.046   1595
  Dihedral  :  5.577  85.442   1294
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.94 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.25), residues: 1154
  helix:  1.70 (0.20), residues: 708
  sheet:  0.38 (0.77), residues: 47
  loop : -0.92 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 139 
 TYR   0.013   0.001   TYR D  88 
 PHE   0.019   0.001   PHE C 346 
 TRP   0.015   0.001   TRP D  81 
 HIS   0.003   0.000   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 9192)
  covalent geometry    : angle       0.48580 (12496)
  hydrogen bonds       : bond        0.03824 (  536)
  hydrogen bonds       : angle       3.88970 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.343 
Fit side-chains
REVERT: C  118 GLU cc_start: 0.7403 (pt0) cc_final: 0.7167 (pp20)
REVERT: C  343 ASP cc_start: 0.8341 (t0) cc_final: 0.7762 (t0)
REVERT: C  506 ASP cc_start: 0.7268 (p0) cc_final: 0.6414 (t0)
REVERT: C  541 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7373 (tp-100)
REVERT: D   94 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8900 (mp)
REVERT: D  154 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8425 (mt)
REVERT: D  233 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7812 (mt-10)
REVERT: D  234 ASP cc_start: 0.8227 (t0) cc_final: 0.7959 (t0)
REVERT: D  311 TYR cc_start: 0.7764 (t80) cc_final: 0.7554 (t80)
REVERT: D  460 ASP cc_start: 0.8126 (m-30) cc_final: 0.7922 (m-30)
REVERT: D  529 ASN cc_start: 0.8271 (t0) cc_final: 0.8007 (m-40)
  outliers start: 13
  outliers final: 7
  residues processed: 119
  average time/residue: 0.1110
  time to fit residues: 17.9682
Evaluate side-chains
  110 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0970
   chunk 100 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 557 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.139755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.104490 restraints weight = 10556.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.77
r_work: 0.3024 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9192  Z= 0.121
  Angle     :  0.513   8.650  12496  Z= 0.257
  Chirality :  0.039   0.199   1454
  Planarity :  0.004   0.048   1595
  Dihedral  :  5.507  81.833   1294
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.26 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.25), residues: 1154
  helix:  1.74 (0.20), residues: 709
  sheet:  0.33 (0.77), residues: 47
  loop : -0.89 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 560 
 TYR   0.016   0.001   TYR D  88 
 PHE   0.021   0.001   PHE C 346 
 TRP   0.012   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9192)
  covalent geometry    : angle       0.51273 (12496)
  hydrogen bonds       : bond        0.03933 (  536)
  hydrogen bonds       : angle       3.88157 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.363 
Fit side-chains
REVERT: C  118 GLU cc_start: 0.7505 (pt0) cc_final: 0.7296 (pp20)
REVERT: C  343 ASP cc_start: 0.8391 (t0) cc_final: 0.7828 (t0)
REVERT: C  541 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7485 (tp-100)
REVERT: D   94 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8963 (mp)
REVERT: D  154 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8505 (mt)
REVERT: D  234 ASP cc_start: 0.8291 (t0) cc_final: 0.8057 (t0)
REVERT: D  311 TYR cc_start: 0.7884 (t80) cc_final: 0.7656 (t80)
REVERT: D  460 ASP cc_start: 0.8135 (m-30) cc_final: 0.7920 (m-30)
REVERT: D  529 ASN cc_start: 0.8335 (t0) cc_final: 0.8089 (m-40)
REVERT: D  566 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7086 (mtt180)
  outliers start: 18
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1109
  time to fit residues: 17.1349
Evaluate side-chains
  112 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 40 optimal weight:    0.0040
   chunk 96 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 557 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.140633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.105589 restraints weight = 10640.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.71
r_work: 0.3007 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9192  Z= 0.149
  Angle     :  0.541   7.982  12496  Z= 0.271
  Chirality :  0.041   0.228   1454
  Planarity :  0.004   0.053   1595
  Dihedral  :  5.522  78.817   1294
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.80 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.25), residues: 1154
  helix:  1.64 (0.20), residues: 715
  sheet:  0.21 (0.78), residues: 47
  loop : -0.87 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 560 
 TYR   0.018   0.001   TYR D  88 
 PHE   0.030   0.001   PHE C 346 
 TRP   0.011   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9192)
  covalent geometry    : angle       0.54054 (12496)
  hydrogen bonds       : bond        0.04187 (  536)
  hydrogen bonds       : angle       3.95335 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.214 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8388 (t0) cc_final: 0.7578 (t0)
REVERT: C  506 ASP cc_start: 0.7186 (p0) cc_final: 0.6458 (t0)
REVERT: C  541 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7509 (tp-100)
REVERT: D   94 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9008 (mp)
REVERT: D  154 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8544 (mt)
REVERT: D  234 ASP cc_start: 0.8282 (t0) cc_final: 0.8054 (t0)
REVERT: D  311 TYR cc_start: 0.7948 (t80) cc_final: 0.7726 (t80)
REVERT: D  342 LEU cc_start: 0.8934 (tp) cc_final: 0.8631 (tp)
REVERT: D  529 ASN cc_start: 0.8390 (t0) cc_final: 0.8140 (m-40)
REVERT: D  566 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7076 (mtt180)
  outliers start: 16
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1119
  time to fit residues: 17.0562
Evaluate side-chains
  115 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0270
   chunk 64 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 456 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.142127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.107493 restraints weight = 10525.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.70
r_work: 0.3068 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9192  Z= 0.120
  Angle     :  0.519   7.419  12496  Z= 0.262
  Chirality :  0.039   0.191   1454
  Planarity :  0.004   0.051   1595
  Dihedral  :  5.416  77.997   1294
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.33 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.25), residues: 1154
  helix:  1.84 (0.20), residues: 704
  sheet:  0.20 (0.78), residues: 47
  loop : -0.91 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 560 
 TYR   0.018   0.001   TYR D  88 
 PHE   0.033   0.001   PHE C 346 
 TRP   0.018   0.001   TRP C 390 
 HIS   0.003   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9192)
  covalent geometry    : angle       0.51857 (12496)
  hydrogen bonds       : bond        0.03924 (  536)
  hydrogen bonds       : angle       3.88088 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.343 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8317 (t0) cc_final: 0.7510 (t0)
REVERT: C  506 ASP cc_start: 0.7188 (p0) cc_final: 0.6450 (t0)
REVERT: C  541 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7416 (tp-100)
REVERT: D   94 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8970 (mp)
REVERT: D  154 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8523 (mt)
REVERT: D  234 ASP cc_start: 0.8241 (t0) cc_final: 0.8010 (t0)
REVERT: D  311 TYR cc_start: 0.7859 (t80) cc_final: 0.7639 (t80)
REVERT: D  342 LEU cc_start: 0.8893 (tp) cc_final: 0.8661 (tp)
REVERT: D  529 ASN cc_start: 0.8339 (t0) cc_final: 0.8127 (m-40)
REVERT: D  566 ARG cc_start: 0.7493 (mtp85) cc_final: 0.7100 (mmt180)
  outliers start: 16
  outliers final: 12
  residues processed: 109
  average time/residue: 0.1177
  time to fit residues: 17.2200
Evaluate side-chains
  112 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0000
   chunk 7 optimal weight:    0.3980
   chunk 111 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
D 442 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.142831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.108050 restraints weight = 10547.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.72
r_work: 0.3057 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9192  Z= 0.113
  Angle     :  0.507   7.780  12496  Z= 0.256
  Chirality :  0.039   0.180   1454
  Planarity :  0.004   0.052   1595
  Dihedral  :  5.322  75.898   1294
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.22 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.25), residues: 1154
  helix:  1.92 (0.20), residues: 704
  sheet:  0.15 (0.78), residues: 47
  loop : -0.90 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 560 
 TYR   0.017   0.001   TYR D  88 
 PHE   0.039   0.001   PHE C 346 
 TRP   0.017   0.001   TRP C 390 
 HIS   0.003   0.000   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9192)
  covalent geometry    : angle       0.50734 (12496)
  hydrogen bonds       : bond        0.03813 (  536)
  hydrogen bonds       : angle       3.83756 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.368 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8318 (t0) cc_final: 0.7496 (t0)
REVERT: C  506 ASP cc_start: 0.7219 (p0) cc_final: 0.6475 (t0)
REVERT: C  541 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7402 (tp-100)
REVERT: D   94 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8970 (mp)
REVERT: D  234 ASP cc_start: 0.8269 (t0) cc_final: 0.8041 (t0)
REVERT: D  311 TYR cc_start: 0.7855 (t80) cc_final: 0.7626 (t80)
REVERT: D  342 LEU cc_start: 0.8820 (tp) cc_final: 0.8575 (tp)
REVERT: D  463 TRP cc_start: 0.8917 (m100) cc_final: 0.8689 (m100)
REVERT: D  529 ASN cc_start: 0.8328 (t0) cc_final: 0.8056 (m110)
REVERT: D  566 ARG cc_start: 0.7506 (mtp85) cc_final: 0.7108 (mmt180)
  outliers start: 18
  outliers final: 11
  residues processed: 110
  average time/residue: 0.1121
  time to fit residues: 16.8947
Evaluate side-chains
  106 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0050
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
D 442 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.142502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.107727 restraints weight = 10623.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.71
r_work: 0.3073 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9192  Z= 0.123
  Angle     :  0.525   8.983  12496  Z= 0.264
  Chirality :  0.040   0.191   1454
  Planarity :  0.004   0.054   1595
  Dihedral  :  5.304  74.195   1294
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.76 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.25), residues: 1154
  helix:  1.87 (0.20), residues: 704
  sheet:  0.08 (0.77), residues: 47
  loop : -0.89 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D 560 
 TYR   0.018   0.001   TYR D  88 
 PHE   0.036   0.001   PHE C 346 
 TRP   0.018   0.001   TRP C 390 
 HIS   0.004   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9192)
  covalent geometry    : angle       0.52545 (12496)
  hydrogen bonds       : bond        0.03882 (  536)
  hydrogen bonds       : angle       3.83706 ( 1569)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.337 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8279 (t0) cc_final: 0.7472 (t0)
REVERT: C  506 ASP cc_start: 0.7212 (p0) cc_final: 0.6466 (t0)
REVERT: C  541 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7403 (tp-100)
REVERT: D   94 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8952 (mp)
REVERT: D  234 ASP cc_start: 0.8261 (t0) cc_final: 0.8022 (t0)
REVERT: D  311 TYR cc_start: 0.7873 (t80) cc_final: 0.7634 (t80)
REVERT: D  342 LEU cc_start: 0.8792 (tp) cc_final: 0.8553 (tp)
REVERT: D  566 ARG cc_start: 0.7491 (mtp85) cc_final: 0.7084 (mmt180)
  outliers start: 13
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1193
  time to fit residues: 16.8212
Evaluate side-chains
  106 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  167 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.141712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.106665 restraints weight = 10481.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.72
r_work: 0.3039 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9192  Z= 0.135
  Angle     :  0.538  10.532  12496  Z= 0.270
  Chirality :  0.040   0.200   1454
  Planarity :  0.004   0.056   1595
  Dihedral  :  5.321  73.040   1294
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.97 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.25), residues: 1154
  helix:  1.81 (0.20), residues: 705
  sheet:  0.04 (0.77), residues: 47
  loop : -0.90 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D 560 
 TYR   0.019   0.001   TYR D  88 
 PHE   0.036   0.001   PHE C 346 
 TRP   0.019   0.001   TRP C 390 
 HIS   0.004   0.001   HIS C 368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9192)
  covalent geometry    : angle       0.53840 (12496)
  hydrogen bonds       : bond        0.04020 (  536)
  hydrogen bonds       : angle       3.88045 ( 1569)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2316.70 seconds
wall clock time: 40 minutes 20.56 seconds (2420.56 seconds total)