Starting phenix.real_space_refine
on Tue Sep 24 01:07:11 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/09_2024/8aqt_15589.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/09_2024/8aqt_15589.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/09_2024/8aqt_15589.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/09_2024/8aqt_15589.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/09_2024/8aqt_15589.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/09_2024/8aqt_15589.cif"
  }
  resolution = 4.4
  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=  -0.001 sd=   0.049
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      37      5.16       5
     C    4033      2.51       5
     N    1055      2.21       5
     O    1196      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 6321
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4744
          Classifications: {'peptide': 584}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 557}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 1535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1535
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 10, 'TRANS': 182}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.32, per 1000 atoms: 0.68
  Number of scatterers: 6321
  At special positions: 0
  Unit cell: (86.086, 91.3836, 116.547, 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      37     16.00
     O    1196      8.00
     N    1055      7.00
     C    4033      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG C   1 " - " ASN A  53 "
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1466

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      48.9% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 53
    Processing helix  chain 'A' and resid 56 through 80
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 111 through 117
      removed outlier: 3.623A  pdb=" N   GLN A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 129
      removed outlier: 4.350A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   TYR A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 153
      removed outlier: 4.222A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 3.509A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 187
      removed outlier: 3.847A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 193
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.827A  pdb=" N   TRP A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ARG A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 230
      removed outlier: 3.592A  pdb=" N   GLU A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLU A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ARG A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR A 229 " --> pdb=" O   ASP A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 4.030A  pdb=" N   GLU A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 234 through 239'
    Processing helix  chain 'A' and resid 239 through 252
      removed outlier: 3.756A  pdb=" N   TYR A 243 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ARG A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   LYS A 247 " --> pdb=" O   TYR A 243 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A 248 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASP A 250 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   TYR A 252 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 298
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.503A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 319
      removed outlier: 4.330A  pdb=" N   GLU A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   SER A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 330
      removed outlier: 3.733A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.368A  pdb=" N   LEU A 370 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   HIS A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   HIS A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ILE A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN A 380 " --> pdb=" O   MET A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 4.070A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 4.076A  pdb=" N   ILE A 421 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 446
      removed outlier: 3.995A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   GLN A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 464
      removed outlier: 3.682A  pdb=" N   LYS A 458 " --> pdb=" O   TYR A 454 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   PHE A 464 " --> pdb=" O   ARG A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 485
      removed outlier: 3.645A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 531
      removed outlier: 4.258A  pdb=" N   ARG A 518 " --> pdb=" O   ARG A 514 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR A 521 " --> pdb=" O   THR A 517 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN A 522 " --> pdb=" O   ARG A 518 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.777A  pdb=" N   LYS A 556 " --> pdb=" O   GLN A 552 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.968A  pdb=" N   GLU A 564 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 581 through 589
      removed outlier: 3.721A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 598
      removed outlier: 3.934A  pdb=" N   GLN A 598 " --> pdb=" O   TRP A 594 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 4.210A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 3.875A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 408
      removed outlier: 4.241A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 405 through 408'
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 349
      removed outlier: 3.885A  pdb=" N   THR A 347 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS A 359 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TRP A 349 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.597A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   TYR B 396 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE B 402 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 434 " --> pdb=" O   VAL B 511 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   VAL B 433 " --> pdb=" O   LYS B 378 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS B 378 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)

    191 hydrogen bonds defined for protein.
    564 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: 1.54

  Time building geometry restraints manager: 1.96 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: 1476
        1.33 -     1.45: 1554
        1.45 -     1.58: 3405
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6494
  Sorted by residual:
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.476 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" CA  SER B 477 "
       pdb=" CB  SER B 477 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.044 1.69e-02 3.50e+03 6.75e+00
  bond pdb=" C   PRO B 479 "
       pdb=" O   PRO B 479 "
    ideal  model  delta    sigma   weight residual
    1.235  1.208  0.027 1.30e-02 5.92e+03 4.40e+00
  bond pdb=" CB  PRO A 389 "
       pdb=" CG  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.492  1.578 -0.086 5.00e-02 4.00e+02 2.95e+00
  bond pdb=" N   THR B 478 "
       pdb=" CA  THR B 478 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.41e-02 5.03e+03 2.44e+00
  ... (remaining 6489 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 8664
        2.27 -     4.53: 133
        4.53 -     6.80: 17
        6.80 -     9.06: 4
        9.06 -    11.33: 1
  Bond angle restraints: 8819
  Sorted by residual:
  angle pdb=" C   PRO B 479 "
        pdb=" CA  PRO B 479 "
        pdb=" CB  PRO B 479 "
      ideal   model   delta    sigma   weight residual
     111.56  100.23   11.33 1.65e+00 3.67e-01 4.71e+01
  angle pdb=" N   PRO B 479 "
        pdb=" CA  PRO B 479 "
        pdb=" C   PRO B 479 "
      ideal   model   delta    sigma   weight residual
     112.47  121.36   -8.89 2.06e+00 2.36e-01 1.86e+01
  angle pdb=" N   GLN A 287 "
        pdb=" CA  GLN A 287 "
        pdb=" C   GLN A 287 "
      ideal   model   delta    sigma   weight residual
     114.31  109.56    4.75 1.29e+00 6.01e-01 1.35e+01
  angle pdb=" N   PRO A 389 "
        pdb=" CA  PRO A 389 "
        pdb=" C   PRO A 389 "
      ideal   model   delta    sigma   weight residual
     112.47  119.46   -6.99 2.06e+00 2.36e-01 1.15e+01
  angle pdb=" C   ILE A 468 "
        pdb=" CA  ILE A 468 "
        pdb=" CB  ILE A 468 "
      ideal   model   delta    sigma   weight residual
     109.33  112.46   -3.13 9.80e-01 1.04e+00 1.02e+01
  ... (remaining 8814 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.45: 3664
       24.45 -    48.90: 187
       48.90 -    73.36: 28
       73.36 -    97.81: 3
       97.81 -   122.26: 3
  Dihedral angle restraints: 3885
    sinusoidal: 1600
      harmonic: 2285
  Sorted by residual:
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.68  -63.68     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.48   53.48     1      1.00e+01 1.00e-02 3.89e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.79   53.21     1      1.00e+01 1.00e-02 3.85e+01
  ... (remaining 3882 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 730
       0.050 -    0.101: 170
       0.101 -    0.151: 26
       0.151 -    0.201: 2
       0.201 -    0.252: 1
  Chirality restraints: 929
  Sorted by residual:
  chirality pdb=" CA  PRO A 389 "
            pdb=" N   PRO A 389 "
            pdb=" C   PRO A 389 "
            pdb=" CB  PRO A 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" C2  NAG C   2 "
            pdb=" C1  NAG C   2 "
            pdb=" C3  NAG C   2 "
            pdb=" N2  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CA  CYS B 480 "
            pdb=" N   CYS B 480 "
            pdb=" C   CYS B 480 "
            pdb=" CB  CYS B 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.15 2.00e-01 2.50e+01 6.01e-01
  ... (remaining 926 not shown)

  Planarity restraints: 1144
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 388 "    0.081 5.00e-02 4.00e+02   1.22e-01 2.40e+01
        pdb=" N   PRO A 389 "   -0.212 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "    0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "    0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 475 "   -0.012 2.00e-02 2.50e+03   2.53e-02 6.39e+00
        pdb=" C   ALA B 475 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ALA B 475 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY B 476 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 468 "    0.036 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO A 469 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 469 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 469 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1141 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 207
        2.71 -     3.26: 6506
        3.26 -     3.81: 9278
        3.81 -     4.35: 11190
        4.35 -     4.90: 17785
  Nonbonded interactions: 44966
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 370 "
            pdb=" ND1 HIS A 374 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OG1 THR B 500 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE2 GLU A 227 "
            pdb=" OH  TYR A 454 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   LEU A 278 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" NZ  LYS A 247 "
            pdb=" O   LEU A 281 "
     model   vdw
     2.240 3.120
  ... (remaining 44961 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.950
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.600
  Find NCS groups from input model:        0.060
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5934
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   6494  Z= 0.215
  Angle     :  0.695  11.326   8819  Z= 0.394
  Chirality :  0.044   0.252    929
  Planarity :  0.006   0.122   1142
  Dihedral  : 14.457 122.259   2401
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  5.43 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.15 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.14 %
  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: -1.80 (0.29), residues: 773
  helix: -0.56 (0.30), residues: 297
  sheet:  2.44 (1.08), residues: 22
  loop : -1.91 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  48 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.016   0.001   PHE A 390 
 TYR   0.009   0.001   TYR A 215 
 ARG   0.005   0.000   ARG A 161 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.8580 (mt0) cc_final: 0.8254 (mt0)
REVERT: A   74 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: A  461 TRP cc_start: 0.7929 (m-10) cc_final: 0.7554 (m-10)
REVERT: A  539 LEU cc_start: 0.7599 (mt) cc_final: 0.7331 (tp)
REVERT: B  386 LYS cc_start: 0.9115 (pttm) cc_final: 0.8733 (tttm)
REVERT: B  421 TYR cc_start: 0.8677 (m-80) cc_final: 0.8354 (m-80)
REVERT: B  466 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7391 (mmm160)
  outliers start: 3
  outliers final: 3
  residues processed: 173
  average time/residue: 0.1904
  time to fit residues: 42.3075
Evaluate side-chains
  96 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0170
   chunk 19 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0770
   chunk 60 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 188 ASN
A 508 ASN
B 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6062
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   6494  Z= 0.228
  Angle     :  0.668  10.043   8819  Z= 0.336
  Chirality :  0.047   0.339    929
  Planarity :  0.006   0.121   1142
  Dihedral  :  8.966 109.920    913
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.43 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  4.45 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.56 (0.29), residues: 773
  helix: -0.21 (0.31), residues: 284
  sheet:  1.44 (1.06), residues: 25
  loop : -1.79 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.030   0.002   PHE A 592 
 TYR   0.012   0.001   TYR A 215 
 ARG   0.005   0.001   ARG A 273 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8237 (m-30) cc_final: 0.7820 (m-30)
REVERT: A   74 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7683 (tm-30)
REVERT: A  539 LEU cc_start: 0.7908 (mt) cc_final: 0.7290 (tp)
REVERT: A  579 MET cc_start: 0.1368 (ttp) cc_final: 0.1129 (ttt)
REVERT: B  386 LYS cc_start: 0.9113 (pttm) cc_final: 0.8629 (tttm)
REVERT: B  466 ARG cc_start: 0.7883 (ttp-170) cc_final: 0.7389 (mmm160)
  outliers start: 2
  outliers final: 1
  residues processed: 124
  average time/residue: 0.1827
  time to fit residues: 29.7316
Evaluate side-chains
  92 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0980
   chunk 58 optimal weight:    0.6980
   chunk 47 optimal weight:    7.9990
   chunk 19 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 62 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6061
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   6494  Z= 0.193
  Angle     :  0.627   9.370   8819  Z= 0.312
  Chirality :  0.047   0.333    929
  Planarity :  0.005   0.119   1142
  Dihedral  :  8.633 107.894    913
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.66 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.26 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.57 (0.29), residues: 773
  helix: -0.23 (0.31), residues: 290
  sheet:  1.28 (1.02), residues: 25
  loop : -1.79 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.022   0.002   PHE A 452 
 TYR   0.016   0.001   TYR B 421 
 ARG   0.004   0.000   ARG A 273 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8188 (m-30) cc_final: 0.7928 (m-30)
REVERT: A   74 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: A  383 MET cc_start: 0.7841 (ptp) cc_final: 0.7272 (tpt)
REVERT: A  539 LEU cc_start: 0.7776 (mt) cc_final: 0.7307 (tp)
REVERT: B  390 LEU cc_start: 0.9066 (mp) cc_final: 0.8535 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 121
  average time/residue: 0.2147
  time to fit residues: 34.2341
Evaluate side-chains
  91 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 52 optimal weight:    0.2980
   chunk 36 optimal weight:    7.9990
   chunk 7 optimal weight:    0.3980
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0870
   chunk 70 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.5360

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6067
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   6494  Z= 0.189
  Angle     :  0.617   9.419   8819  Z= 0.304
  Chirality :  0.046   0.339    929
  Planarity :  0.005   0.116   1142
  Dihedral  :  8.292 105.678    913
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.17 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.26 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.41 (0.29), residues: 773
  helix: -0.13 (0.31), residues: 288
  sheet:  0.98 (1.01), residues: 25
  loop : -1.64 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.014   0.001   PHE B 374 
 TYR   0.011   0.001   TYR B 421 
 ARG   0.004   0.000   ARG B 466 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8158 (m-30) cc_final: 0.7830 (m-30)
REVERT: A   74 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: A  356 PHE cc_start: 0.7594 (m-10) cc_final: 0.7390 (m-10)
REVERT: A  539 LEU cc_start: 0.7673 (mt) cc_final: 0.7141 (tp)
REVERT: B  356 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7403 (mmtt)
  outliers start: 1
  outliers final: 1
  residues processed: 118
  average time/residue: 0.2023
  time to fit residues: 30.6175
Evaluate side-chains
  94 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0270
   overall best weight:    1.4044

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
A 417 HIS
A 442 GLN
A 508 ASN
A 572 ASN
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6225
moved from start:          0.4384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6494  Z= 0.229
  Angle     :  0.662   9.181   8819  Z= 0.328
  Chirality :  0.047   0.344    929
  Planarity :  0.005   0.116   1142
  Dihedral  :  8.454 108.622    913
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.43 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.97 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.57 (0.29), residues: 773
  helix: -0.32 (0.30), residues: 298
  sheet:  0.78 (1.09), residues: 23
  loop : -1.71 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 459 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.029   0.002   PHE A 452 
 TYR   0.010   0.001   TYR A 510 
 ARG   0.007   0.001   ARG B 466 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8351 (m-30) cc_final: 0.8027 (m-30)
REVERT: A   74 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7851 (tm-30)
REVERT: A  514 ARG cc_start: 0.7564 (ttt180) cc_final: 0.7274 (tpt170)
REVERT: B  518 LEU cc_start: 0.8520 (tp) cc_final: 0.8309 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 113
  average time/residue: 0.1999
  time to fit residues: 29.1699
Evaluate side-chains
  80 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 67 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0980
   chunk 74 optimal weight:    0.0470
   chunk 61 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
A 373 HIS
A 508 ASN
A 578 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6151
moved from start:          0.4634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6494  Z= 0.193
  Angle     :  0.659  10.405   8819  Z= 0.322
  Chirality :  0.046   0.312    929
  Planarity :  0.005   0.114   1142
  Dihedral  :  8.197 106.222    913
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.27 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.93 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.53 (0.29), residues: 773
  helix: -0.34 (0.31), residues: 297
  sheet:  0.63 (1.09), residues: 23
  loop : -1.63 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.029   0.001   PHE A 452 
 TYR   0.010   0.001   TYR B 421 
 ARG   0.009   0.001   ARG B 466 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8331 (m-30) cc_final: 0.7977 (m-30)
REVERT: A   74 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: B  390 LEU cc_start: 0.9100 (mt) cc_final: 0.8473 (tp)
REVERT: B  440 ASN cc_start: 0.8554 (t0) cc_final: 0.8341 (t0)
REVERT: B  518 LEU cc_start: 0.8489 (tp) cc_final: 0.8275 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 106
  average time/residue: 0.1977
  time to fit residues: 27.4829
Evaluate side-chains
  84 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0270
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6174
moved from start:          0.4806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6494  Z= 0.188
  Angle     :  0.635   9.730   8819  Z= 0.312
  Chirality :  0.046   0.283    929
  Planarity :  0.005   0.112   1142
  Dihedral  :  8.055 105.076    913
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.05 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.74 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.41 (0.30), residues: 773
  helix: -0.21 (0.31), residues: 297
  sheet:  0.66 (1.12), residues: 23
  loop : -1.57 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.037   0.002   PHE A 592 
 TYR   0.010   0.001   TYR A 510 
 ARG   0.009   0.000   ARG B 466 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8370 (m-30) cc_final: 0.8035 (m-30)
REVERT: A   60 GLN cc_start: 0.8733 (mt0) cc_final: 0.8481 (mt0)
REVERT: A   74 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7955 (tm-30)
REVERT: A  202 TYR cc_start: 0.7220 (t80) cc_final: 0.7014 (t80)
REVERT: B  390 LEU cc_start: 0.9046 (mt) cc_final: 0.8418 (tp)
REVERT: B  440 ASN cc_start: 0.8560 (t0) cc_final: 0.8336 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 103
  average time/residue: 0.1968
  time to fit residues: 26.3708
Evaluate side-chains
  77 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 67 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9980
   chunk 64 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
A 578 ASN
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6254
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   6494  Z= 0.207
  Angle     :  0.693   9.333   8819  Z= 0.342
  Chirality :  0.046   0.278    929
  Planarity :  0.005   0.112   1142
  Dihedral  :  8.223 105.929    913
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.95 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.48 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.35 (0.30), residues: 773
  helix: -0.21 (0.31), residues: 298
  sheet:  0.60 (1.13), residues: 23
  loop : -1.49 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.100   0.002   TRP A 461 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.028   0.002   PHE A 592 
 TYR   0.009   0.001   TYR A 510 
 ARG   0.009   0.001   ARG A 460 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8383 (m-30) cc_final: 0.8088 (m-30)
REVERT: A   60 GLN cc_start: 0.8824 (mt0) cc_final: 0.8536 (mt0)
REVERT: A   74 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8042 (tm-30)
REVERT: A  108 LEU cc_start: 0.7395 (tt) cc_final: 0.6404 (mp)
REVERT: A  557 MET cc_start: 0.5738 (mmt) cc_final: 0.5419 (mmt)
REVERT: B  390 LEU cc_start: 0.9095 (mt) cc_final: 0.8443 (tp)
REVERT: B  440 ASN cc_start: 0.8571 (t0) cc_final: 0.8348 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 103
  average time/residue: 0.1861
  time to fit residues: 25.5365
Evaluate side-chains
  79 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0570
   chunk 21 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6246
moved from start:          0.5399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6494  Z= 0.196
  Angle     :  0.671   9.330   8819  Z= 0.329
  Chirality :  0.047   0.303    929
  Planarity :  0.005   0.111   1142
  Dihedral  :  8.096 104.971    913
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.56 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.45 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.38 (0.30), residues: 773
  helix: -0.31 (0.30), residues: 304
  sheet:  1.02 (1.06), residues: 25
  loop : -1.51 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.002   TRP A 461 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.024   0.002   PHE A 452 
 TYR   0.009   0.001   TYR A 510 
 ARG   0.008   0.001   ARG B 466 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8365 (m-30) cc_final: 0.8065 (m-30)
REVERT: A   60 GLN cc_start: 0.8822 (mt0) cc_final: 0.8577 (mt0)
REVERT: A   74 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: A  108 LEU cc_start: 0.7339 (tt) cc_final: 0.6590 (mp)
REVERT: A  557 MET cc_start: 0.5690 (mmt) cc_final: 0.5308 (mmt)
REVERT: B  390 LEU cc_start: 0.9090 (mt) cc_final: 0.8524 (tp)
REVERT: B  440 ASN cc_start: 0.8562 (t0) cc_final: 0.8331 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 103
  average time/residue: 0.1904
  time to fit residues: 26.0820
Evaluate side-chains
  79 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 34 optimal weight:    0.0050
   chunk 50 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 47 optimal weight:    0.1980
   chunk 37 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0370
   chunk 18 optimal weight:    6.9990
   overall best weight:    0.3672

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6222
moved from start:          0.5557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6494  Z= 0.190
  Angle     :  0.687   9.397   8819  Z= 0.335
  Chirality :  0.047   0.290    929
  Planarity :  0.005   0.110   1142
  Dihedral  :  7.923 102.975    913
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.56 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.45 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.41 (0.30), residues: 773
  helix: -0.41 (0.30), residues: 304
  sheet:  0.92 (1.06), residues: 25
  loop : -1.44 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.002   TRP A 461 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.025   0.001   PHE A 592 
 TYR   0.009   0.001   TYR A 510 
 ARG   0.009   0.001   ARG B 466 

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8330 (m-30) cc_final: 0.7991 (m-30)
REVERT: A   60 GLN cc_start: 0.8819 (mt0) cc_final: 0.8617 (mt0)
REVERT: A  557 MET cc_start: 0.5675 (mmt) cc_final: 0.5309 (mmt)
REVERT: A  591 LEU cc_start: 0.8101 (tt) cc_final: 0.7810 (mm)
REVERT: B  390 LEU cc_start: 0.9072 (mt) cc_final: 0.8576 (tp)
REVERT: B  440 ASN cc_start: 0.8555 (t0) cc_final: 0.8323 (t0)
REVERT: B  466 ARG cc_start: 0.8331 (mmm160) cc_final: 0.8003 (tpp80)
  outliers start: 1
  outliers final: 1
  residues processed: 106
  average time/residue: 0.1871
  time to fit residues: 26.1113
Evaluate side-chains
  85 residues out of total 677 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0020
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0170
   chunk 62 optimal weight:    0.0770
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.145465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.132482 restraints weight = 33110.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.134255 restraints weight = 23044.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.135557 restraints weight = 17271.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6229
moved from start:          0.5688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6494  Z= 0.190
  Angle     :  0.679   9.393   8819  Z= 0.330
  Chirality :  0.046   0.290    929
  Planarity :  0.005   0.108   1142
  Dihedral  :  7.747 101.121    913
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.30 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    Favored  : 99.70 %
  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: -1.41 (0.30), residues: 773
  helix: -0.36 (0.30), residues: 304
  sheet:  0.97 (1.06), residues: 25
  loop : -1.49 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.001   TRP A 461 
 HIS   0.002   0.001   HIS A 353 
 PHE   0.021   0.001   PHE A 452 
 TYR   0.010   0.001   TYR A 510 
 ARG   0.007   0.000   ARG B 466 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1616.17 seconds
wall clock time: 29 minutes 15.85 seconds (1755.85 seconds total)