Starting phenix.real_space_refine
on Fri Nov 15 07:09:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfu_39230/11_2024/8yfu_39230.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfu_39230/11_2024/8yfu_39230.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfu_39230/11_2024/8yfu_39230.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfu_39230/11_2024/8yfu_39230.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfu_39230/11_2024/8yfu_39230.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfu_39230/11_2024/8yfu_39230.cif"
  }
  resolution = 4.59
  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=   0.041
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      32      5.16       5
     C    5511      2.51       5
     N    1423      2.21       5
     O    1453      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8419
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4222
          Classifications: {'peptide': 583}
          Incomplete info: {'truncation_to_alanine': 168}
          Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 562}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 647
          Unresolved non-hydrogen angles: 817
          Unresolved non-hydrogen dihedrals: 541
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 391
    Chain: "B"
      Number of atoms: 4197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4197
          Classifications: {'peptide': 578}
          Incomplete info: {'truncation_to_alanine': 164}
          Link IDs: {'PTRANS': 19, 'TRANS': 558}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 624
          Unresolved non-hydrogen angles: 787
          Unresolved non-hydrogen dihedrals: 520
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 370
  Time building chain proxies: 5.71, per 1000 atoms: 0.68
  Number of scatterers: 8419
  At special positions: 0
  Unit cell: (123.2, 126.5, 128.7, 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      32     16.00
     O    1453      8.00
     N    1423      7.00
     C    5511      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " 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
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2230

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      79.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 36
    Processing helix  chain 'A' and resid 43 through 100
    Processing helix  chain 'A' and resid 119 through 168
    Processing helix  chain 'A' and resid 170 through 180
      removed outlier: 4.113A  pdb=" N   ASP A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 189 through 206
      removed outlier: 3.613A  pdb=" N   GLN A 193 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.604A  pdb=" N   ALA A 214 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 258
      removed outlier: 3.847A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 3.563A  pdb=" N   ILE A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY A 296 " --> pdb=" O   TRP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.712A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 4.377A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 402
      removed outlier: 3.625A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.907A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 3.945A  pdb=" N   ILE A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 476 through 501
      removed outlier: 4.119A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 4.067A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 571
      removed outlier: 4.047A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 581
      removed outlier: 3.938A  pdb=" N   ILE A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 616
      removed outlier: 4.457A  pdb=" N   ILE A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   THR A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   VAL A 595 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE A 596 " --> pdb=" O   ILE A 592 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 4.365A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A 612 " --> pdb=" O   ASN A 608 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 36
      removed outlier: 4.026A  pdb=" N   GLN B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ALA B  36 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 100
      removed outlier: 3.573A  pdb=" N   VAL B  47 " --> pdb=" O   ASP B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 168
    Processing helix  chain 'B' and resid 170 through 179
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 3.520A  pdb=" N   THR B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 206
    Processing helix  chain 'B' and resid 210 through 218
    Processing helix  chain 'B' and resid 230 through 258
      removed outlier: 3.522A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.623A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.999A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 337
    Processing helix  chain 'B' and resid 343 through 345
      No H-bonds generated for 'chain 'B' and resid 343 through 345'
    Processing helix  chain 'B' and resid 346 through 360
      removed outlier: 4.108A  pdb=" N   ALA B 350 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LEU B 351 " --> pdb=" O   TYR B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 384
      removed outlier: 3.580A  pdb=" N   ARG B 371 " --> pdb=" O   TYR B 367 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   PHE B 372 " --> pdb=" O   TYR B 368 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   THR B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA B 384 " --> pdb=" O   ARG B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.637A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 420
      removed outlier: 3.760A  pdb=" N   MET B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   LEU B 410 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   GLU B 411 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 473 through 501
      removed outlier: 3.816A  pdb=" N   GLY B 481 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLU B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.727A  pdb=" N   PHE B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   TYR B 512 " --> pdb=" O   MET B 508 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL B 516 " --> pdb=" O   TYR B 512 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER B 521 " --> pdb=" O   PHE B 517 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS B 531 " --> pdb=" O   ILE B 527 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   MET B 532 " --> pdb=" O   TRP B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 571
      removed outlier: 3.939A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 580
      removed outlier: 3.588A  pdb=" N   ILE B 577 " --> pdb=" O   TRP B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 620
      removed outlier: 4.112A  pdb=" N   ILE B 592 " --> pdb=" O   SER B 588 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ALA B 593 " --> pdb=" O   GLY B 589 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 3.629A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG B 604 " --> pdb=" O   GLU B 600 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE B 605 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   VAL B 606 " --> pdb=" O   PHE B 602 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TRP B 607 " --> pdb=" O   ARG B 603 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU B 615 " --> pdb=" O   ARG B 611 " (cutoff:3.500A)

    662 hydrogen bonds defined for protein.
    1980 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.44

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2382
        1.34 -     1.46: 1609
        1.46 -     1.58: 4602
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 8637
  Sorted by residual:
  bond pdb=" CA  VAL A 220 "
       pdb=" CB  VAL A 220 "
    ideal  model  delta    sigma   weight residual
    1.539  1.549 -0.010 5.40e-03 3.43e+04 3.16e+00
  bond pdb=" CG1 ILE B 249 "
       pdb=" CD1 ILE B 249 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.91e+00
  bond pdb=" CB  TRP A 395 "
       pdb=" CG  TRP A 395 "
    ideal  model  delta    sigma   weight residual
    1.498  1.538 -0.040 3.10e-02 1.04e+03 1.67e+00
  bond pdb=" C   ALA B 384 "
       pdb=" N   PRO B 385 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.28e-02 6.10e+03 1.62e+00
  bond pdb=" C   ALA A 226 "
       pdb=" N   GLN A 227 "
    ideal  model  delta    sigma   weight residual
    1.329  1.345 -0.016 1.40e-02 5.10e+03 1.24e+00
  ... (remaining 8632 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.65: 11796
        4.65 -     9.31: 26
        9.31 -    13.96: 0
       13.96 -    18.61: 0
       18.61 -    23.27: 1
  Bond angle restraints: 11823
  Sorted by residual:
  angle pdb=" C   ALA A 226 "
        pdb=" N   GLN A 227 "
        pdb=" CA  GLN A 227 "
      ideal   model   delta    sigma   weight residual
     121.70  144.97  -23.27 1.80e+00 3.09e-01 1.67e+02
  angle pdb=" N   VAL A 341 "
        pdb=" CA  VAL A 341 "
        pdb=" C   VAL A 341 "
      ideal   model   delta    sigma   weight residual
     112.12  108.54    3.58 8.40e-01 1.42e+00 1.82e+01
  angle pdb=" C   THR B 383 "
        pdb=" N   ALA B 384 "
        pdb=" CA  ALA B 384 "
      ideal   model   delta    sigma   weight residual
     121.80  130.99   -9.19 2.44e+00 1.68e-01 1.42e+01
  angle pdb=" C   ALA A 225 "
        pdb=" N   ALA A 226 "
        pdb=" CA  ALA A 226 "
      ideal   model   delta    sigma   weight residual
     121.54  128.27   -6.73 1.91e+00 2.74e-01 1.24e+01
  angle pdb=" CA  ALA A 226 "
        pdb=" C   ALA A 226 "
        pdb=" N   GLN A 227 "
      ideal   model   delta    sigma   weight residual
     116.84  122.00   -5.16 1.71e+00 3.42e-01 9.11e+00
  ... (remaining 11818 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4572
       17.93 -    35.86: 319
       35.86 -    53.79: 55
       53.79 -    71.72: 4
       71.72 -    89.65: 5
  Dihedral angle restraints: 4955
    sinusoidal: 1526
      harmonic: 3429
  Sorted by residual:
  dihedral pdb=" CA  ALA B 473 "
           pdb=" C   ALA B 473 "
           pdb=" N   PHE B 474 "
           pdb=" CA  PHE B 474 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  SER B 521 "
           pdb=" C   SER B 521 "
           pdb=" N   SER B 522 "
           pdb=" CA  SER B 522 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.27  -15.73     0      5.00e+00 4.00e-02 9.90e+00
  dihedral pdb=" CA  ILE A 342 "
           pdb=" C   ILE A 342 "
           pdb=" N   PRO A 343 "
           pdb=" CA  PRO A 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.48  -15.52     0      5.00e+00 4.00e-02 9.64e+00
  ... (remaining 4952 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 959
       0.035 -    0.070: 320
       0.070 -    0.105: 82
       0.105 -    0.140: 11
       0.140 -    0.175: 3
  Chirality restraints: 1375
  Sorted by residual:
  chirality pdb=" CA  ALA A 226 "
            pdb=" N   ALA A 226 "
            pdb=" C   ALA A 226 "
            pdb=" CB  ALA A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.31    0.18 2.00e-01 2.50e+01 7.67e-01
  chirality pdb=" CA  ALA B 384 "
            pdb=" N   ALA B 384 "
            pdb=" C   ALA B 384 "
            pdb=" CB  ALA B 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.34    0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CB  THR A 261 "
            pdb=" CA  THR A 261 "
            pdb=" OG1 THR A 261 "
            pdb=" CG2 THR A 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.08e-01
  ... (remaining 1372 not shown)

  Planarity restraints: 1499
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 395 "   -0.020 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRP A 395 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 395 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 395 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 395 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 395 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 395 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 395 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 395 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 395 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 517 "   -0.015 2.00e-02 2.50e+03   1.48e-02 3.85e+00
        pdb=" CG  PHE A 517 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 517 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 517 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 517 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 517 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 517 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 306 "   -0.030 5.00e-02 4.00e+02   4.63e-02 3.43e+00
        pdb=" N   PRO B 307 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 307 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 307 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1496 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 81
        2.64 -     3.21: 8597
        3.21 -     3.77: 13329
        3.77 -     4.34: 15878
        4.34 -     4.90: 25350
  Nonbonded interactions: 63235
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 575 "
            pdb=" OG  SER A 578 "
     model   vdw
     2.081 3.040
  nonbonded pdb=" OG  SER B 402 "
            pdb=" NH2 ARG B 604 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" O   HIS A 387 "
            pdb=" NH1 ARG A 465 "
     model   vdw
     2.152 3.120
  nonbonded pdb=" O   TYR B 518 "
            pdb=" OG  SER B 521 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   ALA A 384 "
            pdb=" NH1 ARG A 465 "
     model   vdw
     2.161 3.120
  ... (remaining 63230 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 26 through 620)
  selection = chain 'B'
}

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:             1.650
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.860
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.050
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
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   0.055   8637  Z= 0.197
  Angle     :  0.672  23.267  11823  Z= 0.370
  Chirality :  0.038   0.175   1375
  Planarity :  0.004   0.046   1499
  Dihedral  : 12.845  89.649   2719
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.29 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  1.47 (0.26), residues: 1153
  helix:  2.05 (0.18), residues: 843
  sheet:  None (None), residues: 0
  loop : -2.22 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP A 395 
 HIS   0.010   0.001   HIS B 441 
 PHE   0.034   0.001   PHE A 517 
 TYR   0.017   0.001   TYR B 345 
 ARG   0.006   0.001   ARG A 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.9315 (mt) cc_final: 0.9098 (mt)
REVERT: A  318 GLU cc_start: 0.8482 (pp20) cc_final: 0.8216 (pp20)
REVERT: A  319 ILE cc_start: 0.8491 (mt) cc_final: 0.8285 (mt)
REVERT: A  413 MET cc_start: 0.8920 (ppp) cc_final: 0.8573 (ppp)
REVERT: A  508 MET cc_start: 0.6607 (mmt) cc_final: 0.6158 (mmt)
REVERT: A  558 TYR cc_start: 0.8090 (m-80) cc_final: 0.7773 (m-80)
REVERT: B  241 CYS cc_start: 0.8770 (t) cc_final: 0.8495 (t)
REVERT: B  248 ASN cc_start: 0.9206 (t0) cc_final: 0.8952 (t0)
REVERT: B  280 GLU cc_start: 0.9164 (tt0) cc_final: 0.8508 (tp30)
REVERT: B  281 PHE cc_start: 0.8803 (t80) cc_final: 0.8603 (t80)
REVERT: B  288 ASN cc_start: 0.9278 (m110) cc_final: 0.8766 (m-40)
REVERT: B  403 LEU cc_start: 0.9108 (mt) cc_final: 0.8887 (mt)
REVERT: B  411 GLU cc_start: 0.9493 (tm-30) cc_final: 0.9147 (tm-30)
REVERT: B  524 TYR cc_start: 0.7476 (t80) cc_final: 0.7192 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1635
  time to fit residues: 43.5871
Evaluate side-chains
  146 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.0980
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:   30.0000
   chunk 46 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    7.9990
   chunk 67 optimal weight:   50.0000
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
B 387 HIS
B 619 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8637  Z= 0.168
  Angle     :  0.581  12.277  11823  Z= 0.312
  Chirality :  0.038   0.256   1375
  Planarity :  0.004   0.055   1499
  Dihedral  :  3.823  19.265   1239
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.16 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.70 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  1.91 (0.26), residues: 1153
  helix:  2.32 (0.17), residues: 861
  sheet:  None (None), residues: 0
  loop : -2.17 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 395 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.022   0.001   PHE A 517 
 TYR   0.023   0.001   TYR A 512 
 ARG   0.003   0.000   ARG B 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.9169 (mt) cc_final: 0.8835 (mt)
REVERT: A  413 MET cc_start: 0.8980 (ppp) cc_final: 0.8637 (ppp)
REVERT: A  508 MET cc_start: 0.6513 (mmt) cc_final: 0.5804 (mmp)
REVERT: A  558 TYR cc_start: 0.8088 (m-80) cc_final: 0.7747 (m-80)
REVERT: A  596 PHE cc_start: 0.8040 (m-80) cc_final: 0.7498 (m-10)
REVERT: A  600 GLU cc_start: 0.8643 (mp0) cc_final: 0.7942 (mm-30)
REVERT: B  241 CYS cc_start: 0.8600 (t) cc_final: 0.8264 (t)
REVERT: B  248 ASN cc_start: 0.9227 (t0) cc_final: 0.8915 (t0)
REVERT: B  280 GLU cc_start: 0.9171 (tt0) cc_final: 0.8609 (tp30)
REVERT: B  288 ASN cc_start: 0.9373 (m110) cc_final: 0.9090 (t0)
REVERT: B  398 ASP cc_start: 0.8840 (m-30) cc_final: 0.8592 (m-30)
REVERT: B  411 GLU cc_start: 0.9504 (tm-30) cc_final: 0.9145 (tm-30)
REVERT: B  462 GLN cc_start: 0.9149 (mp10) cc_final: 0.8887 (mp10)
REVERT: B  496 TYR cc_start: 0.8549 (t80) cc_final: 0.8266 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1633
  time to fit residues: 44.1037
Evaluate side-chains
  153 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:   30.0000
   chunk 32 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 71 optimal weight:   40.0000
   chunk 28 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0170
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.9622

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8637  Z= 0.172
  Angle     :  0.563  11.668  11823  Z= 0.299
  Chirality :  0.037   0.244   1375
  Planarity :  0.003   0.055   1499
  Dihedral  :  3.751  17.172   1239
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.42 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.84 %
    Favored  : 95.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.06 (0.26), residues: 1153
  helix:  2.45 (0.17), residues: 857
  sheet:  None (None), residues: 0
  loop : -2.11 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 395 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.013   0.001   PHE A 394 
 TYR   0.019   0.001   TYR A 512 
 ARG   0.005   0.000   ARG A 270 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.9050 (mt) cc_final: 0.8767 (mt)
REVERT: A  292 TRP cc_start: 0.7772 (m-10) cc_final: 0.7513 (m-10)
REVERT: A  394 PHE cc_start: 0.8056 (p90) cc_final: 0.7676 (p90)
REVERT: A  413 MET cc_start: 0.9017 (ppp) cc_final: 0.8720 (ppp)
REVERT: A  508 MET cc_start: 0.6344 (mmt) cc_final: 0.5773 (mmp)
REVERT: A  512 TYR cc_start: 0.8443 (m-80) cc_final: 0.8233 (m-10)
REVERT: A  558 TYR cc_start: 0.8152 (m-80) cc_final: 0.7754 (m-80)
REVERT: A  565 GLU cc_start: 0.9088 (tp30) cc_final: 0.8862 (tp30)
REVERT: A  600 GLU cc_start: 0.8620 (mp0) cc_final: 0.8015 (mm-30)
REVERT: A  607 TRP cc_start: 0.8113 (t60) cc_final: 0.7697 (t60)
REVERT: B  241 CYS cc_start: 0.8572 (t) cc_final: 0.8286 (t)
REVERT: B  248 ASN cc_start: 0.9207 (t0) cc_final: 0.8860 (t0)
REVERT: B  280 GLU cc_start: 0.9096 (tt0) cc_final: 0.8577 (tp30)
REVERT: B  304 GLU cc_start: 0.8543 (pp20) cc_final: 0.8274 (pm20)
REVERT: B  328 CYS cc_start: 0.8917 (m) cc_final: 0.8688 (m)
REVERT: B  411 GLU cc_start: 0.9507 (tm-30) cc_final: 0.9207 (tm-30)
REVERT: B  489 MET cc_start: 0.8388 (ttt) cc_final: 0.8120 (ttt)
REVERT: B  496 TYR cc_start: 0.8597 (t80) cc_final: 0.8321 (t80)
REVERT: B  610 PHE cc_start: 0.9129 (m-10) cc_final: 0.8852 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1586
  time to fit residues: 44.5455
Evaluate side-chains
  154 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 11 optimal weight:   50.0000
   chunk 49 optimal weight:    1.9990
   chunk 70 optimal weight:   20.0000
   chunk 104 optimal weight:    3.9990
   chunk 111 optimal weight:    0.2980
   chunk 99 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0370
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
B 555 GLN
B 608 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8637  Z= 0.157
  Angle     :  0.567  10.961  11823  Z= 0.298
  Chirality :  0.037   0.233   1375
  Planarity :  0.003   0.059   1499
  Dihedral  :  3.714  16.457   1239
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.34 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.13 %
    Favored  : 96.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.14 (0.26), residues: 1153
  helix:  2.51 (0.17), residues: 861
  sheet:  None (None), residues: 0
  loop : -2.14 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 292 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.020   0.001   PHE A 235 
 TYR   0.016   0.001   TYR A 512 
 ARG   0.006   0.001   ARG B 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ARG cc_start: 0.8893 (ptt180) cc_final: 0.8374 (ptt180)
REVERT: A  284 LEU cc_start: 0.9022 (mt) cc_final: 0.8769 (mt)
REVERT: A  292 TRP cc_start: 0.7750 (m-10) cc_final: 0.7444 (m-10)
REVERT: A  413 MET cc_start: 0.9089 (ppp) cc_final: 0.8714 (ppp)
REVERT: A  508 MET cc_start: 0.6115 (mmt) cc_final: 0.5620 (mmp)
REVERT: A  512 TYR cc_start: 0.8557 (m-80) cc_final: 0.8301 (m-10)
REVERT: A  534 TRP cc_start: 0.8152 (m-10) cc_final: 0.7818 (m-90)
REVERT: A  558 TYR cc_start: 0.8149 (m-80) cc_final: 0.7730 (m-80)
REVERT: A  565 GLU cc_start: 0.9101 (tp30) cc_final: 0.8848 (tp30)
REVERT: A  566 ASP cc_start: 0.9293 (t0) cc_final: 0.9056 (t0)
REVERT: A  600 GLU cc_start: 0.8648 (mp0) cc_final: 0.8125 (mm-30)
REVERT: A  607 TRP cc_start: 0.8189 (t60) cc_final: 0.7675 (t60)
REVERT: B  241 CYS cc_start: 0.8789 (t) cc_final: 0.8450 (t)
REVERT: B  248 ASN cc_start: 0.9239 (t0) cc_final: 0.8861 (t0)
REVERT: B  280 GLU cc_start: 0.9136 (tt0) cc_final: 0.8713 (tp30)
REVERT: B  281 PHE cc_start: 0.8753 (t80) cc_final: 0.8547 (t80)
REVERT: B  328 CYS cc_start: 0.8887 (m) cc_final: 0.8625 (m)
REVERT: B  403 LEU cc_start: 0.8993 (mt) cc_final: 0.8793 (mt)
REVERT: B  411 GLU cc_start: 0.9483 (tm-30) cc_final: 0.9212 (tm-30)
REVERT: B  462 GLN cc_start: 0.9132 (mp10) cc_final: 0.8840 (mp10)
REVERT: B  496 TYR cc_start: 0.8565 (t80) cc_final: 0.8280 (t80)
REVERT: B  509 VAL cc_start: 0.9330 (t) cc_final: 0.9083 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1659
  time to fit residues: 46.0410
Evaluate side-chains
  158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
B 555 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8637  Z= 0.175
  Angle     :  0.559  10.289  11823  Z= 0.295
  Chirality :  0.037   0.240   1375
  Planarity :  0.004   0.057   1499
  Dihedral  :  3.719  16.577   1239
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.25 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.23 (0.26), residues: 1153
  helix:  2.54 (0.17), residues: 865
  sheet:  None (None), residues: 0
  loop : -2.08 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 395 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.017   0.001   PHE A 235 
 TYR   0.012   0.001   TYR A 512 
 ARG   0.007   0.000   ARG A 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.8970 (t80) cc_final: 0.8741 (t80)
REVERT: A  273 ARG cc_start: 0.8993 (ptt180) cc_final: 0.8530 (ptt90)
REVERT: A  284 LEU cc_start: 0.9035 (mt) cc_final: 0.8786 (mt)
REVERT: A  413 MET cc_start: 0.9017 (ppp) cc_final: 0.8713 (ppp)
REVERT: A  508 MET cc_start: 0.6149 (mmt) cc_final: 0.5561 (mmp)
REVERT: A  534 TRP cc_start: 0.8238 (m-10) cc_final: 0.7813 (m-90)
REVERT: A  558 TYR cc_start: 0.7923 (m-80) cc_final: 0.7532 (m-80)
REVERT: A  565 GLU cc_start: 0.8946 (tp30) cc_final: 0.8661 (tp30)
REVERT: A  566 ASP cc_start: 0.9479 (t0) cc_final: 0.9055 (t0)
REVERT: A  600 GLU cc_start: 0.8648 (mp0) cc_final: 0.8140 (mm-30)
REVERT: A  607 TRP cc_start: 0.8232 (t60) cc_final: 0.7696 (t60)
REVERT: B  241 CYS cc_start: 0.8712 (t) cc_final: 0.8423 (t)
REVERT: B  248 ASN cc_start: 0.9233 (t0) cc_final: 0.8878 (t0)
REVERT: B  280 GLU cc_start: 0.9153 (tt0) cc_final: 0.8767 (tp30)
REVERT: B  281 PHE cc_start: 0.8796 (t80) cc_final: 0.8545 (t80)
REVERT: B  408 MET cc_start: 0.9090 (pmm) cc_final: 0.8819 (pmm)
REVERT: B  411 GLU cc_start: 0.9493 (tm-30) cc_final: 0.9052 (tm-30)
REVERT: B  489 MET cc_start: 0.8227 (ttt) cc_final: 0.7970 (ttt)
REVERT: B  496 TYR cc_start: 0.8591 (t80) cc_final: 0.8293 (t80)
REVERT: B  509 VAL cc_start: 0.9322 (t) cc_final: 0.9020 (t)
REVERT: B  524 TYR cc_start: 0.7298 (t80) cc_final: 0.7034 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1600
  time to fit residues: 43.7915
Evaluate side-chains
  153 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 9 optimal weight:   30.0000
   chunk 36 optimal weight:    0.5980
   chunk 58 optimal weight:   20.0000
   chunk 107 optimal weight:    9.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS
B 387 HIS
B 504 HIS
B 555 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8637  Z= 0.212
  Angle     :  0.579   9.631  11823  Z= 0.309
  Chirality :  0.038   0.146   1375
  Planarity :  0.004   0.061   1499
  Dihedral  :  3.832  20.043   1239
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.42 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.19 (0.26), residues: 1153
  helix:  2.51 (0.17), residues: 863
  sheet:  None (None), residues: 0
  loop : -2.05 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 395 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.015   0.001   PHE A 235 
 TYR   0.013   0.001   TYR B 558 
 ARG   0.007   0.001   ARG A 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A  244 PHE cc_start: 0.9031 (t80) cc_final: 0.8784 (t80)
REVERT: A  273 ARG cc_start: 0.9011 (ptt180) cc_final: 0.8761 (ptt90)
REVERT: A  284 LEU cc_start: 0.9115 (mt) cc_final: 0.8909 (mt)
REVERT: A  413 MET cc_start: 0.9110 (ppp) cc_final: 0.8710 (ppp)
REVERT: A  489 MET cc_start: 0.8433 (tpt) cc_final: 0.7901 (tpp)
REVERT: A  508 MET cc_start: 0.6572 (mmt) cc_final: 0.5816 (mmp)
REVERT: A  558 TYR cc_start: 0.7970 (m-80) cc_final: 0.7559 (m-80)
REVERT: A  565 GLU cc_start: 0.9090 (tp30) cc_final: 0.8669 (tp30)
REVERT: A  566 ASP cc_start: 0.9478 (t0) cc_final: 0.9224 (t0)
REVERT: A  600 GLU cc_start: 0.8771 (mp0) cc_final: 0.8237 (mm-30)
REVERT: A  604 ARG cc_start: 0.8027 (ttm170) cc_final: 0.7804 (tpp80)
REVERT: B  241 CYS cc_start: 0.8706 (t) cc_final: 0.8436 (t)
REVERT: B  248 ASN cc_start: 0.9251 (t0) cc_final: 0.8886 (t0)
REVERT: B  280 GLU cc_start: 0.9164 (tt0) cc_final: 0.8745 (tp30)
REVERT: B  281 PHE cc_start: 0.8828 (t80) cc_final: 0.8506 (t80)
REVERT: B  328 CYS cc_start: 0.8981 (m) cc_final: 0.8667 (m)
REVERT: B  408 MET cc_start: 0.9057 (pmm) cc_final: 0.8799 (pmm)
REVERT: B  411 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9054 (tm-30)
REVERT: B  462 GLN cc_start: 0.9110 (mp10) cc_final: 0.8638 (mp10)
REVERT: B  489 MET cc_start: 0.8110 (ttt) cc_final: 0.7809 (ttt)
REVERT: B  496 TYR cc_start: 0.8615 (t80) cc_final: 0.8306 (t80)
REVERT: B  509 VAL cc_start: 0.9240 (t) cc_final: 0.9008 (t)
REVERT: B  510 PHE cc_start: 0.8538 (m-10) cc_final: 0.8197 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1566
  time to fit residues: 41.2677
Evaluate side-chains
  147 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:   30.0000
   chunk 63 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 62 optimal weight:   30.0000
   chunk 93 optimal weight:    0.7980
   chunk 110 optimal weight:    0.9980
   chunk 69 optimal weight:   30.0000
   chunk 67 optimal weight:   40.0000
   chunk 51 optimal weight:    3.9990
   chunk 68 optimal weight:   40.0000
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 504 HIS
B 555 GLN
B 618 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8637  Z= 0.224
  Angle     :  0.595   9.640  11823  Z= 0.319
  Chirality :  0.038   0.143   1375
  Planarity :  0.004   0.069   1499
  Dihedral  :  3.874  18.554   1239
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.77 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.20 (0.26), residues: 1153
  helix:  2.51 (0.17), residues: 859
  sheet:  None (None), residues: 0
  loop : -1.96 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 395 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.014   0.001   PHE B 510 
 TYR   0.013   0.001   TYR B 558 
 ARG   0.006   0.001   ARG A 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.9047 (t80) cc_final: 0.8791 (t80)
REVERT: A  273 ARG cc_start: 0.9049 (ptt180) cc_final: 0.8547 (ptt180)
REVERT: A  413 MET cc_start: 0.8916 (ppp) cc_final: 0.8691 (ppp)
REVERT: A  508 MET cc_start: 0.6651 (mmt) cc_final: 0.5644 (mmp)
REVERT: A  558 TYR cc_start: 0.7801 (m-80) cc_final: 0.7343 (m-80)
REVERT: A  566 ASP cc_start: 0.9509 (t0) cc_final: 0.9299 (t0)
REVERT: A  600 GLU cc_start: 0.8786 (mp0) cc_final: 0.8222 (mm-30)
REVERT: B  241 CYS cc_start: 0.8820 (t) cc_final: 0.8517 (t)
REVERT: B  248 ASN cc_start: 0.9284 (t0) cc_final: 0.8919 (t0)
REVERT: B  280 GLU cc_start: 0.9156 (tt0) cc_final: 0.8742 (tp30)
REVERT: B  328 CYS cc_start: 0.8999 (m) cc_final: 0.8681 (m)
REVERT: B  462 GLN cc_start: 0.9134 (mp10) cc_final: 0.8755 (mp10)
REVERT: B  489 MET cc_start: 0.8137 (ttt) cc_final: 0.7800 (ttt)
REVERT: B  496 TYR cc_start: 0.8615 (t80) cc_final: 0.8293 (t80)
REVERT: B  509 VAL cc_start: 0.9333 (t) cc_final: 0.9015 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1694
  time to fit residues: 45.0910
Evaluate side-chains
  144 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:   40.0000
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0370
   chunk 10 optimal weight:   40.0000
   chunk 87 optimal weight:    0.0980
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0980
   overall best weight:    0.3458

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS
B 298 ASN
B 555 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8637  Z= 0.160
  Angle     :  0.567   9.077  11823  Z= 0.298
  Chirality :  0.038   0.193   1375
  Planarity :  0.004   0.079   1499
  Dihedral  :  3.782  17.425   1239
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.99 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.26 (0.26), residues: 1153
  helix:  2.54 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -1.96 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 395 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.022   0.001   PHE A 235 
 TYR   0.010   0.001   TYR B 524 
 ARG   0.003   0.000   ARG B 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.063 
Fit side-chains
REVERT: A  273 ARG cc_start: 0.8994 (ptt180) cc_final: 0.8533 (ptt90)
REVERT: A  413 MET cc_start: 0.9133 (ppp) cc_final: 0.8767 (ppp)
REVERT: A  489 MET cc_start: 0.8381 (tpt) cc_final: 0.7858 (tpp)
REVERT: A  508 MET cc_start: 0.6498 (mmt) cc_final: 0.5673 (mmp)
REVERT: A  524 TYR cc_start: 0.8229 (t80) cc_final: 0.7932 (t80)
REVERT: A  534 TRP cc_start: 0.8149 (m-10) cc_final: 0.7794 (m-90)
REVERT: A  558 TYR cc_start: 0.7675 (m-80) cc_final: 0.7289 (m-80)
REVERT: A  600 GLU cc_start: 0.8566 (mp0) cc_final: 0.7978 (mm-30)
REVERT: B  241 CYS cc_start: 0.8732 (t) cc_final: 0.8456 (t)
REVERT: B  248 ASN cc_start: 0.9259 (t0) cc_final: 0.8900 (t0)
REVERT: B  280 GLU cc_start: 0.9142 (tt0) cc_final: 0.8641 (tp30)
REVERT: B  281 PHE cc_start: 0.8730 (t80) cc_final: 0.8426 (t80)
REVERT: B  328 CYS cc_start: 0.8912 (m) cc_final: 0.8693 (m)
REVERT: B  377 LEU cc_start: 0.8453 (mm) cc_final: 0.7896 (mm)
REVERT: B  462 GLN cc_start: 0.9139 (mp10) cc_final: 0.8807 (mp10)
REVERT: B  489 MET cc_start: 0.8050 (ttt) cc_final: 0.7702 (ttt)
REVERT: B  496 TYR cc_start: 0.8593 (t80) cc_final: 0.8270 (t80)
REVERT: B  509 VAL cc_start: 0.9263 (t) cc_final: 0.9027 (t)
REVERT: B  510 PHE cc_start: 0.8176 (m-10) cc_final: 0.7846 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1526
  time to fit residues: 41.7852
Evaluate side-chains
  149 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 62 optimal weight:   40.0000
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 93 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0060
   chunk 102 optimal weight:    0.6980
   chunk 67 optimal weight:   50.0000
   chunk 109 optimal weight:    0.0670
   overall best weight:    0.4334

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

Flipped N/Q/H residues before XYZ refinement:
A 499 HIS
** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 HIS
B 555 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8637  Z= 0.160
  Angle     :  0.585  13.539  11823  Z= 0.302
  Chirality :  0.038   0.181   1375
  Planarity :  0.004   0.059   1499
  Dihedral  :  3.734  17.746   1239
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.82 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.28 (0.26), residues: 1153
  helix:  2.56 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -1.96 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 395 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.024   0.001   TYR A 512 
 ARG   0.005   0.000   ARG B 465 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 ARG cc_start: 0.9003 (ptt180) cc_final: 0.8564 (ptt90)
REVERT: A  413 MET cc_start: 0.9085 (ppp) cc_final: 0.8732 (ppp)
REVERT: A  489 MET cc_start: 0.8396 (tpt) cc_final: 0.8020 (tpp)
REVERT: A  508 MET cc_start: 0.6594 (mmt) cc_final: 0.5963 (mmp)
REVERT: A  512 TYR cc_start: 0.8558 (m-80) cc_final: 0.8295 (m-10)
REVERT: A  524 TYR cc_start: 0.8194 (t80) cc_final: 0.7882 (t80)
REVERT: A  534 TRP cc_start: 0.8112 (m-10) cc_final: 0.7753 (m-90)
REVERT: A  558 TYR cc_start: 0.7694 (m-80) cc_final: 0.7300 (m-80)
REVERT: A  600 GLU cc_start: 0.8533 (mp0) cc_final: 0.7914 (mm-30)
REVERT: B  241 CYS cc_start: 0.8734 (t) cc_final: 0.8459 (t)
REVERT: B  251 LEU cc_start: 0.8721 (tt) cc_final: 0.8423 (pp)
REVERT: B  280 GLU cc_start: 0.9142 (tt0) cc_final: 0.8589 (tp30)
REVERT: B  281 PHE cc_start: 0.8679 (t80) cc_final: 0.8355 (t80)
REVERT: B  328 CYS cc_start: 0.8946 (m) cc_final: 0.8717 (m)
REVERT: B  377 LEU cc_start: 0.8332 (mm) cc_final: 0.7772 (mm)
REVERT: B  403 LEU cc_start: 0.9076 (mt) cc_final: 0.8842 (mt)
REVERT: B  462 GLN cc_start: 0.9126 (mp10) cc_final: 0.8788 (mp10)
REVERT: B  489 MET cc_start: 0.8041 (ttt) cc_final: 0.7680 (ttt)
REVERT: B  496 TYR cc_start: 0.8587 (t80) cc_final: 0.8286 (t80)
REVERT: B  509 VAL cc_start: 0.9293 (t) cc_final: 0.9001 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1552
  time to fit residues: 41.8946
Evaluate side-chains
  161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:   40.0000
   chunk 51 optimal weight:    7.9990
   chunk 75 optimal weight:    0.0030
   chunk 114 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 9 optimal weight:   30.0000
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 72 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 555 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8637  Z= 0.196
  Angle     :  0.589   9.772  11823  Z= 0.312
  Chirality :  0.038   0.179   1375
  Planarity :  0.004   0.060   1499
  Dihedral  :  3.776  18.077   1239
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.34 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.24 (0.26), residues: 1153
  helix:  2.53 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -1.98 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 395 
 HIS   0.015   0.001   HIS B 441 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.021   0.001   TYR A 512 
 ARG   0.006   0.001   ARG A 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ARG cc_start: 0.9040 (ptt180) cc_final: 0.8510 (ptt180)
REVERT: A  413 MET cc_start: 0.9050 (ppp) cc_final: 0.8645 (ppp)
REVERT: A  489 MET cc_start: 0.8374 (tpt) cc_final: 0.8001 (tpp)
REVERT: A  508 MET cc_start: 0.6859 (mmt) cc_final: 0.6248 (mmp)
REVERT: A  512 TYR cc_start: 0.8605 (m-80) cc_final: 0.8350 (m-10)
REVERT: A  524 TYR cc_start: 0.8248 (t80) cc_final: 0.7999 (t80)
REVERT: A  534 TRP cc_start: 0.8221 (m-10) cc_final: 0.7987 (m-90)
REVERT: A  558 TYR cc_start: 0.7824 (m-80) cc_final: 0.7395 (m-80)
REVERT: A  600 GLU cc_start: 0.8684 (mp0) cc_final: 0.8239 (mm-30)
REVERT: B  241 CYS cc_start: 0.8753 (t) cc_final: 0.8469 (t)
REVERT: B  280 GLU cc_start: 0.9155 (tt0) cc_final: 0.8533 (tp30)
REVERT: B  281 PHE cc_start: 0.8758 (t80) cc_final: 0.8455 (t80)
REVERT: B  328 CYS cc_start: 0.8990 (m) cc_final: 0.8723 (m)
REVERT: B  377 LEU cc_start: 0.8352 (mm) cc_final: 0.7809 (mm)
REVERT: B  403 LEU cc_start: 0.9117 (mt) cc_final: 0.8912 (mt)
REVERT: B  462 GLN cc_start: 0.9200 (mp10) cc_final: 0.8822 (mp10)
REVERT: B  489 MET cc_start: 0.8114 (ttt) cc_final: 0.7753 (ttt)
REVERT: B  496 TYR cc_start: 0.8578 (t80) cc_final: 0.8279 (t80)
REVERT: B  509 VAL cc_start: 0.9296 (t) cc_final: 0.8919 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1485
  time to fit residues: 40.4783
Evaluate side-chains
  144 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0980
   chunk 91 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 11 optimal weight:   30.0000
   chunk 16 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 5 optimal weight:   40.0000
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 GLN
B 608 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.138128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.105121 restraints weight = 25747.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.107745 restraints weight = 16257.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.109566 restraints weight = 11591.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8637  Z= 0.185
  Angle     :  0.603  13.652  11823  Z= 0.316
  Chirality :  0.038   0.181   1375
  Planarity :  0.004   0.059   1499
  Dihedral  :  3.779  17.578   1239
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.25 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    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:  2.21 (0.26), residues: 1153
  helix:  2.49 (0.17), residues: 865
  sheet:  None (None), residues: 0
  loop : -1.94 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 395 
 HIS   0.013   0.001   HIS B 441 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.019   0.001   TYR A 512 
 ARG   0.004   0.000   ARG B 459 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1772.78 seconds
wall clock time: 33 minutes 11.74 seconds (1991.74 seconds total)