Starting phenix.real_space_refine
on Fri Nov 15 04:21:46 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irj_35676/11_2024/8irj_35676.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irj_35676/11_2024/8irj_35676.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irj_35676/11_2024/8irj_35676.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irj_35676/11_2024/8irj_35676.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irj_35676/11_2024/8irj_35676.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irj_35676/11_2024/8irj_35676.cif"
  }
  resolution = 3.49
  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=   0.005 sd=   0.018
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      54      5.16       5
     C    5314      2.51       5
     N    1422      2.21       5
     O    1438      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8228
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 4114
          Classifications: {'peptide': 531}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 30, 'TRANS': 500}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.52, per 1000 atoms: 1.04
  Number of scatterers: 8228
  At special positions: 0
  Unit cell: (66.3966, 96.1899, 167.694, 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      54     16.00
     O    1438      8.00
     N    1422      7.00
     C    5314      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  76 " - pdb=" SG  CYS A 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 295 " - pdb=" SG  CYS A 317 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 319 " - pdb=" SG  CYS A 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 359 " - pdb=" SG  CYS A 366 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 445 " - pdb=" SG  CYS A 537 " 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: 1.97
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      50.5% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 92 through 116
      removed outlier: 3.603A  pdb=" N   THR A 101 " --> pdb=" O   GLY A  97 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA A 105 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ALA A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 139
      removed outlier: 3.842A  pdb=" N   TYR A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 328 through 332
    Processing helix  chain 'A' and resid 378 through 402
      removed outlier: 3.861A  pdb=" N   ALA A 382 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS A 391 " --> pdb=" O   CYS A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 408
      removed outlier: 3.980A  pdb=" N   ARG A 407 " --> pdb=" O   TYR A 403 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASN A 408 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 403 through 408'
    Processing helix  chain 'A' and resid 416 through 431
      removed outlier: 3.559A  pdb=" N   PHE A 431 " --> pdb=" O   LEU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 436
    Processing helix  chain 'A' and resid 441 through 475
      removed outlier: 3.870A  pdb=" N   THR A 462 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LEU A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 519
      Proline residue:  A 500  - end of helix
    Processing helix  chain 'A' and resid 540 through 565
      removed outlier: 3.570A  pdb=" N   GLY A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THR A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 599
      removed outlier: 3.980A  pdb=" N   TYR A 576 " --> pdb=" O   HIS A 572 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   MET A 577 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE A 579 " --> pdb=" O   ARG A 575 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA A 580 " --> pdb=" O   TYR A 576 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'A' and resid 603 through 632
      Proline residue:  A 629  - end of helix
      removed outlier: 3.657A  pdb=" N   TRP A 632 " --> pdb=" O   ILE A 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 68 through 72
    Processing helix  chain 'B' and resid 92 through 116
      removed outlier: 3.602A  pdb=" N   THR B 101 " --> pdb=" O   GLY B  97 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN B 104 " --> pdb=" O   GLY B 100 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA B 105 " --> pdb=" O   THR B 101 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ALA B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 139
      removed outlier: 3.842A  pdb=" N   TYR B 130 " --> pdb=" O   ASP B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 227
    Processing helix  chain 'B' and resid 328 through 332
    Processing helix  chain 'B' and resid 378 through 402
      removed outlier: 3.862A  pdb=" N   ALA B 382 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS B 391 " --> pdb=" O   CYS B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 408
      removed outlier: 3.980A  pdb=" N   ARG B 407 " --> pdb=" O   TYR B 403 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN B 408 " --> pdb=" O   ARG B 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 403 through 408'
    Processing helix  chain 'B' and resid 416 through 431
      removed outlier: 3.559A  pdb=" N   PHE B 431 " --> pdb=" O   LEU B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 436
    Processing helix  chain 'B' and resid 441 through 475
      removed outlier: 3.869A  pdb=" N   THR B 462 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   LEU B 475 " --> pdb=" O   LEU B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 519
      Proline residue:  B 500  - end of helix
    Processing helix  chain 'B' and resid 540 through 565
      removed outlier: 3.571A  pdb=" N   GLY B 557 " --> pdb=" O   LEU B 553 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   THR B 564 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 599
      removed outlier: 3.979A  pdb=" N   TYR B 576 " --> pdb=" O   HIS B 572 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   MET B 577 " --> pdb=" O   GLU B 573 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE B 579 " --> pdb=" O   ARG B 575 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 580 " --> pdb=" O   TYR B 576 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   VAL B 597 " --> pdb=" O   THR B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 602
      No H-bonds generated for 'chain 'B' and resid 600 through 602'
    Processing helix  chain 'B' and resid 603 through 632
      Proline residue:  B 629  - end of helix
      removed outlier: 3.658A  pdb=" N   TRP B 632 " --> pdb=" O   ILE B 628 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81
      removed outlier: 3.910A  pdb=" N   TYR A  80 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229
      removed outlier: 3.852A  pdb=" N   PHE A 253 " --> pdb=" O   GLY A 266 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY A 266 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   ARG A 265 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   PHE A 151 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLN A 267 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LEU A 149 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   GLN A 269 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ALA A 147 " --> pdb=" O   GLN A 269 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ASP A 271 " --> pdb=" O   TYR A 145 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   LEU A 162 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR B 203 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 221
      removed outlier: 7.872A  pdb=" N   THR B 173 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL A 201 " --> pdb=" O   THR B 173 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   LEU B 175 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   THR A 203 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU B 162 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ASP B 271 " --> pdb=" O   TYR B 145 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ALA B 147 " --> pdb=" O   GLN B 269 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   GLN B 269 " --> pdb=" O   ALA B 147 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LEU B 149 " --> pdb=" O   GLN B 267 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLN B 267 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   PHE B 151 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   ARG B 265 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY B 266 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   PHE B 253 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 237
    Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 304
    Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 527
      removed outlier: 3.764A  pdb=" N   PHE A 534 " --> pdb=" O   GLY A 526 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 81
      removed outlier: 3.909A  pdb=" N   TYR B  80 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 236 through 237
    Processing sheet with id=AA9, first strand: chain 'B' and resid 300 through 304
    Processing sheet with id=AB1, first strand: chain 'B' and resid 526 through 527
      removed outlier: 3.763A  pdb=" N   PHE B 534 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1230 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: 2.32

  Time building geometry restraints manager: 2.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2482
        1.34 -     1.46: 1974
        1.46 -     1.58: 3900
        1.58 -     1.71: 2
        1.71 -     1.83: 68
  Bond restraints: 8426
  Sorted by residual:
  bond pdb=" C   GLN A 225 "
       pdb=" N   GLN A 226 "
    ideal  model  delta    sigma   weight residual
    1.335  1.411 -0.076 1.33e-02 5.65e+03 3.31e+01
  bond pdb=" C   GLN B 225 "
       pdb=" N   GLN B 226 "
    ideal  model  delta    sigma   weight residual
    1.335  1.411 -0.076 1.33e-02 5.65e+03 3.29e+01
  bond pdb=" C   LEU A 473 "
       pdb=" N   PHE A 474 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.055 1.27e-02 6.20e+03 1.89e+01
  bond pdb=" C   LEU B 473 "
       pdb=" N   PHE B 474 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.055 1.27e-02 6.20e+03 1.86e+01
  bond pdb=" N   VAL B 523 "
       pdb=" CA  VAL B 523 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.043 1.23e-02 6.61e+03 1.25e+01
  ... (remaining 8421 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 10955
        2.56 -     5.12: 455
        5.12 -     7.68: 48
        7.68 -    10.24: 4
       10.24 -    12.80: 2
  Bond angle restraints: 11464
  Sorted by residual:
  angle pdb=" N   PRO A 521 "
        pdb=" CA  PRO A 521 "
        pdb=" C   PRO A 521 "
      ideal   model   delta    sigma   weight residual
     113.65  100.85   12.80 1.35e+00 5.49e-01 8.99e+01
  angle pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
        pdb=" C   PRO B 521 "
      ideal   model   delta    sigma   weight residual
     113.65  100.87   12.78 1.35e+00 5.49e-01 8.96e+01
  angle pdb=" N   ARG B 406 "
        pdb=" CA  ARG B 406 "
        pdb=" C   ARG B 406 "
      ideal   model   delta    sigma   weight residual
     114.62  106.47    8.15 1.14e+00 7.69e-01 5.12e+01
  angle pdb=" N   ARG A 406 "
        pdb=" CA  ARG A 406 "
        pdb=" C   ARG A 406 "
      ideal   model   delta    sigma   weight residual
     114.62  106.50    8.12 1.14e+00 7.69e-01 5.07e+01
  angle pdb=" C   ARG A 525 "
        pdb=" CA  ARG A 525 "
        pdb=" CB  ARG A 525 "
      ideal   model   delta    sigma   weight residual
     110.34  118.05   -7.71 1.40e+00 5.10e-01 3.03e+01
  ... (remaining 11459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4492
       17.96 -    35.91: 394
       35.91 -    53.87: 73
       53.87 -    71.82: 12
       71.82 -    89.78: 10
  Dihedral angle restraints: 4981
    sinusoidal: 1937
      harmonic: 3044
  Sorted by residual:
  dihedral pdb=" CA  PHE B 431 "
           pdb=" C   PHE B 431 "
           pdb=" N   PRO B 432 "
           pdb=" CA  PRO B 432 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.66  -29.34     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  PHE A 431 "
           pdb=" C   PHE A 431 "
           pdb=" N   PRO A 432 "
           pdb=" CA  PRO A 432 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.68  -29.32     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  SER A 486 "
           pdb=" C   SER A 486 "
           pdb=" N   SER A 487 "
           pdb=" CA  SER A 487 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.52   25.48     0      5.00e+00 4.00e-02 2.60e+01
  ... (remaining 4978 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.136: 1273
       0.136 -    0.271: 27
       0.271 -    0.407: 6
       0.407 -    0.542: 0
       0.542 -    0.678: 2
  Chirality restraints: 1308
  Sorted by residual:
  chirality pdb=" CG  LEU B 428 "
            pdb=" CB  LEU B 428 "
            pdb=" CD1 LEU B 428 "
            pdb=" CD2 LEU B 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.91   -0.68 2.00e-01 2.50e+01 1.15e+01
  chirality pdb=" CG  LEU A 428 "
            pdb=" CB  LEU A 428 "
            pdb=" CD1 LEU A 428 "
            pdb=" CD2 LEU A 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.92   -0.67 2.00e-01 2.50e+01 1.14e+01
  chirality pdb=" CA  THR B 150 "
            pdb=" N   THR B 150 "
            pdb=" C   THR B 150 "
            pdb=" CB  THR B 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.15    0.38 2.00e-01 2.50e+01 3.52e+00
  ... (remaining 1305 not shown)

  Planarity restraints: 1456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 585 "   -0.018 2.00e-02 2.50e+03   3.68e-02 1.35e+01
        pdb=" C   LEU A 585 "    0.064 2.00e-02 2.50e+03
        pdb=" O   LEU A 585 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU A 586 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 585 "    0.018 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" C   LEU B 585 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   LEU B 585 "    0.024 2.00e-02 2.50e+03
        pdb=" N   LEU B 586 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 405 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.73e+00
        pdb=" C   CYS A 405 "    0.045 2.00e-02 2.50e+03
        pdb=" O   CYS A 405 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 406 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1453 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 66
        2.60 -     3.18: 7029
        3.18 -     3.75: 12067
        3.75 -     4.33: 16169
        4.33 -     4.90: 26699
  Nonbonded interactions: 62030
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 295 "
            pdb=" SG  CYS B 317 "
     model   vdw
     2.027 3.760
  nonbonded pdb=" SG  CYS B 282 "
            pdb=" SG  CYS B 302 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B  76 "
            pdb=" SG  CYS B 236 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 445 "
            pdb=" SG  CYS B 537 "
     model   vdw
     2.033 3.760
  nonbonded pdb=" SG  CYS B 363 "
            pdb=" SG  CYS B 372 "
     model   vdw
     2.035 3.760
  ... (remaining 62025 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'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.980
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
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      :  0.007   0.076   8426  Z= 0.482
  Angle     :  1.097  12.798  11464  Z= 0.681
  Chirality :  0.063   0.678   1308
  Planarity :  0.007   0.060   1456
  Dihedral  : 14.433  89.775   3000
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  1.84 %
    Favored  : 97.01 %
  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: -1.75 (0.24), residues: 1034
  helix: -0.16 (0.23), residues: 452
  sheet: -0.02 (0.49), residues: 122
  loop : -2.58 (0.25), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 450 
 HIS   0.006   0.001   HIS A 603 
 PHE   0.019   0.002   PHE B 253 
 TYR   0.028   0.002   TYR B 468 
 ARG   0.008   0.001   ARG B 525 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 162
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A  452 ARG cc_start: 0.7990 (tpt170) cc_final: 0.7740 (tpp80)
REVERT: B  452 ARG cc_start: 0.7951 (tpt170) cc_final: 0.7724 (tpp80)
  outliers start: 10
  outliers final: 4
  residues processed: 172
  average time/residue: 0.2341
  time to fit residues: 54.7260
Evaluate side-chains
  125 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  522 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0670
   chunk 61 optimal weight:    0.7980
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 388 GLN
A 519 HIS
B 388 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8426  Z= 0.245
  Angle     :  0.765  12.541  11464  Z= 0.372
  Chirality :  0.042   0.139   1308
  Planarity :  0.006   0.064   1456
  Dihedral  :  5.098  32.984   1156
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.00 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.25), residues: 1034
  helix:  0.68 (0.23), residues: 468
  sheet: -0.16 (0.43), residues: 158
  loop : -2.30 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 508 
 HIS   0.003   0.001   HIS A 538 
 PHE   0.020   0.001   PHE B 253 
 TYR   0.021   0.002   TYR B 468 
 ARG   0.004   0.000   ARG A  83 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 ARG cc_start: 0.6424 (tpt90) cc_final: 0.5233 (ttt180)
REVERT: B  392 MET cc_start: 0.7772 (mmm) cc_final: 0.7337 (mtp)
  outliers start: 19
  outliers final: 11
  residues processed: 167
  average time/residue: 0.2259
  time to fit residues: 52.0032
Evaluate side-chains
  147 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  463 ILE
Chi-restraints excluded: chain B residue  501 VAL
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0870
   chunk 104 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.9162

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
B 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8426  Z= 0.281
  Angle     :  0.751  13.317  11464  Z= 0.367
  Chirality :  0.043   0.157   1308
  Planarity :  0.005   0.053   1456
  Dihedral  :  4.917  19.248   1150
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.36 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.26), residues: 1034
  helix:  1.03 (0.23), residues: 468
  sheet: -0.19 (0.43), residues: 160
  loop : -2.16 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 450 
 HIS   0.002   0.001   HIS A 538 
 PHE   0.022   0.002   PHE B 434 
 TYR   0.018   0.002   TYR B 468 
 ARG   0.007   0.000   ARG A 240 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A  354 LEU cc_start: 0.4941 (tp) cc_final: 0.4512 (tp)
REVERT: A  404 ARG cc_start: 0.6464 (tpt90) cc_final: 0.5254 (ttt180)
REVERT: B  118 ILE cc_start: 0.8793 (mt) cc_final: 0.8547 (mt)
REVERT: B  392 MET cc_start: 0.7862 (mmm) cc_final: 0.7521 (mtp)
  outliers start: 25
  outliers final: 12
  residues processed: 160
  average time/residue: 0.1999
  time to fit residues: 44.1583
Evaluate side-chains
  138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 96 optimal weight:    0.1980
   chunk 102 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8426  Z= 0.229
  Angle     :  0.728  12.426  11464  Z= 0.348
  Chirality :  0.042   0.159   1308
  Planarity :  0.005   0.041   1456
  Dihedral  :  4.696  19.127   1150
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.08 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.26), residues: 1034
  helix:  1.12 (0.24), residues: 468
  sheet: -0.41 (0.41), residues: 170
  loop : -2.15 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 450 
 HIS   0.002   0.000   HIS A 519 
 PHE   0.019   0.001   PHE A 253 
 TYR   0.013   0.001   TYR B 468 
 ARG   0.006   0.000   ARG A 240 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A  392 MET cc_start: 0.7616 (mmt) cc_final: 0.7159 (mtp)
REVERT: A  404 ARG cc_start: 0.6434 (tpt90) cc_final: 0.5340 (ttt180)
REVERT: A  452 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7435 (tpp80)
REVERT: B  392 MET cc_start: 0.7876 (mmm) cc_final: 0.7586 (mtp)
REVERT: B  452 ARG cc_start: 0.7797 (tpt170) cc_final: 0.7451 (tpp80)
  outliers start: 30
  outliers final: 17
  residues processed: 154
  average time/residue: 0.2095
  time to fit residues: 43.8959
Evaluate side-chains
  146 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0170
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 91 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
B 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.4093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8426  Z= 0.187
  Angle     :  0.701  12.204  11464  Z= 0.330
  Chirality :  0.041   0.148   1308
  Planarity :  0.004   0.048   1456
  Dihedral  :  4.413  19.010   1150
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.23 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.26), residues: 1034
  helix:  1.30 (0.23), residues: 470
  sheet: -0.31 (0.40), residues: 170
  loop : -2.09 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 450 
 HIS   0.002   0.000   HIS A 519 
 PHE   0.021   0.001   PHE A 434 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.007   0.000   ARG A 240 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: A  392 MET cc_start: 0.7545 (mmt) cc_final: 0.7150 (mtp)
REVERT: A  404 ARG cc_start: 0.6571 (tpt90) cc_final: 0.5450 (ttt180)
REVERT: B  392 MET cc_start: 0.7849 (mmm) cc_final: 0.7616 (mtp)
REVERT: B  404 ARG cc_start: 0.6549 (tpt170) cc_final: 0.5411 (ttt180)
  outliers start: 30
  outliers final: 20
  residues processed: 152
  average time/residue: 0.1802
  time to fit residues: 38.9137
Evaluate side-chains
  148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  628 ILE
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
A 533 HIS
B 204 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8426  Z= 0.238
  Angle     :  0.726  12.357  11464  Z= 0.347
  Chirality :  0.042   0.153   1308
  Planarity :  0.005   0.046   1456
  Dihedral  :  4.548  19.102   1150
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.57 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.26), residues: 1034
  helix:  1.42 (0.23), residues: 470
  sheet: -0.33 (0.40), residues: 170
  loop : -2.05 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 182 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.020   0.002   PHE A 253 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.005   0.000   ARG B  83 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: A  392 MET cc_start: 0.7606 (mmt) cc_final: 0.7229 (mtp)
REVERT: A  404 ARG cc_start: 0.6559 (tpt90) cc_final: 0.5444 (ttt180)
REVERT: A  452 ARG cc_start: 0.7695 (tpt170) cc_final: 0.7385 (tpp80)
REVERT: B  392 MET cc_start: 0.7927 (mmm) cc_final: 0.7690 (mtp)
REVERT: B  404 ARG cc_start: 0.6435 (tpt170) cc_final: 0.5629 (ttt180)
REVERT: B  452 ARG cc_start: 0.7716 (tpt170) cc_final: 0.7394 (tpp80)
  outliers start: 34
  outliers final: 22
  residues processed: 157
  average time/residue: 0.1981
  time to fit residues: 42.9607
Evaluate side-chains
  154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 58 optimal weight:    0.2980
   chunk 74 optimal weight:    0.5980
   chunk 86 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
B 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8426  Z= 0.180
  Angle     :  0.692  13.005  11464  Z= 0.327
  Chirality :  0.040   0.148   1308
  Planarity :  0.004   0.042   1456
  Dihedral  :  4.298  19.433   1150
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.84 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.26), residues: 1034
  helix:  1.66 (0.23), residues: 474
  sheet: -0.23 (0.40), residues: 170
  loop : -2.00 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 182 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.020   0.001   PHE B 504 
 TYR   0.009   0.001   TYR A  80 
 ARG   0.006   0.000   ARG B  83 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: A  392 MET cc_start: 0.7566 (mmt) cc_final: 0.7237 (mtp)
REVERT: A  404 ARG cc_start: 0.6637 (tpt90) cc_final: 0.5517 (ttt180)
REVERT: A  452 ARG cc_start: 0.7676 (tpt170) cc_final: 0.7378 (tpp80)
REVERT: B  392 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7671 (mtp)
REVERT: B  404 ARG cc_start: 0.6712 (tpt170) cc_final: 0.5848 (ttt180)
REVERT: B  452 ARG cc_start: 0.7706 (tpt170) cc_final: 0.7410 (tpp80)
  outliers start: 26
  outliers final: 17
  residues processed: 146
  average time/residue: 0.2089
  time to fit residues: 42.0246
Evaluate side-chains
  145 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  524 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0670
   chunk 9 optimal weight:    0.5980
   chunk 80 optimal weight:    0.3980
   chunk 92 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
B 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.4705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8426  Z= 0.182
  Angle     :  0.705  14.698  11464  Z= 0.331
  Chirality :  0.040   0.131   1308
  Planarity :  0.004   0.037   1456
  Dihedral  :  4.241  19.592   1150
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.99 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 1034
  helix:  1.71 (0.23), residues: 478
  sheet: -0.19 (0.40), residues: 170
  loop : -1.97 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 182 
 HIS   0.003   0.000   HIS A 533 
 PHE   0.020   0.001   PHE A 504 
 TYR   0.010   0.001   TYR A  62 
 ARG   0.007   0.000   ARG B  83 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 GLN cc_start: 0.7461 (tm-30) cc_final: 0.7246 (tt0)
REVERT: A  392 MET cc_start: 0.7581 (mmt) cc_final: 0.7291 (mtp)
REVERT: A  404 ARG cc_start: 0.6622 (tpt90) cc_final: 0.5517 (ttt180)
REVERT: A  450 TRP cc_start: 0.7383 (m100) cc_final: 0.7117 (m100)
REVERT: A  452 ARG cc_start: 0.7666 (tpt170) cc_final: 0.7385 (tpp80)
REVERT: B  392 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7504 (mtp)
REVERT: B  404 ARG cc_start: 0.6753 (tpt170) cc_final: 0.5884 (ttt180)
REVERT: B  452 ARG cc_start: 0.7712 (tpt170) cc_final: 0.7445 (tpp80)
  outliers start: 25
  outliers final: 18
  residues processed: 144
  average time/residue: 0.1967
  time to fit residues: 39.3609
Evaluate side-chains
  146 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.0870
   chunk 97 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 41 optimal weight:    3.9990
   chunk 74 optimal weight:    0.1980
   chunk 29 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 100 optimal weight:    8.9990
   overall best weight:    0.4560

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.4839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8426  Z= 0.181
  Angle     :  0.717  14.603  11464  Z= 0.334
  Chirality :  0.040   0.131   1308
  Planarity :  0.004   0.036   1456
  Dihedral  :  4.193  19.559   1150
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.64 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.26), residues: 1034
  helix:  1.82 (0.23), residues: 476
  sheet: -0.27 (0.38), residues: 186
  loop : -2.09 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.020   0.001   PHE A 504 
 TYR   0.010   0.001   TYR A  80 
 ARG   0.007   0.000   ARG A  83 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.8652 (tt) cc_final: 0.8175 (mt)
REVERT: A  392 MET cc_start: 0.7604 (mmt) cc_final: 0.7295 (mtp)
REVERT: A  404 ARG cc_start: 0.6600 (tpt90) cc_final: 0.5477 (ttt180)
REVERT: A  452 ARG cc_start: 0.7615 (tpt170) cc_final: 0.7368 (tpp80)
REVERT: A  577 MET cc_start: 0.7556 (mtt) cc_final: 0.7294 (mtt)
REVERT: B   60 LEU cc_start: 0.8612 (tt) cc_final: 0.8128 (mt)
REVERT: B  392 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7508 (mtp)
REVERT: B  404 ARG cc_start: 0.6643 (tpt170) cc_final: 0.5795 (ttt180)
REVERT: B  452 ARG cc_start: 0.7724 (tpt170) cc_final: 0.7437 (tpp80)
  outliers start: 25
  outliers final: 20
  residues processed: 148
  average time/residue: 0.2052
  time to fit residues: 41.7518
Evaluate side-chains
  146 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 582 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8426  Z= 0.236
  Angle     :  0.764  15.673  11464  Z= 0.356
  Chirality :  0.041   0.136   1308
  Planarity :  0.005   0.035   1456
  Dihedral  :  4.392  29.782   1150
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 23.33 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.26), residues: 1034
  helix:  1.66 (0.23), residues: 484
  sheet: -0.26 (0.39), residues: 184
  loop : -2.05 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 450 
 HIS   0.017   0.001   HIS A 582 
 PHE   0.030   0.002   PHE B 434 
 TYR   0.010   0.001   TYR A  62 
 ARG   0.008   0.000   ARG A  83 

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8678 (tt) cc_final: 0.8214 (mt)
REVERT: A  392 MET cc_start: 0.7624 (mmt) cc_final: 0.7325 (mtp)
REVERT: A  404 ARG cc_start: 0.6676 (tpt90) cc_final: 0.5575 (ttt180)
REVERT: A  452 ARG cc_start: 0.7678 (tpt170) cc_final: 0.7403 (tpp80)
REVERT: A  551 LEU cc_start: 0.8223 (mm) cc_final: 0.7014 (tp)
REVERT: A  577 MET cc_start: 0.7596 (mtt) cc_final: 0.7331 (mtt)
REVERT: B   60 LEU cc_start: 0.8615 (tt) cc_final: 0.8110 (mt)
REVERT: B  392 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7553 (mtp)
REVERT: B  404 ARG cc_start: 0.6566 (tpt170) cc_final: 0.5678 (ttt180)
REVERT: B  452 ARG cc_start: 0.7742 (tpt170) cc_final: 0.7450 (tpp80)
  outliers start: 23
  outliers final: 21
  residues processed: 145
  average time/residue: 0.2076
  time to fit residues: 41.4147
Evaluate side-chains
  148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  431 PHE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.148908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.124846 restraints weight = 15990.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.79
r_work: 0.3323 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8426  Z= 0.248
  Angle     :  0.767  15.148  11464  Z= 0.361
  Chirality :  0.042   0.136   1308
  Planarity :  0.005   0.035   1456
  Dihedral  :  4.381  20.045   1150
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 23.79 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 1034
  helix:  1.65 (0.23), residues: 484
  sheet: -0.14 (0.41), residues: 170
  loop : -1.90 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 450 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.027   0.002   PHE B 434 
 TYR   0.012   0.001   TYR A  80 
 ARG   0.007   0.000   ARG A  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2084.15 seconds
wall clock time: 38 minutes 50.49 seconds (2330.49 seconds total)