Starting phenix.real_space_refine
on Thu Mar  6 10:25:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wpz_32693/03_2025/7wpz_32693.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wpz_32693/03_2025/7wpz_32693.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wpz_32693/03_2025/7wpz_32693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wpz_32693/03_2025/7wpz_32693.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wpz_32693/03_2025/7wpz_32693.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wpz_32693/03_2025/7wpz_32693.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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      31      5.16       5
     C    3672      2.51       5
     N    1016      2.21       5
     O    1037      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5756
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4361
          Classifications: {'peptide': 595}
          Incomplete info: {'truncation_to_alanine': 186}
          Link IDs: {'PTRANS': 24, 'TRANS': 570}
          Unresolved non-hydrogen bonds: 531
          Unresolved non-hydrogen angles: 671
          Unresolved non-hydrogen dihedrals: 401
          Unresolved non-hydrogen chiralities: 58
          Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 23, 'GLU:plan': 36}
          Unresolved non-hydrogen planarities: 284
    Chain: "B"
      Number of atoms: 1194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1194
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 111}
          Link IDs: {'PTRANS': 11, 'TRANS': 180}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 341
          Unresolved non-hydrogen angles: 441
          Unresolved non-hydrogen dihedrals: 265
          Unresolved non-hydrogen chiralities: 49
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 159
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "J"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.15, per 1000 atoms: 0.72
  Number of scatterers: 5756
  At special positions: 0
  Unit cell: (88.56, 94.3, 117.26, 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      31     16.00
     O    1037      8.00
     N    1016      7.00
     C    3672      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 134 " - pdb=" SG  CYS A 142 " distance=2.20
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.11
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 387 " - pdb=" SG  CYS B 411 " distance=2.08
    Simple disulfide: pdb=" SG  CYS B 441 " - pdb=" SG  CYS B 583 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B 506 " - pdb=" SG  CYS B 527 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG J   1 " - " NAG J   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 329 "
      " NAG A 702 " - " ASN A 546 "
      " NAG A 703 " - " ASN A  91 "
      " NAG B 601 " - " ASN B 489 "
      " NAG C   1 " - " ASN A  54 "
      " NAG D   1 " - " ASN A 104 "
      " NAG E   1 " - " ASN A 280 "
      " NAG J   1 " - " ASN A 432 "
  Time building additional restraints: 1.74
  Conformation dependent library (CDL) restraints added in 825.8 milliseconds
  

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1486

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      58.7% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 53
    Processing helix  chain 'A' and resid 56 through 82
      removed outlier: 4.082A  pdb=" N   GLN A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS A  62 " --> pdb=" O   GLU A  58 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN A  64 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 102
    Processing helix  chain 'A' and resid 110 through 130
    Processing helix  chain 'A' and resid 145 through 153
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.911A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.824A  pdb=" N   MET A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.994A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.500A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 385
      removed outlier: 4.473A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 397 through 414
      removed outlier: 3.599A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.706A  pdb=" N   ILE A 436 " --> pdb=" O   ASN A 432 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASN A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 534
      removed outlier: 3.531A  pdb=" N   PHE A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.855A  pdb=" N   ILE A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 600
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 4.072A  pdb=" N   GLN A 615 " --> pdb=" O   TYR A 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 393
    Processing helix  chain 'B' and resid 417 through 422
      removed outlier: 3.657A  pdb=" N   VAL B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 438
    Processing helix  chain 'B' and resid 453 through 460
      removed outlier: 4.424A  pdb=" N   SER B 458 " --> pdb=" O   ALA B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 471
    Processing helix  chain 'B' and resid 524 through 533
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.365A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'B' and resid 404 through 408
      removed outlier: 3.561A  pdb=" N   LYS B 404 " --> pdb=" O   TRP B 449 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   HIS B 485 " --> pdb=" O   ASP B 425 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 411 through 412
      removed outlier: 6.101A  pdb=" N   CYS B 411 " --> pdb=" O   CYS B 583 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 513 through 514
      removed outlier: 6.607A  pdb=" N   SER B 553 " --> pdb=" O   THR B 504 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   CYS B 506 " --> pdb=" O   ARG B 551 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ARG B 551 " --> pdb=" O   CYS B 506 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   TYR B 508 " --> pdb=" O   PRO B 549 " (cutoff:3.500A)

    334 hydrogen bonds defined for protein.
    942 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 1245
        1.33 -     1.46: 2088
        1.46 -     1.60: 2530
        1.60 -     1.73: 1
        1.73 -     1.87: 49
  Bond restraints: 5913
  Sorted by residual:
  bond pdb=" CA  LEU A 491 "
       pdb=" C   LEU A 491 "
    ideal  model  delta    sigma   weight residual
    1.522  1.566 -0.044 8.40e-03 1.42e+04 2.71e+01
  bond pdb=" CA  ASN A 546 "
       pdb=" C   ASN A 546 "
    ideal  model  delta    sigma   weight residual
    1.525  1.579 -0.054 1.40e-02 5.10e+03 1.49e+01
  bond pdb=" NE  ARG B 483 "
       pdb=" CZ  ARG B 483 "
    ideal  model  delta    sigma   weight residual
    1.326  1.368 -0.042 1.10e-02 8.26e+03 1.46e+01
  bond pdb=" N   PRO A 492 "
       pdb=" CD  PRO A 492 "
    ideal  model  delta    sigma   weight residual
    1.473  1.420  0.053 1.40e-02 5.10e+03 1.44e+01
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.488 -0.075 2.00e-02 2.50e+03 1.42e+01
  ... (remaining 5908 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.35: 7829
        3.35 -     6.70: 242
        6.70 -    10.05: 12
       10.05 -    13.41: 1
       13.41 -    16.76: 1
  Bond angle restraints: 8085
  Sorted by residual:
  angle pdb=" N   ILE B 494 "
        pdb=" CA  ILE B 494 "
        pdb=" C   ILE B 494 "
      ideal   model   delta    sigma   weight residual
     109.34   92.58   16.76 2.08e+00 2.31e-01 6.49e+01
  angle pdb=" C   GLY A 537 "
        pdb=" N   PRO A 538 "
        pdb=" CA  PRO A 538 "
      ideal   model   delta    sigma   weight residual
     119.76  127.80   -8.04 1.03e+00 9.43e-01 6.09e+01
  angle pdb=" C   GLU A 489 "
        pdb=" N   PRO A 490 "
        pdb=" CA  PRO A 490 "
      ideal   model   delta    sigma   weight residual
     119.56  126.92   -7.36 1.02e+00 9.61e-01 5.21e+01
  angle pdb=" C   GLU A 335 "
        pdb=" N   PRO A 336 "
        pdb=" CA  PRO A 336 "
      ideal   model   delta    sigma   weight residual
     119.85  126.95   -7.10 1.01e+00 9.80e-01 4.94e+01
  angle pdb=" C   GLU B 576 "
        pdb=" N   PRO B 577 "
        pdb=" CA  PRO B 577 "
      ideal   model   delta    sigma   weight residual
     119.78  126.84   -7.06 1.03e+00 9.43e-01 4.70e+01
  ... (remaining 8080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.29: 3529
       21.29 -    42.59: 71
       42.59 -    63.88: 14
       63.88 -    85.17: 9
       85.17 -   106.47: 4
  Dihedral angle restraints: 3627
    sinusoidal: 1321
      harmonic: 2306
  Sorted by residual:
  dihedral pdb=" N   ILE B 494 "
           pdb=" C   ILE B 494 "
           pdb=" CA  ILE B 494 "
           pdb=" CB  ILE B 494 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  106.22   17.18     0      2.50e+00 1.60e-01 4.72e+01
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -124.14   38.14     1      1.00e+01 1.00e-02 2.05e+01
  dihedral pdb=" C   ILE B 494 "
           pdb=" N   ILE B 494 "
           pdb=" CA  ILE B 494 "
           pdb=" CB  ILE B 494 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -110.76  -11.24     0      2.50e+00 1.60e-01 2.02e+01
  ... (remaining 3624 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.232: 862
       0.232 -    0.463: 37
       0.463 -    0.695: 0
       0.695 -    0.927: 1
       0.927 -    1.159: 1
  Chirality restraints: 901
  Sorted by residual:
  chirality pdb=" C1  NAG J   2 "
            pdb=" O4  NAG J   1 "
            pdb=" C2  NAG J   2 "
            pdb=" O5  NAG J   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.64    0.24 2.00e-02 2.50e+03 1.45e+02
  chirality pdb=" C1  MAN C   4 "
            pdb=" O3  BMA C   3 "
            pdb=" C2  MAN C   4 "
            pdb=" O5  MAN C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.60   -0.20 2.00e-02 2.50e+03 9.87e+01
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.58    0.18 2.00e-02 2.50e+03 8.25e+01
  ... (remaining 898 not shown)

  Planarity restraints: 1055
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 491 "    0.018 2.00e-02 2.50e+03   3.78e-02 1.43e+01
        pdb=" C   LEU A 491 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   LEU A 491 "    0.025 2.00e-02 2.50e+03
        pdb=" N   PRO A 492 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 329 "   -0.027 2.00e-02 2.50e+03   2.77e-02 9.58e+00
        pdb=" CG  ASN A 329 "    0.011 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 329 "    0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 329 "    0.043 2.00e-02 2.50e+03
        pdb=" C1  NAG A 701 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  91 "   -0.022 2.00e-02 2.50e+03   2.68e-02 8.98e+00
        pdb=" CG  ASN A  91 "   -0.000 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  91 "    0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  91 "    0.045 2.00e-02 2.50e+03
        pdb=" C1  NAG A 703 "   -0.032 2.00e-02 2.50e+03
  ... (remaining 1052 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 2433
        2.93 -     3.42: 5498
        3.42 -     3.91: 9550
        3.91 -     4.41: 10552
        4.41 -     4.90: 16754
  Nonbonded interactions: 44787
  Sorted by model distance:
  nonbonded pdb=" N   VAL A 108 "
            pdb=" N   LEU A 109 "
     model   vdw
     2.431 2.560
  nonbonded pdb=" N   ALA B 523 "
            pdb=" O   ALA B 523 "
     model   vdw
     2.519 2.496
  nonbonded pdb=" N   LYS B 562 "
            pdb=" O   LYS B 562 "
     model   vdw
     2.581 2.496
  nonbonded pdb=" O   GLN A 239 "
            pdb=" ND2 ASN A 599 "
     model   vdw
     2.581 3.120
  nonbonded pdb=" N   ARG B 467 "
            pdb=" N   ILE B 468 "
     model   vdw
     2.587 2.560
  ... (remaining 44782 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 'D'
  selection = chain 'E'
  selection = chain 'J'
}

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:             1.350
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.000
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
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      :  0.013   0.094   5913  Z= 0.891
  Angle     :  1.409  16.756   8085  Z= 0.971
  Chirality :  0.111   1.159    901
  Planarity :  0.006   0.038   1047
  Dihedral  : 11.149 106.467   2123
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  2.19 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  0.99 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.13 %
  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: -0.13 (0.27), residues: 777
  helix: -0.10 (0.23), residues: 405
  sheet:  0.71 (0.69), residues: 50
  loop :  0.05 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.005   TRP A 328 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.024   0.004   PHE A 592 
 TYR   0.035   0.005   TYR A 217 
 ARG   0.006   0.001   ARG A 161 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.7652 (ttp) cc_final: 0.7421 (ttp)
REVERT: A  223 MET cc_start: 0.7557 (mtm) cc_final: 0.7319 (mtt)
REVERT: A  510 TYR cc_start: 0.6825 (m-80) cc_final: 0.6512 (m-10)
REVERT: B  474 ASN cc_start: 0.7697 (t0) cc_final: 0.7387 (t0)
REVERT: B  475 GLN cc_start: 0.8105 (tt0) cc_final: 0.7542 (tt0)
  outliers start: 3
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2335
  time to fit residues: 36.0632
Evaluate side-chains
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  42 HIS
A 330 ASN
A 535 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.123081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.109090 restraints weight = 12038.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.111418 restraints weight = 6191.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.112862 restraints weight = 3754.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   5913  Z= 0.230
  Angle     :  0.634  10.396   8085  Z= 0.338
  Chirality :  0.045   0.223    901
  Planarity :  0.005   0.044   1047
  Dihedral  :  7.392  73.219   1156
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  0.90 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  7.94 %
    Favored  : 90.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.29), residues: 777
  helix:  1.45 (0.25), residues: 405
  sheet:  1.22 (0.63), residues: 54
  loop :  0.20 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 163 
 HIS   0.007   0.001   HIS A 345 
 PHE   0.023   0.002   PHE A 592 
 TYR   0.027   0.002   TYR A 315 
 ARG   0.004   0.001   ARG A 219 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6583 (mmm)
REVERT: B  474 ASN cc_start: 0.7717 (t0) cc_final: 0.7352 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 76
  average time/residue: 0.2287
  time to fit residues: 24.5277
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  294 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.114919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.100825 restraints weight = 12475.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102959 restraints weight = 6520.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.104345 restraints weight = 4043.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5913  Z= 0.202
  Angle     :  0.547   6.140   8085  Z= 0.291
  Chirality :  0.043   0.165    901
  Planarity :  0.004   0.037   1047
  Dihedral  :  6.815  61.422   1156
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.32 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.17 %
    Favored  : 87.59 %
  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:  1.52 (0.30), residues: 777
  helix:  1.78 (0.25), residues: 406
  sheet:  1.50 (0.64), residues: 53
  loop : -0.02 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 165 
 HIS   0.003   0.001   HIS B 485 
 PHE   0.021   0.002   PHE A 592 
 TYR   0.021   0.002   TYR A 385 
 ARG   0.003   0.001   ARG A 575 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8209 (t0)
REVERT: A  207 TYR cc_start: 0.8419 (m-80) cc_final: 0.7461 (m-80)
REVERT: A  512 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7568 (m-80)
REVERT: B  474 ASN cc_start: 0.7752 (t0) cc_final: 0.7365 (t0)
REVERT: B  500 TYR cc_start: 0.5534 (m-80) cc_final: 0.5241 (m-80)
  outliers start: 9
  outliers final: 6
  residues processed: 77
  average time/residue: 0.1573
  time to fit residues: 16.7128
Evaluate side-chains
  78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  442 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0470
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.9282

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.112284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098582 restraints weight = 12766.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.100652 restraints weight = 6702.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.102029 restraints weight = 4156.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5913  Z= 0.177
  Angle     :  0.519   5.957   8085  Z= 0.266
  Chirality :  0.042   0.171    901
  Planarity :  0.004   0.035   1047
  Dihedral  :  5.981  47.957   1156
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.54 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.41 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.64 (0.31), residues: 777
  helix:  1.91 (0.25), residues: 413
  sheet:  1.18 (0.65), residues: 53
  loop :  0.00 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.016   0.001   PHE A 592 
 TYR   0.018   0.002   TYR B 550 
 ARG   0.004   0.001   ARG A 575 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 SER cc_start: 0.8731 (p) cc_final: 0.8397 (m)
REVERT: A  201 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8177 (t0)
REVERT: A  207 TYR cc_start: 0.8403 (m-80) cc_final: 0.7488 (m-80)
REVERT: A  512 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7673 (m-80)
REVERT: B  474 ASN cc_start: 0.7844 (t0) cc_final: 0.7470 (t0)
REVERT: B  500 TYR cc_start: 0.5577 (m-80) cc_final: 0.5312 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 80
  average time/residue: 0.1825
  time to fit residues: 19.7056
Evaluate side-chains
  80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue  442 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 25 optimal weight:    0.3980
   chunk 63 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 67 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.109662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.095451 restraints weight = 12502.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.097594 restraints weight = 6381.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.099005 restraints weight = 3908.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5913  Z= 0.189
  Angle     :  0.516   5.572   8085  Z= 0.265
  Chirality :  0.042   0.168    901
  Planarity :  0.004   0.035   1047
  Dihedral  :  5.825  44.668   1156
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.41 %
    Favored  : 86.60 %
  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:  1.63 (0.31), residues: 777
  helix:  1.97 (0.25), residues: 415
  sheet:  0.92 (0.67), residues: 53
  loop : -0.06 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 373 
 PHE   0.016   0.002   PHE A 525 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 192 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8395 (m)
REVERT: A  201 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8224 (t0)
REVERT: A  207 TYR cc_start: 0.8457 (m-80) cc_final: 0.7588 (m-80)
REVERT: A  512 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7691 (m-80)
REVERT: B  474 ASN cc_start: 0.7824 (t0) cc_final: 0.7445 (t0)
REVERT: B  500 TYR cc_start: 0.5610 (m-80) cc_final: 0.5333 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 79
  average time/residue: 0.2355
  time to fit residues: 24.9802
Evaluate side-chains
  80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  442 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3422 r_free = 0.3422 target = 0.109475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.095734 restraints weight = 12432.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.097743 restraints weight = 6560.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.099038 restraints weight = 4100.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5913  Z= 0.172
  Angle     :  0.500   5.579   8085  Z= 0.254
  Chirality :  0.041   0.173    901
  Planarity :  0.004   0.032   1047
  Dihedral  :  5.407  39.959   1156
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.91 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.31), residues: 777
  helix:  2.10 (0.25), residues: 415
  sheet:  0.40 (0.67), residues: 55
  loop : -0.14 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.019   0.001   PHE B 543 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.012   0.001   ARG A 192 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 TRP cc_start: 0.8157 (t-100) cc_final: 0.7693 (t-100)
REVERT: A   68 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8404 (m)
REVERT: A  201 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8200 (t0)
REVERT: A  207 TYR cc_start: 0.8463 (m-80) cc_final: 0.7604 (m-80)
REVERT: A  512 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7622 (m-80)
REVERT: B  474 ASN cc_start: 0.7850 (t0) cc_final: 0.7536 (t0)
REVERT: B  500 TYR cc_start: 0.5595 (m-80) cc_final: 0.5324 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 75
  average time/residue: 0.2004
  time to fit residues: 20.3999
Evaluate side-chains
  77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue  442 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   chunk 74 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0000
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0030
   overall best weight:    0.3994

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.112025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.098373 restraints weight = 12709.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.100445 restraints weight = 6697.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101829 restraints weight = 4171.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.4960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5913  Z= 0.129
  Angle     :  0.471   5.527   8085  Z= 0.239
  Chirality :  0.040   0.160    901
  Planarity :  0.003   0.028   1047
  Dihedral  :  4.857  35.452   1156
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.91 %
    Favored  : 85.86 %
  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:  1.77 (0.31), residues: 777
  helix:  2.27 (0.26), residues: 412
  sheet:  0.66 (0.65), residues: 53
  loop : -0.20 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.016   0.001   PHE A 525 
 TYR   0.015   0.001   TYR A 385 
 ARG   0.006   0.001   ARG A 192 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 TRP cc_start: 0.8181 (t-100) cc_final: 0.7715 (t-100)
REVERT: A   68 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8330 (m)
REVERT: A  201 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8170 (t0)
REVERT: A  207 TYR cc_start: 0.8414 (m-80) cc_final: 0.7567 (m-80)
REVERT: A  474 MET cc_start: 0.7667 (tpp) cc_final: 0.7082 (mmt)
REVERT: A  512 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7624 (m-80)
REVERT: B  474 ASN cc_start: 0.7838 (t0) cc_final: 0.7531 (t0)
REVERT: B  500 TYR cc_start: 0.5500 (m-80) cc_final: 0.5250 (m-80)
  outliers start: 9
  outliers final: 4
  residues processed: 82
  average time/residue: 0.1760
  time to fit residues: 19.0023
Evaluate side-chains
  82 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue  442 TYR
Chi-restraints excluded: chain B residue  459 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 66 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.110057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096469 restraints weight = 12650.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.098490 restraints weight = 6735.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.099845 restraints weight = 4224.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.5111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5913  Z= 0.168
  Angle     :  0.489   5.516   8085  Z= 0.248
  Chirality :  0.041   0.168    901
  Planarity :  0.004   0.032   1047
  Dihedral  :  4.871  33.638   1156
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.67 %
    Favored  : 87.34 %
  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 (0.31), residues: 777
  helix:  2.27 (0.26), residues: 415
  sheet:  0.54 (0.67), residues: 53
  loop : -0.25 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.014   0.001   PHE A 525 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.006   0.001   ARG B 483 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 TRP cc_start: 0.8212 (t-100) cc_final: 0.7739 (t-100)
REVERT: A   68 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8333 (m)
REVERT: A  201 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8249 (t0)
REVERT: A  207 TYR cc_start: 0.8458 (m-80) cc_final: 0.7616 (m-80)
REVERT: A  474 MET cc_start: 0.7743 (tpp) cc_final: 0.7171 (mmt)
REVERT: A  512 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7620 (m-80)
REVERT: B  474 ASN cc_start: 0.7874 (t0) cc_final: 0.7550 (t0)
REVERT: B  500 TYR cc_start: 0.5624 (m-80) cc_final: 0.5321 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1708
  time to fit residues: 18.2163
Evaluate side-chains
  81 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue  442 TYR
Chi-restraints excluded: chain B residue  459 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 68 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.105454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.091599 restraints weight = 12771.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.093623 restraints weight = 6627.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.094937 restraints weight = 4110.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5913  Z= 0.238
  Angle     :  0.553   5.667   8085  Z= 0.282
  Chirality :  0.043   0.172    901
  Planarity :  0.004   0.036   1047
  Dihedral  :  5.568  34.719   1156
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.92 %
    Favored  : 87.34 %
  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:  1.43 (0.31), residues: 777
  helix:  2.05 (0.25), residues: 415
  sheet:  0.45 (0.69), residues: 53
  loop : -0.49 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 165 
 HIS   0.003   0.001   HIS B 485 
 PHE   0.019   0.002   PHE A 308 
 TYR   0.018   0.002   TYR A 385 
 ARG   0.006   0.001   ARG B 483 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 TRP cc_start: 0.8323 (t-100) cc_final: 0.7875 (t-100)
REVERT: A   68 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8470 (m)
REVERT: A  201 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8398 (t0)
REVERT: A  207 TYR cc_start: 0.8510 (m-80) cc_final: 0.7684 (m-80)
REVERT: A  474 MET cc_start: 0.7749 (tpp) cc_final: 0.7347 (mmp)
REVERT: A  512 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7737 (m-80)
REVERT: B  474 ASN cc_start: 0.7889 (t0) cc_final: 0.7516 (t0)
REVERT: B  500 TYR cc_start: 0.5761 (m-80) cc_final: 0.5438 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 82
  average time/residue: 0.2007
  time to fit residues: 22.3962
Evaluate side-chains
  81 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  442 TYR
Chi-restraints excluded: chain B residue  459 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.108177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.094460 restraints weight = 12684.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.096501 restraints weight = 6582.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.097809 restraints weight = 4092.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5913  Z= 0.155
  Angle     :  0.492   6.030   8085  Z= 0.249
  Chirality :  0.041   0.152    901
  Planarity :  0.004   0.031   1047
  Dihedral  :  5.073  32.312   1156
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.41 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.31), residues: 777
  helix:  2.26 (0.26), residues: 415
  sheet:  0.22 (0.67), residues: 55
  loop : -0.45 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 159 
 PHE   0.013   0.001   PHE B 543 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.006   0.001   ARG B 483 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TRP cc_start: 0.8284 (t-100) cc_final: 0.7820 (t-100)
REVERT: A   68 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8440 (m)
REVERT: A  201 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8261 (t0)
REVERT: A  207 TYR cc_start: 0.8459 (m-80) cc_final: 0.7677 (m-80)
REVERT: A  512 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7664 (m-80)
REVERT: B  474 ASN cc_start: 0.7841 (t0) cc_final: 0.7488 (t0)
REVERT: B  500 TYR cc_start: 0.5597 (m-80) cc_final: 0.5301 (m-80)
  outliers start: 6
  outliers final: 3
  residues processed: 78
  average time/residue: 0.1850
  time to fit residues: 19.2418
Evaluate side-chains
  76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  442 TYR
Chi-restraints excluded: chain B residue  459 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.0020
   chunk 65 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.4966

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

Flipped N/Q/H residues before XYZ refinement:
A 159 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.109246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.095507 restraints weight = 12744.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.097590 restraints weight = 6646.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.098952 restraints weight = 4128.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5913  Z= 0.145
  Angle     :  0.496   5.733   8085  Z= 0.252
  Chirality :  0.040   0.146    901
  Planarity :  0.004   0.034   1047
  Dihedral  :  4.798  31.133   1156
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.91 %
    Favored  : 86.35 %
  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:  1.69 (0.31), residues: 777
  helix:  2.35 (0.26), residues: 415
  sheet:  0.36 (0.68), residues: 53
  loop : -0.46 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 159 
 PHE   0.037   0.002   PHE A 327 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.006   0.001   ARG A 192 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2014.70 seconds
wall clock time: 36 minutes 59.82 seconds (2219.82 seconds total)