Starting phenix.real_space_refine
on Wed Mar  4 04:46:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lby_23267/03_2026/7lby_23267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lby_23267/03_2026/7lby_23267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lby_23267/03_2026/7lby_23267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lby_23267/03_2026/7lby_23267.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lby_23267/03_2026/7lby_23267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lby_23267/03_2026/7lby_23267.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2664 atoms to isotropic.
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      23      5.16       5
     C    5441      2.51       5
     N    1624      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8800
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 755, 3724
          Classifications: {'peptide': 755}
          Incomplete info: {'truncation_to_alanine': 648}
          Link IDs: {'PTRANS': 40, 'TRANS': 714}
          Chain breaks: 2
          Unresolved chain link angles: 40
          Unresolved non-hydrogen bonds: 2559
          Unresolved non-hydrogen angles: 3319
          Unresolved non-hydrogen dihedrals: 2205
          Unresolved non-hydrogen chiralities: 231
          Planarities with less than four sites: {'ARG:plan': 54, 'TYR:plan': 28, 'ASP:plan': 25, 'HIS:plan': 24, 'PHE:plan': 40, 'TRP:plan': 22, 'GLU:plan': 32, 'GLN:plan1': 28, 'ASN:plan1': 28}
          Unresolved non-hydrogen planarities: 1423
    Chain: "B"
      Number of atoms: 5076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5076
          Classifications: {'peptide': 663}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 612}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 39
  Time building chain proxies: 2.33, per 1000 atoms: 0.26
  Number of scatterers: 8800
  At special positions: 0
  Unit cell: (135, 150.12, 124.2, 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      23     16.00
     O    1712      8.00
     N    1624      7.00
     C    5441      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 182 " - pdb=" SG  CYS B 500 " 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: 0.79
  Conformation dependent library (CDL) restraints added in 506.4 milliseconds
  

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2648

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 13 sheets defined
      40.6% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 42
    Processing helix  chain 'A' and resid 124 through 142
      Proline residue:  A 129  - end of helix
      Proline residue:  A 133  - end of helix
      removed outlier: 3.859A  pdb=" N   HIS A 142 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 153
      removed outlier: 3.510A  pdb=" N   SER A 152 " --> pdb=" O   HIS A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 178 through 191
    Processing helix  chain 'A' and resid 196 through 219
      removed outlier: 3.894A  pdb=" N   MET A 200 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
      Proline residue:  A 204  - end of helix
    Processing helix  chain 'A' and resid 222 through 227
    Processing helix  chain 'A' and resid 228 through 256
      Proline residue:  A 250  - end of helix
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 287 through 300
      removed outlier: 3.576A  pdb=" N   SER A 300 " --> pdb=" O   TRP A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 328
    Processing helix  chain 'A' and resid 343 through 352
    Processing helix  chain 'A' and resid 353 through 355
      No H-bonds generated for 'chain 'A' and resid 353 through 355'
    Processing helix  chain 'A' and resid 373 through 377
      removed outlier: 3.632A  pdb=" N   SER A 376 " --> pdb=" O   ILE A 373 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 377 " --> pdb=" O   TYR A 374 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 373 through 377'
    Processing helix  chain 'A' and resid 400 through 407
    Processing helix  chain 'A' and resid 416 through 421
    Processing helix  chain 'A' and resid 422 through 430
      removed outlier: 3.703A  pdb=" N   ASN A 426 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 468
      removed outlier: 3.825A  pdb=" N   GLN A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU A 463 " --> pdb=" O   LYS A 459 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLN A 467 " --> pdb=" O   LEU A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 513
    Processing helix  chain 'A' and resid 519 through 551
      removed outlier: 3.903A  pdb=" N   THR A 535 " --> pdb=" O   VAL A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 582
    Processing helix  chain 'A' and resid 589 through 610
      removed outlier: 4.249A  pdb=" N   GLY A 593 " --> pdb=" O   ASN A 589 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG A 601 " --> pdb=" O   LYS A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 659
      Proline residue:  A 646  - end of helix
    Processing helix  chain 'A' and resid 663 through 688
      Proline residue:  A 670  - end of helix
    Processing helix  chain 'A' and resid 791 through 802
      removed outlier: 3.822A  pdb=" N   ARG A 802 " --> pdb=" O   ARG A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 831
      removed outlier: 3.592A  pdb=" N   GLY A 830 " --> pdb=" O   PHE A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 838 through 860
    Processing helix  chain 'A' and resid 861 through 863
      No H-bonds generated for 'chain 'A' and resid 861 through 863'
    Processing helix  chain 'B' and resid 145 through 149
      removed outlier: 3.692A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 259
    Processing helix  chain 'B' and resid 260 through 262
      No H-bonds generated for 'chain 'B' and resid 260 through 262'
    Processing helix  chain 'B' and resid 321 through 335
    Processing helix  chain 'B' and resid 532 through 538
    Processing helix  chain 'B' and resid 560 through 578
      removed outlier: 3.558A  pdb=" N   MET B 564 " --> pdb=" O   ASN B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 614
      No H-bonds generated for 'chain 'B' and resid 612 through 614'
    Processing helix  chain 'B' and resid 615 through 630
      removed outlier: 3.907A  pdb=" N   LEU B 619 " --> pdb=" O   LYS B 615 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU B 620 " --> pdb=" O   GLN B 616 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   VAL B 621 " --> pdb=" O   ILE B 617 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLN B 622 " --> pdb=" O   ASP B 618 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TRP B 627 " --> pdb=" O   ALA B 623 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR B 630 " --> pdb=" O   SER B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 697
      removed outlier: 3.517A  pdb=" N   TYR B 688 " --> pdb=" O   SER B 684 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASP B 697 " --> pdb=" O   ASP B 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 743
      removed outlier: 4.047A  pdb=" N   VAL B 736 " --> pdb=" O   TRP B 732 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   TRP B 737 " --> pdb=" O   PHE B 733 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   TYR B 738 " --> pdb=" O   GLU B 734 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ASN B 742 " --> pdb=" O   TYR B 738 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   HIS B 743 " --> pdb=" O   ALA B 739 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 743 through 772
    Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 282
      removed outlier: 3.766A  pdb=" N   ALA A 279 " --> pdb=" O   SER A 309 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A 311 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 392
      removed outlier: 3.546A  pdb=" N   PHE A 478 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 700 through 704
      removed outlier: 6.586A  pdb=" N   TYR A 702 " --> pdb=" O   THR A 722 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   THR A 722 " --> pdb=" O   TYR A 702 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ALA A 704 " --> pdb=" O   ASN A 720 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   GLU A 729 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 716 through 717
    Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 101
      removed outlier: 4.078A  pdb=" N   PHE B 100 " --> pdb=" O   ASN B 168 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ASN B 168 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU B 173 " --> pdb=" O   LYS B 131 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL B 132 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   GLY B 140 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 159
      removed outlier: 4.207A  pdb=" N   THR B 153 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   TYR B 117 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ALA B 111 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LYS B 110 " --> pdb=" O   THR B 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 267 through 269
      removed outlier: 4.116A  pdb=" N   LEU B 268 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE B 235 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   VAL B 234 " --> pdb=" O   PHE B 280 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   VAL B 279 " --> pdb=" O   VAL B 317 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL B 316 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 384
    Processing sheet with id=AB1, first strand: chain 'B' and resid 395 through 396
      removed outlier: 3.942A  pdb=" N   LEU B 396 " --> pdb=" O   ASN B 480 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASN B 480 " --> pdb=" O   LEU B 396 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442
      removed outlier: 3.880A  pdb=" N   GLN B 439 " --> pdb=" O   ILE B 431 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET B 429 " --> pdb=" O   PHE B 441 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG B 428 " --> pdb=" O   GLU B 487 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLU B 487 " --> pdb=" O   ARG B 428 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ASP B 430 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ASP B 485 " --> pdb=" O   ASP B 430 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 527 through 528
      removed outlier: 4.022A  pdb=" N   ILE B 527 " --> pdb=" O   VAL B 727 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL B 727 " --> pdb=" O   ILE B 527 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 586 through 588
      removed outlier: 6.163A  pdb=" N   THR B 553 " --> pdb=" O   THR B 588 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE B 552 " --> pdb=" O   MET B 602 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   ILE B 604 " --> pdb=" O   ILE B 552 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   VAL B 554 " --> pdb=" O   ILE B 604 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ILE B 601 " --> pdb=" O   SER B 676 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE B 678 " --> pdb=" O   ILE B 601 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA B 662 " --> pdb=" O   ILE B 711 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL B 710 " --> pdb=" O   ASN B 717 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN B 717 " --> pdb=" O   VAL B 710 " (cutoff:3.500A)

    434 hydrogen bonds defined for protein.
    1269 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: 1.11

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3201
        1.34 -     1.46: 1632
        1.46 -     1.58: 4037
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 8914
  Sorted by residual:
  bond pdb=" CA  VAL A 343 "
       pdb=" CB  VAL A 343 "
    ideal  model  delta    sigma   weight residual
    1.537  1.508  0.028 5.00e-03 4.00e+04 3.22e+01
  bond pdb=" C   THR A 540 "
       pdb=" O   THR A 540 "
    ideal  model  delta    sigma   weight residual
    1.236  1.272 -0.036 1.15e-02 7.56e+03 9.71e+00
  bond pdb=" N   THR A 540 "
       pdb=" CA  THR A 540 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.031 1.19e-02 7.06e+03 6.89e+00
  bond pdb=" N   SER A 635 "
       pdb=" CA  SER A 635 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.28e-02 6.10e+03 6.04e+00
  bond pdb=" N   GLY A 636 "
       pdb=" CA  GLY A 636 "
    ideal  model  delta    sigma   weight residual
    1.454  1.481 -0.027 1.24e-02 6.50e+03 4.60e+00
  ... (remaining 8909 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 11846
        1.82 -     3.65: 307
        3.65 -     5.47: 45
        5.47 -     7.30: 37
        7.30 -     9.12: 13
  Bond angle restraints: 12248
  Sorted by residual:
  angle pdb=" N   PRO A 445 "
        pdb=" CA  PRO A 445 "
        pdb=" CB  PRO A 445 "
      ideal   model   delta    sigma   weight residual
     102.25  110.63   -8.38 7.00e-01 2.04e+00 1.43e+02
  angle pdb=" N   PRO A 764 "
        pdb=" CA  PRO A 764 "
        pdb=" CB  PRO A 764 "
      ideal   model   delta    sigma   weight residual
     103.36  110.96   -7.60 8.30e-01 1.45e+00 8.38e+01
  angle pdb=" N   PRO A 337 "
        pdb=" CA  PRO A 337 "
        pdb=" CB  PRO A 337 "
      ideal   model   delta    sigma   weight residual
     103.36  110.62   -7.26 8.30e-01 1.45e+00 7.66e+01
  angle pdb=" N   PRO A 706 "
        pdb=" CA  PRO A 706 "
        pdb=" CB  PRO A 706 "
      ideal   model   delta    sigma   weight residual
     103.25  112.37   -9.12 1.05e+00 9.07e-01 7.55e+01
  angle pdb=" N   PRO A 763 "
        pdb=" CA  PRO A 763 "
        pdb=" CB  PRO A 763 "
      ideal   model   delta    sigma   weight residual
     103.08  111.30   -8.22 9.70e-01 1.06e+00 7.18e+01
  ... (remaining 12243 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 5008
       17.93 -    35.86: 233
       35.86 -    53.79: 43
       53.79 -    71.71: 13
       71.71 -    89.64: 7
  Dihedral angle restraints: 5304
    sinusoidal: 1226
      harmonic: 4078
  Sorted by residual:
  dihedral pdb=" N   PRO A 342 "
           pdb=" C   PRO A 342 "
           pdb=" CA  PRO A 342 "
           pdb=" CB  PRO A 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  124.59   -9.49     0      2.50e+00 1.60e-01 1.44e+01
  dihedral pdb=" CB  GLU B 183 "
           pdb=" CG  GLU B 183 "
           pdb=" CD  GLU B 183 "
           pdb=" OE1 GLU B 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.64  -89.64     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" N   PRO A 307 "
           pdb=" C   PRO A 307 "
           pdb=" CA  PRO A 307 "
           pdb=" CB  PRO A 307 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  123.23   -8.13     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 5301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1195
       0.052 -    0.104: 227
       0.104 -    0.155: 31
       0.155 -    0.207: 11
       0.207 -    0.259: 33
  Chirality restraints: 1497
  Sorted by residual:
  chirality pdb=" CA  PRO A 307 "
            pdb=" N   PRO A 307 "
            pdb=" C   PRO A 307 "
            pdb=" CB  PRO A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  PRO A 342 "
            pdb=" N   PRO A 342 "
            pdb=" C   PRO A 342 "
            pdb=" CB  PRO A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  PRO A 660 "
            pdb=" N   PRO A 660 "
            pdb=" C   PRO A 660 "
            pdb=" CB  PRO A 660 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 1494 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  83 "   -0.047 5.00e-02 4.00e+02   7.15e-02 8.19e+00
        pdb=" N   PRO B  84 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B  84 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B  84 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 538 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.66e+00
        pdb=" C   ALA A 538 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ALA A 538 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   HIS A 539 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 537 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   ASP A 537 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ASP A 537 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A 538 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 174
        2.70 -     3.25: 8609
        3.25 -     3.80: 13241
        3.80 -     4.35: 14118
        4.35 -     4.90: 24343
  Nonbonded interactions: 60485
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 705 "
            pdb=" OG  SER B 718 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" ND2 ASN B 569 "
            pdb=" OD1 ASN B 692 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OG  SER B 432 "
            pdb=" O   ARG B 483 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG1 THR B 118 "
            pdb=" OD1 ASP B 193 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   ASN B  67 "
            pdb=" OH  TYR B 311 "
     model   vdw
     2.289 3.040
  ... (remaining 60480 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.540
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8915  Z= 0.217
  Angle     :  0.780   9.122  12250  Z= 0.603
  Chirality :  0.054   0.259   1497
  Planarity :  0.003   0.072   1689
  Dihedral  : 12.333  89.643   2653
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  :  6.19 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.24), residues: 1406
  helix:  2.83 (0.22), residues: 539
  sheet: -1.18 (0.40), residues: 194
  loop : -2.55 (0.23), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 257 
 TYR   0.005   0.001   TYR B 524 
 PHE   0.024   0.001   PHE B 289 
 TRP   0.011   0.000   TRP B 253 
 HIS   0.001   0.000   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8914)
  covalent geometry    : angle       0.78034 (12248)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.05338 (    2)
  hydrogen bonds       : bond        0.17919 (  434)
  hydrogen bonds       : angle       5.94837 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: B  172 LEU cc_start: 0.8714 (mp) cc_final: 0.8465 (mt)
REVERT: B  338 LEU cc_start: 0.8362 (pt) cc_final: 0.7990 (pp)
REVERT: B  429 MET cc_start: 0.8745 (tmm) cc_final: 0.8237 (tmm)
REVERT: B  482 LEU cc_start: 0.8744 (tp) cc_final: 0.8481 (tt)
REVERT: B  676 SER cc_start: 0.8473 (p) cc_final: 0.7910 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0743
  time to fit residues: 16.9081
Evaluate side-chains
  115 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 168 ASN
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 305 ASN
** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 729 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.173359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.158535 restraints weight = 20850.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.153513 restraints weight = 42640.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.149977 restraints weight = 39074.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.149291 restraints weight = 45325.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.149109 restraints weight = 37190.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8915  Z= 0.167
  Angle     :  0.544   5.528  12250  Z= 0.290
  Chirality :  0.044   0.153   1497
  Planarity :  0.004   0.071   1689
  Dihedral  :  3.605  17.971   1460
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.12 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  6.09 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.24), residues: 1406
  helix:  3.08 (0.22), residues: 561
  sheet: -1.20 (0.43), residues: 168
  loop : -2.55 (0.22), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 368 
 TYR   0.009   0.001   TYR B 416 
 PHE   0.017   0.001   PHE B 221 
 TRP   0.013   0.001   TRP B 737 
 HIS   0.003   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8914)
  covalent geometry    : angle       0.54393 (12248)
  SS BOND              : bond        0.00420 (    1)
  SS BOND              : angle       0.93502 (    2)
  hydrogen bonds       : bond        0.03348 (  434)
  hydrogen bonds       : angle       4.36621 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.276 
Fit side-chains
REVERT: B   88 VAL cc_start: 0.8226 (t) cc_final: 0.7996 (m)
REVERT: B   95 ASN cc_start: 0.8549 (m110) cc_final: 0.8152 (p0)
REVERT: B  258 SER cc_start: 0.9245 (t) cc_final: 0.8857 (t)
REVERT: B  338 LEU cc_start: 0.8755 (pt) cc_final: 0.8514 (pp)
REVERT: B  372 PHE cc_start: 0.7646 (m-80) cc_final: 0.7282 (m-10)
REVERT: B  466 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7178 (ttmm)
REVERT: B  482 LEU cc_start: 0.9103 (tp) cc_final: 0.8753 (tt)
REVERT: B  529 MET cc_start: 0.7160 (tpp) cc_final: 0.6914 (tpt)
REVERT: B  547 ASP cc_start: 0.8212 (p0) cc_final: 0.7984 (p0)
REVERT: B  580 PHE cc_start: 0.8596 (t80) cc_final: 0.8330 (t80)
REVERT: B  690 MET cc_start: 0.7289 (ptt) cc_final: 0.7084 (ptt)
  outliers start: 1
  outliers final: 1
  residues processed: 138
  average time/residue: 0.0858
  time to fit residues: 16.9775
Evaluate side-chains
  113 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 28 optimal weight:   30.0000
   chunk 44 optimal weight:   20.0000
   chunk 73 optimal weight:   30.0000
   chunk 43 optimal weight:    7.9990
   chunk 138 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 35 optimal weight:   20.0000
   chunk 20 optimal weight:    0.0970
   chunk 79 optimal weight:    2.9990
   overall best weight:    3.8186

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
B 244 GLN
B 305 ASN
B 397 ASN
** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.161316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.137464 restraints weight = 20665.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.132276 restraints weight = 24604.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.131951 restraints weight = 28186.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.132073 restraints weight = 23134.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.132141 restraints weight = 22523.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.088   8915  Z= 0.453
  Angle     :  0.851  11.269  12250  Z= 0.464
  Chirality :  0.053   0.185   1497
  Planarity :  0.006   0.069   1689
  Dihedral  :  5.356  24.229   1460
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  9.89 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  7.56 %
    Favored  : 91.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.24), residues: 1406
  helix:  2.56 (0.22), residues: 559
  sheet: -2.21 (0.37), residues: 165
  loop : -2.86 (0.22), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 196 
 TYR   0.024   0.003   TYR B 378 
 PHE   0.038   0.004   PHE B 580 
 TRP   0.013   0.002   TRP B 253 
 HIS   0.010   0.003   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00995 ( 8914)
  covalent geometry    : angle       0.85076 (12248)
  SS BOND              : bond        0.01520 (    1)
  SS BOND              : angle       1.91535 (    2)
  hydrogen bonds       : bond        0.04312 (  434)
  hydrogen bonds       : angle       4.89888 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.332 
Fit side-chains
REVERT: B  210 LYS cc_start: 0.7886 (pttp) cc_final: 0.7299 (tppt)
REVERT: B  466 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8229 (ttmm)
REVERT: B  489 MET cc_start: 0.7370 (pmm) cc_final: 0.7088 (pmm)
REVERT: B  690 MET cc_start: 0.8184 (ptt) cc_final: 0.7923 (ptt)
  outliers start: 3
  outliers final: 2
  residues processed: 118
  average time/residue: 0.0822
  time to fit residues: 14.2298
Evaluate side-chains
  93 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 102 optimal weight:    0.4980
   chunk 96 optimal weight:    0.6980
   chunk 36 optimal weight:   40.0000
   chunk 86 optimal weight:    0.0070
   chunk 29 optimal weight:    7.9990
   chunk 63 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   overall best weight:    1.2200

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

Flipped N/Q/H residues before XYZ refinement:
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.166539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.152399 restraints weight = 21124.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.151690 restraints weight = 45168.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.151363 restraints weight = 43057.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.150093 restraints weight = 36402.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.150114 restraints weight = 33212.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8915  Z= 0.163
  Angle     :  0.582   7.884  12250  Z= 0.308
  Chirality :  0.044   0.171   1497
  Planarity :  0.004   0.072   1689
  Dihedral  :  4.513  23.007   1460
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  6.76 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.24), residues: 1406
  helix:  2.82 (0.23), residues: 562
  sheet: -2.02 (0.38), residues: 165
  loop : -2.75 (0.22), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 196 
 TYR   0.013   0.001   TYR B 378 
 PHE   0.024   0.002   PHE B 540 
 TRP   0.006   0.001   TRP B 760 
 HIS   0.004   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8914)
  covalent geometry    : angle       0.58232 (12248)
  SS BOND              : bond        0.00515 (    1)
  SS BOND              : angle       1.22204 (    2)
  hydrogen bonds       : bond        0.03158 (  434)
  hydrogen bonds       : angle       4.26955 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.322 
Fit side-chains
REVERT: B  210 LYS cc_start: 0.7653 (pttp) cc_final: 0.7314 (tppt)
REVERT: B  263 GLN cc_start: 0.8857 (mp10) cc_final: 0.8406 (mp10)
REVERT: B  466 LYS cc_start: 0.8299 (mmmt) cc_final: 0.7944 (ttmm)
REVERT: B  627 TRP cc_start: 0.8900 (t-100) cc_final: 0.8598 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0770
  time to fit residues: 13.7993
Evaluate side-chains
  94 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 127 optimal weight:    0.0980
   chunk 93 optimal weight:    0.6980
   chunk 26 optimal weight:    0.1980
   chunk 120 optimal weight:    0.2980
   chunk 45 optimal weight:    6.9990
   chunk 1 optimal weight:   50.0000
   chunk 99 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 137 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
B 244 GLN
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.169694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.153951 restraints weight = 20986.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.152958 restraints weight = 47094.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.153216 restraints weight = 46212.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.152424 restraints weight = 33983.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.152871 restraints weight = 26644.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8915  Z= 0.100
  Angle     :  0.531   8.013  12250  Z= 0.275
  Chirality :  0.043   0.164   1497
  Planarity :  0.004   0.075   1689
  Dihedral  :  4.021  20.953   1460
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.18 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.24), residues: 1406
  helix:  2.95 (0.22), residues: 563
  sheet: -1.76 (0.39), residues: 166
  loop : -2.63 (0.22), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 368 
 TYR   0.009   0.001   TYR B 416 
 PHE   0.023   0.001   PHE B 441 
 TRP   0.005   0.000   TRP B 760 
 HIS   0.002   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 8914)
  covalent geometry    : angle       0.53049 (12248)
  SS BOND              : bond        0.00238 (    1)
  SS BOND              : angle       0.82756 (    2)
  hydrogen bonds       : bond        0.02762 (  434)
  hydrogen bonds       : angle       3.93455 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.335 
Fit side-chains
REVERT: B  395 SER cc_start: 0.8141 (m) cc_final: 0.7291 (m)
REVERT: B  412 MET cc_start: 0.8503 (mmm) cc_final: 0.8217 (mmp)
REVERT: B  466 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8030 (ttmm)
REVERT: B  627 TRP cc_start: 0.8848 (t-100) cc_final: 0.8533 (t-100)
REVERT: B  668 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8325 (tp40)
REVERT: B  681 LEU cc_start: 0.8105 (tp) cc_final: 0.7864 (tp)
REVERT: B  690 MET cc_start: 0.7349 (ptt) cc_final: 0.7077 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0696
  time to fit residues: 13.2519
Evaluate side-chains
  101 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 112 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 60 optimal weight:   40.0000
   chunk 26 optimal weight:    0.8980
   chunk 46 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 244 GLN
** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.157761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.143038 restraints weight = 20956.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.141617 restraints weight = 58167.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.141164 restraints weight = 46523.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139771 restraints weight = 37823.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139848 restraints weight = 33180.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.095   8915  Z= 0.512
  Angle     :  0.910  11.865  12250  Z= 0.495
  Chirality :  0.054   0.201   1497
  Planarity :  0.007   0.068   1689
  Dihedral  :  5.662  33.207   1460
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 11.66 %
    Favored  : 87.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.24), residues: 1406
  helix:  2.26 (0.23), residues: 563
  sheet: -2.63 (0.36), residues: 166
  loop : -2.98 (0.22), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 196 
 TYR   0.032   0.003   TYR B 378 
 PHE   0.035   0.004   PHE B 580 
 TRP   0.011   0.002   TRP B 253 
 HIS   0.008   0.003   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.01129 ( 8914)
  covalent geometry    : angle       0.90946 (12248)
  SS BOND              : bond        0.01397 (    1)
  SS BOND              : angle       1.75319 (    2)
  hydrogen bonds       : bond        0.04442 (  434)
  hydrogen bonds       : angle       4.97575 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: B  412 MET cc_start: 0.8543 (mmm) cc_final: 0.8277 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0677
  time to fit residues: 10.2280
Evaluate side-chains
  87 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 120 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 104 optimal weight:    0.9980
   chunk 118 optimal weight:    0.8980
   chunk 131 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 244 GLN
B 263 GLN
B 509 HIS
B 569 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.164875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.140660 restraints weight = 20919.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.133939 restraints weight = 24986.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.133363 restraints weight = 33472.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.134193 restraints weight = 26770.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.134285 restraints weight = 20830.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8915  Z= 0.146
  Angle     :  0.602   7.537  12250  Z= 0.319
  Chirality :  0.044   0.179   1497
  Planarity :  0.004   0.069   1689
  Dihedral  :  4.717  28.239   1460
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.54 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.85 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.24), residues: 1406
  helix:  2.69 (0.23), residues: 565
  sheet: -2.27 (0.39), residues: 155
  loop : -2.74 (0.22), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 196 
 TYR   0.025   0.001   TYR B 378 
 PHE   0.015   0.002   PHE B 289 
 TRP   0.006   0.001   TRP B 760 
 HIS   0.004   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8914)
  covalent geometry    : angle       0.60193 (12248)
  SS BOND              : bond        0.00485 (    1)
  SS BOND              : angle       1.12465 (    2)
  hydrogen bonds       : bond        0.03143 (  434)
  hydrogen bonds       : angle       4.23963 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.365 
Fit side-chains
REVERT: B  139 MET cc_start: 0.8790 (pmm) cc_final: 0.8500 (pmm)
REVERT: B  210 LYS cc_start: 0.8157 (tppt) cc_final: 0.7607 (pttm)
REVERT: B  411 ASP cc_start: 0.7813 (p0) cc_final: 0.7444 (p0)
REVERT: B  412 MET cc_start: 0.8742 (mmm) cc_final: 0.8519 (mmm)
REVERT: B  627 TRP cc_start: 0.9047 (t-100) cc_final: 0.8708 (t-100)
REVERT: B  690 MET cc_start: 0.8097 (ptt) cc_final: 0.7515 (ptt)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0610
  time to fit residues: 11.1862
Evaluate side-chains
  92 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0470
   chunk 102 optimal weight:    0.0470
   chunk 96 optimal weight:    0.5980
   chunk 14 optimal weight:    9.9990
   chunk 129 optimal weight:    0.8980
   chunk 119 optimal weight:    0.3980
   chunk 123 optimal weight:    0.8980
   chunk 41 optimal weight:   20.0000
   chunk 39 optimal weight:   30.0000
   overall best weight:    0.3976

-------------------------------------------------------------------------------
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 = 0.4248 r_free = 0.4248 target = 0.167768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.152404 restraints weight = 21044.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.151482 restraints weight = 51955.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.151549 restraints weight = 45597.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.150823 restraints weight = 34550.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.151126 restraints weight = 26182.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8915  Z= 0.102
  Angle     :  0.560   8.068  12250  Z= 0.289
  Chirality :  0.043   0.171   1497
  Planarity :  0.004   0.074   1689
  Dihedral  :  4.114  23.542   1460
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.11 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.24), residues: 1406
  helix:  2.89 (0.22), residues: 564
  sheet: -2.10 (0.39), residues: 166
  loop : -2.66 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 428 
 TYR   0.028   0.001   TYR B 378 
 PHE   0.018   0.001   PHE B 289 
 TRP   0.006   0.000   TRP B 760 
 HIS   0.003   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8914)
  covalent geometry    : angle       0.56029 (12248)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       0.63502 (    2)
  hydrogen bonds       : bond        0.02716 (  434)
  hydrogen bonds       : angle       3.87186 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: B  112 MET cc_start: 0.6949 (mtp) cc_final: 0.6716 (mtp)
REVERT: B  412 MET cc_start: 0.8561 (mmm) cc_final: 0.8200 (mmp)
REVERT: B  690 MET cc_start: 0.7635 (ptt) cc_final: 0.7203 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0552
  time to fit residues: 10.7854
Evaluate side-chains
  92 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 139 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 132 optimal weight:    0.6980
   chunk 130 optimal weight:    0.5980
   chunk 43 optimal weight:   30.0000
   chunk 67 optimal weight:   40.0000
   chunk 96 optimal weight:    0.4980
   chunk 17 optimal weight:    9.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 381 GLN
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.166150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.152159 restraints weight = 21001.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.149048 restraints weight = 46372.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.145673 restraints weight = 38407.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.144675 restraints weight = 44790.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.144216 restraints weight = 34532.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8915  Z= 0.133
  Angle     :  0.573  10.185  12250  Z= 0.295
  Chirality :  0.044   0.168   1497
  Planarity :  0.004   0.074   1689
  Dihedral  :  4.119  25.360   1460
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.25 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.24), residues: 1406
  helix:  2.95 (0.22), residues: 563
  sheet: -2.11 (0.39), residues: 165
  loop : -2.62 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 196 
 TYR   0.024   0.001   TYR B 378 
 PHE   0.028   0.002   PHE B 174 
 TRP   0.006   0.001   TRP B 760 
 HIS   0.004   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8914)
  covalent geometry    : angle       0.57262 (12248)
  SS BOND              : bond        0.00414 (    1)
  SS BOND              : angle       0.60168 (    2)
  hydrogen bonds       : bond        0.02772 (  434)
  hydrogen bonds       : angle       3.84034 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.344 
Fit side-chains
REVERT: B  210 LYS cc_start: 0.7778 (pttm) cc_final: 0.7174 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0576
  time to fit residues: 10.8769
Evaluate side-chains
  92 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:   20.0000
   chunk 107 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0980
   chunk 112 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0370
   chunk 17 optimal weight:   20.0000
   chunk 54 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
B 381 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.167589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.152439 restraints weight = 20850.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.151414 restraints weight = 49371.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.151565 restraints weight = 43978.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.150794 restraints weight = 32573.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.151247 restraints weight = 24685.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8915  Z= 0.108
  Angle     :  0.573  12.257  12250  Z= 0.291
  Chirality :  0.043   0.166   1497
  Planarity :  0.004   0.075   1689
  Dihedral  :  4.011  23.757   1460
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.11 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.24), residues: 1406
  helix:  2.98 (0.22), residues: 564
  sheet: -1.89 (0.40), residues: 165
  loop : -2.60 (0.23), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 196 
 TYR   0.020   0.001   TYR B 378 
 PHE   0.026   0.002   PHE B 174 
 TRP   0.021   0.001   TRP B 627 
 HIS   0.003   0.001   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8914)
  covalent geometry    : angle       0.57282 (12248)
  SS BOND              : bond        0.00286 (    1)
  SS BOND              : angle       0.51035 (    2)
  hydrogen bonds       : bond        0.02735 (  434)
  hydrogen bonds       : angle       3.80263 ( 1269)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: B  210 LYS cc_start: 0.7671 (pttm) cc_final: 0.7180 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0627
  time to fit residues: 11.6924
Evaluate side-chains
  100 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 123 optimal weight:    0.5980
   chunk 118 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 114 optimal weight:    5.9990
   chunk 29 optimal weight:   20.0000
   chunk 120 optimal weight:    2.9990
   chunk 69 optimal weight:   30.0000
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
B 381 GLN
B 481 GLN
** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.160826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.143302 restraints weight = 20858.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.140276 restraints weight = 49707.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.140581 restraints weight = 47857.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139987 restraints weight = 32032.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.140273 restraints weight = 27047.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   8915  Z= 0.315
  Angle     :  0.745  11.618  12250  Z= 0.392
  Chirality :  0.048   0.209   1497
  Planarity :  0.005   0.071   1689
  Dihedral  :  4.837  31.268   1460
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 10.24 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.24), residues: 1406
  helix:  2.78 (0.23), residues: 559
  sheet: -2.26 (0.35), residues: 194
  loop : -2.84 (0.23), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 196 
 TYR   0.022   0.002   TYR B 378 
 PHE   0.031   0.003   PHE B 540 
 TRP   0.024   0.002   TRP B 627 
 HIS   0.008   0.002   HIS B 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00696 ( 8914)
  covalent geometry    : angle       0.74538 (12248)
  SS BOND              : bond        0.00889 (    1)
  SS BOND              : angle       0.89231 (    2)
  hydrogen bonds       : bond        0.03523 (  434)
  hydrogen bonds       : angle       4.31706 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1437.41 seconds
wall clock time: 25 minutes 22.68 seconds (1522.68 seconds total)