Starting phenix.real_space_refine
on Tue Feb  3 22:32:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bfc_44492/02_2026/9bfc_44492.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bfc_44492/02_2026/9bfc_44492.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bfc_44492/02_2026/9bfc_44492.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bfc_44492/02_2026/9bfc_44492.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bfc_44492/02_2026/9bfc_44492.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bfc_44492/02_2026/9bfc_44492.map"
  }
  resolution = 3.2
  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=  -0.002 sd=   0.031
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      50      5.16       5
     C    4646      2.51       5
     N    1259      2.21       5
     O    1428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7383
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "F"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 20
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
    Chain: "H"
      Number of atoms: 6810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 876, 6810
          Classifications: {'peptide': 876}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 37, 'TRANS': 838}
    Chain: "I"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 441
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 1, 'TRANS': 51}
    Chain: "J"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 53
          Classifications: {'peptide': 7}
          Link IDs: {'PTRANS': 1, 'TRANS': 5}
    Chain: "C"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 33
          Classifications: {'peptide': 4}
          Link IDs: {'TRANS': 3}
    Chain: "H"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
    Chain: "H"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Classifications: {'peptide': 1}
    Chain: "H"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
  Time building chain proxies: 1.76, per 1000 atoms: 0.24
  Number of scatterers: 7383
  At special positions: 0
  Unit cell: (89.187, 90.146, 115.08, 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      50     16.00
     O    1428      8.00
     N    1259      7.00
     C    4646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
    TRANS
      " GLY H 902 " - " PHE H 901 "
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 300.6 milliseconds
  

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1808

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 0 sheets defined
      82.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'H' and resid 2 through 12
      removed outlier: 3.786A  pdb=" N   ILE H   6 " --> pdb=" O   GLU H   2 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 14 through 32
      removed outlier: 4.491A  pdb=" N   ALA H  20 " --> pdb=" O   LEU H  16 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN H  32 " --> pdb=" O   ALA H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 32 through 46
      removed outlier: 3.770A  pdb=" N   ASN H  46 " --> pdb=" O   ARG H  42 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 50 through 66
      removed outlier: 3.904A  pdb=" N   GLN H  60 " --> pdb=" O   ALA H  56 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE H  61 " --> pdb=" O   ALA H  57 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 69 through 82
    Processing helix  chain 'H' and resid 84 through 98
    Processing helix  chain 'H' and resid 108 through 121
      removed outlier: 3.527A  pdb=" N   GLU H 120 " --> pdb=" O   ILE H 116 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 122 through 124
      No H-bonds generated for 'chain 'H' and resid 122 through 124'
    Processing helix  chain 'H' and resid 128 through 139
    Processing helix  chain 'H' and resid 143 through 158
    Processing helix  chain 'H' and resid 162 through 167
      removed outlier: 4.020A  pdb=" N   LEU H 166 " --> pdb=" O   ASP H 162 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 171 through 181
      removed outlier: 3.846A  pdb=" N   THR H 175 " --> pdb=" O   ASN H 171 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 187 through 201
      removed outlier: 3.580A  pdb=" N   LYS H 191 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU H 199 " --> pdb=" O   THR H 195 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASN H 200 " --> pdb=" O   ASN H 196 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 205 through 211
      removed outlier: 3.558A  pdb=" N   LYS H 211 " --> pdb=" O   ALA H 207 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 211 through 223
      removed outlier: 3.661A  pdb=" N   PHE H 217 " --> pdb=" O   SER H 213 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 224 through 228
      removed outlier: 3.841A  pdb=" N   CYS H 228 " --> pdb=" O   ALA H 225 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 231 through 248
      removed outlier: 3.745A  pdb=" N   ASN H 240 " --> pdb=" O   ALA H 236 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LYS H 243 " --> pdb=" O   GLN H 239 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 252 through 257
      removed outlier: 4.357A  pdb=" N   GLY H 257 " --> pdb=" O   GLU H 253 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 259 through 269
    Processing helix  chain 'H' and resid 272 through 303
      removed outlier: 4.034A  pdb=" N   GLN H 278 " --> pdb=" O   GLU H 274 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY H 279 " --> pdb=" O   VAL H 275 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   TRP H 283 " --> pdb=" O   GLY H 279 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   MET H 291 " --> pdb=" O   CYS H 287 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA H 294 " --> pdb=" O   GLU H 290 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA H 301 " --> pdb=" O   ALA H 297 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN H 303 " --> pdb=" O   GLU H 299 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 318 through 330
      Proline residue:  H 324  - end of helix
      removed outlier: 3.702A  pdb=" N   GLN H 328 " --> pdb=" O   PRO H 324 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU H 330 " --> pdb=" O   LEU H 326 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 343 through 360
      removed outlier: 3.684A  pdb=" N   GLY H 349 " --> pdb=" O   CYS H 345 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL H 350 " --> pdb=" O   LYS H 346 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 363 through 375
      Proline residue:  H 369  - end of helix
    Processing helix  chain 'H' and resid 379 through 393
      removed outlier: 4.098A  pdb=" N   ILE H 393 " --> pdb=" O   ALA H 389 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 398 through 401
    Processing helix  chain 'H' and resid 402 through 417
      removed outlier: 3.658A  pdb=" N   VAL H 406 " --> pdb=" O   LEU H 402 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLN H 408 " --> pdb=" O   PRO H 404 " (cutoff:3.500A)
      Proline residue:  H 411  - end of helix
      removed outlier: 3.558A  pdb=" N   GLU H 415 " --> pdb=" O   PRO H 411 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 421 through 439
    Processing helix  chain 'H' and resid 440 through 445
      removed outlier: 3.673A  pdb=" N   ASN H 445 " --> pdb=" O   GLU H 441 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 448 through 460
    Processing helix  chain 'H' and resid 463 through 489
      removed outlier: 3.835A  pdb=" N   SER H 468 " --> pdb=" O   PRO H 464 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   ASN H 469 " --> pdb=" O   ARG H 465 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TRP H 472 " --> pdb=" O   SER H 468 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ALA H 473 " --> pdb=" O   ASN H 469 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLU H 479 " --> pdb=" O   SER H 475 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ALA H 488 " --> pdb=" O   ALA H 484 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 502 through 515
      removed outlier: 3.698A  pdb=" N   ILE H 506 " --> pdb=" O   SER H 502 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   GLN H 508 " --> pdb=" O   GLU H 504 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ASP H 515 " --> pdb=" O   LEU H 511 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 520 through 522
      No H-bonds generated for 'chain 'H' and resid 520 through 522'
    Processing helix  chain 'H' and resid 523 through 538
    Processing helix  chain 'H' and resid 540 through 542
      No H-bonds generated for 'chain 'H' and resid 540 through 542'
    Processing helix  chain 'H' and resid 543 through 562
      removed outlier: 3.663A  pdb=" N   LEU H 562 " --> pdb=" O   LEU H 558 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 563 through 568
      removed outlier: 4.400A  pdb=" N   SER H 566 " --> pdb=" O   GLN H 563 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE H 568 " --> pdb=" O   GLU H 565 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 570 through 593
      removed outlier: 3.570A  pdb=" N   ASP H 579 " --> pdb=" O   ILE H 575 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 596 through 601
    Processing helix  chain 'H' and resid 603 through 618
      removed outlier: 3.773A  pdb=" N   THR H 618 " --> pdb=" O   MET H 614 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 622 through 640
    Processing helix  chain 'H' and resid 641 through 645
      removed outlier: 3.982A  pdb=" N   LEU H 644 " --> pdb=" O   GLY H 641 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LYS H 645 " --> pdb=" O   GLU H 642 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 641 through 645'
    Processing helix  chain 'H' and resid 646 through 660
      Proline residue:  H 652  - end of helix
    Processing helix  chain 'H' and resid 663 through 682
      removed outlier: 4.013A  pdb=" N   CYS H 667 " --> pdb=" O   GLU H 663 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 683 through 687
      removed outlier: 4.004A  pdb=" N   ILE H 686 " --> pdb=" O   SER H 683 " (cutoff:3.500A)
      Proline residue:  H 687  - end of helix
      No H-bonds generated for 'chain 'H' and resid 683 through 687'
    Processing helix  chain 'H' and resid 688 through 702
      removed outlier: 3.921A  pdb=" N   VAL H 692 " --> pdb=" O   PHE H 688 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 706 through 708
      No H-bonds generated for 'chain 'H' and resid 706 through 708'
    Processing helix  chain 'H' and resid 709 through 725
      removed outlier: 3.760A  pdb=" N   ILE H 713 " --> pdb=" O   VAL H 709 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LEU H 714 " --> pdb=" O   LYS H 710 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER H 715 " --> pdb=" O   PRO H 711 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 728 through 744
      removed outlier: 4.529A  pdb=" N   GLU H 733 " --> pdb=" O   LYS H 729 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   VAL H 734 " --> pdb=" O   LYS H 730 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 751 through 778
      removed outlier: 4.528A  pdb=" N   TYR H 757 " --> pdb=" O   ASP H 753 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY H 778 " --> pdb=" O   GLN H 774 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 784 through 792
      removed outlier: 3.519A  pdb=" N   VAL H 787 " --> pdb=" O   HIS H 784 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLN H 791 " --> pdb=" O   MET H 788 " (cutoff:3.500A)
      Proline residue:  H 792  - end of helix
    Processing helix  chain 'H' and resid 793 through 806
    Processing helix  chain 'H' and resid 811 through 829
      removed outlier: 3.850A  pdb=" N   VAL H 815 " --> pdb=" O   THR H 811 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLY H 820 " --> pdb=" O   ALA H 816 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE H 829 " --> pdb=" O   LEU H 825 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 830 through 832
      No H-bonds generated for 'chain 'H' and resid 830 through 832'
    Processing helix  chain 'H' and resid 833 through 838
    Processing helix  chain 'H' and resid 841 through 853
      removed outlier: 3.748A  pdb=" N   THR H 848 " --> pdb=" O   HIS H 844 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ARG H 851 " --> pdb=" O   LEU H 847 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 855 through 875
      removed outlier: 3.519A  pdb=" N   LYS H 859 " --> pdb=" O   THR H 855 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN H 875 " --> pdb=" O   LYS H 871 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 8 through 13
    Processing helix  chain 'I' and resid 14 through 17
    Processing helix  chain 'I' and resid 23 through 52
      removed outlier: 3.591A  pdb=" N   ASN I  35 " --> pdb=" O   ARG I  31 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ARG I  39 " --> pdb=" O   ASN I  35 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU I  48 " --> pdb=" O   ASP I  44 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LYS I  49 " --> pdb=" O   ASP I  45 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ARG I  50 " --> pdb=" O   GLN I  46 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG I  51 " --> pdb=" O   MET I  47 " (cutoff:3.500A)

    468 hydrogen bonds defined for protein.
    1383 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: 1.02

  Time building geometry restraints manager: 0.81 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: 2480
        1.34 -     1.46: 1306
        1.46 -     1.58: 3636
        1.58 -     1.70: 0
        1.70 -     1.81: 77
  Bond restraints: 7499
  Sorted by residual:
  bond pdb=" CA  CYS H 223 "
       pdb=" C   CYS H 223 "
    ideal  model  delta    sigma   weight residual
    1.522  1.564 -0.042 1.72e-02 3.38e+03 5.98e+00
  bond pdb=" CA  VAL H 364 "
       pdb=" C   VAL H 364 "
    ideal  model  delta    sigma   weight residual
    1.520  1.537 -0.017 8.80e-03 1.29e+04 3.75e+00
  bond pdb=" C   ILE H 121 "
       pdb=" N   PRO H 122 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.017 9.40e-03 1.13e+04 3.21e+00
  bond pdb=" CA  VAL H 323 "
       pdb=" C   VAL H 323 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.016 8.80e-03 1.29e+04 3.20e+00
  bond pdb=" CA  TYR H 544 "
       pdb=" C   TYR H 544 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.021 1.26e-02 6.30e+03 2.77e+00
  ... (remaining 7494 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 9923
        2.24 -     4.49: 181
        4.49 -     6.73: 33
        6.73 -     8.97: 13
        8.97 -    11.21: 3
  Bond angle restraints: 10153
  Sorted by residual:
  angle pdb=" C   ILE H 363 "
        pdb=" N   VAL H 364 "
        pdb=" CA  VAL H 364 "
      ideal   model   delta    sigma   weight residual
     120.24  124.02   -3.78 6.30e-01 2.52e+00 3.61e+01
  angle pdb=" C   GLU H 504 "
        pdb=" N   LEU H 505 "
        pdb=" CA  LEU H 505 "
      ideal   model   delta    sigma   weight residual
     121.54  130.19   -8.65 1.91e+00 2.74e-01 2.05e+01
  angle pdb=" C   ASP H 230 "
        pdb=" N   THR H 231 "
        pdb=" CA  THR H 231 "
      ideal   model   delta    sigma   weight residual
     121.54  130.14   -8.60 1.91e+00 2.74e-01 2.03e+01
  angle pdb=" C   SER H 142 "
        pdb=" CA  SER H 142 "
        pdb=" CB  SER H 142 "
      ideal   model   delta    sigma   weight residual
     116.34  110.31    6.03 1.40e+00 5.10e-01 1.86e+01
  angle pdb=" N   GLN H 791 "
        pdb=" CA  GLN H 791 "
        pdb=" C   GLN H 791 "
      ideal   model   delta    sigma   weight residual
     109.81  119.30   -9.49 2.21e+00 2.05e-01 1.84e+01
  ... (remaining 10148 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4174
       17.62 -    35.24: 342
       35.24 -    52.85: 87
       52.85 -    70.47: 14
       70.47 -    88.09: 9
  Dihedral angle restraints: 4626
    sinusoidal: 1856
      harmonic: 2770
  Sorted by residual:
  dihedral pdb=" CA  HIS H 810 "
           pdb=" C   HIS H 810 "
           pdb=" N   THR H 811 "
           pdb=" CA  THR H 811 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.23   23.77     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  ASP H 490 "
           pdb=" C   ASP H 490 "
           pdb=" N   GLN H 491 "
           pdb=" CA  GLN H 491 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.41  -22.59     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  ASP H 489 "
           pdb=" C   ASP H 489 "
           pdb=" N   ASP H 490 "
           pdb=" CA  ASP H 490 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.54   22.46     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 4623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 811
       0.043 -    0.086: 269
       0.086 -    0.129: 74
       0.129 -    0.172: 16
       0.172 -    0.215: 3
  Chirality restraints: 1173
  Sorted by residual:
  chirality pdb=" CA  GLN H 791 "
            pdb=" N   GLN H 791 "
            pdb=" C   GLN H 791 "
            pdb=" CB  GLN H 791 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  THR I   9 "
            pdb=" N   THR I   9 "
            pdb=" C   THR I   9 "
            pdb=" CB  THR I   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  THR H 231 "
            pdb=" N   THR H 231 "
            pdb=" C   THR H 231 "
            pdb=" CB  THR H 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.52e-01
  ... (remaining 1170 not shown)

  Planarity restraints: 1327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS H 784 "    0.041 5.00e-02 4.00e+02   6.29e-02 6.33e+00
        pdb=" N   PRO H 785 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO H 785 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO H 785 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN H 343 "   -0.040 5.00e-02 4.00e+02   5.94e-02 5.64e+00
        pdb=" N   PRO H 344 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO H 344 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO H 344 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 403 "    0.037 5.00e-02 4.00e+02   5.44e-02 4.74e+00
        pdb=" N   PRO H 404 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO H 404 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO H 404 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1324 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1279
        2.77 -     3.31: 7236
        3.31 -     3.84: 11701
        3.84 -     4.37: 13366
        4.37 -     4.90: 23002
  Nonbonded interactions: 56584
  Sorted by model distance:
  nonbonded pdb=" O   VAL H 134 "
            pdb=" OG1 THR H 138 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   PRO H 711 "
            pdb=" OG  SER H 764 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   LYS H 191 "
            pdb=" OG1 THR H 195 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" OH  TYR H 544 "
            pdb=" OD2 ASP H 599 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OD1 ASP H 426 "
            pdb=" ND2 ASN H 469 "
     model   vdw
     2.356 3.120
  ... (remaining 56579 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.270
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
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      :  0.004   0.048   7500  Z= 0.235
  Angle     :  0.838  11.214  10156  Z= 0.471
  Chirality :  0.047   0.215   1173
  Planarity :  0.007   0.063   1326
  Dihedral  : 14.558  88.090   2815
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  7.65 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.40 (0.24), residues: 933
  helix: -0.68 (0.18), residues: 691
  sheet:  None (None), residues: 0
  loop : -1.18 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H 525 
 TYR   0.017   0.002   TYR H 156 
 PHE   0.017   0.002   PHE H 643 
 TRP   0.011   0.002   TRP H 380 
 HIS   0.004   0.001   HIS H  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 7499)
  covalent geometry    : angle       0.83773 (10153)
  hydrogen bonds       : bond        0.13319 (  468)
  hydrogen bonds       : angle       4.82689 ( 1383)
  link_TRANS           : bond        0.00017 (    1)
  link_TRANS           : angle       0.16067 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  101 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8235 (p)
  outliers start: 16
  outliers final: 3
  residues processed: 143
  average time/residue: 0.1000
  time to fit residues: 18.2066
Evaluate side-chains
  75 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   98 THR
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  864 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.0002

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

Flipped N/Q/H residues before XYZ refinement:
H 196 ASN
H 333 GLN
H 521 GLN
H 569 GLN
H 589 GLN
H 596 GLN
H 598 GLN
H 741 GLN
H 744 GLN
I   6 ASN
I  35 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.056368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.040419 restraints weight = 38863.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 5.38
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7500  Z= 0.142
  Angle     :  0.679  13.939  10156  Z= 0.344
  Chirality :  0.041   0.176   1173
  Planarity :  0.005   0.042   1326
  Dihedral  :  5.187  43.553   1010
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 10.74 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.45 (0.28), residues: 933
  helix:  0.68 (0.20), residues: 695
  sheet:  None (None), residues: 0
  loop : -0.56 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 105 
 TYR   0.010   0.001   TYR H 251 
 PHE   0.013   0.001   PHE H 204 
 TRP   0.008   0.001   TRP H  80 
 HIS   0.001   0.000   HIS H 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7499)
  covalent geometry    : angle       0.67929 (10153)
  hydrogen bonds       : bond        0.04973 (  468)
  hydrogen bonds       : angle       4.01594 ( 1383)
  link_TRANS           : bond        0.00002 (    1)
  link_TRANS           : angle       0.07250 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  164 GLU cc_start: 0.9662 (mp0) cc_final: 0.9416 (pm20)
REVERT: H  181 MET cc_start: 0.8005 (ttm) cc_final: 0.7775 (tpt)
REVERT: H  219 MET cc_start: 0.9054 (tpp) cc_final: 0.8803 (mmt)
REVERT: H  410 MET cc_start: 0.9452 (mmm) cc_final: 0.9245 (mmm)
REVERT: H  537 LYS cc_start: 0.9338 (tppt) cc_final: 0.9059 (tppt)
REVERT: H  564 MET cc_start: 0.9246 (ttm) cc_final: 0.8999 (tmm)
REVERT: H  630 MET cc_start: 0.9360 (mtp) cc_final: 0.9060 (mtm)
REVERT: I   42 LYS cc_start: 0.9606 (tptp) cc_final: 0.9320 (tptp)
REVERT: I   47 MET cc_start: 0.9465 (tpt) cc_final: 0.9202 (tpp)
  outliers start: 22
  outliers final: 9
  residues processed: 105
  average time/residue: 0.0965
  time to fit residues: 13.3851
Evaluate side-chains
  73 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  295 ILE
Chi-restraints excluded: chain H residue  375 ILE
Chi-restraints excluded: chain H residue  406 VAL
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  815 VAL
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain H residue  869 LEU
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 55 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0670
   chunk 83 optimal weight:    0.0970
   chunk 82 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.0320

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

Flipped N/Q/H residues before XYZ refinement:
H 167 GLN
H 844 HIS
I  35 ASN
I  46 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.055967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.040186 restraints weight = 38628.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 5.33
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7500  Z= 0.125
  Angle     :  0.622   9.295  10156  Z= 0.312
  Chirality :  0.041   0.243   1173
  Planarity :  0.004   0.043   1326
  Dihedral  :  4.627  41.892   1008
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.22 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.16 (0.28), residues: 933
  helix:  1.18 (0.20), residues: 711
  sheet:  None (None), residues: 0
  loop : -0.37 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  16 
 TYR   0.011   0.001   TYR H 251 
 PHE   0.011   0.001   PHE H 653 
 TRP   0.008   0.001   TRP H 283 
 HIS   0.001   0.000   HIS H 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7499)
  covalent geometry    : angle       0.62193 (10153)
  hydrogen bonds       : bond        0.04186 (  468)
  hydrogen bonds       : angle       3.83133 ( 1383)
  link_TRANS           : bond        0.00008 (    1)
  link_TRANS           : angle       0.05896 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  537 LYS cc_start: 0.9306 (tppt) cc_final: 0.8928 (tppt)
REVERT: I    1 MET cc_start: 0.4686 (ppp) cc_final: 0.4265 (ppp)
REVERT: I   20 LYS cc_start: 0.9504 (mmmm) cc_final: 0.9150 (mmmm)
REVERT: I   47 MET cc_start: 0.9626 (tpt) cc_final: 0.9268 (tpp)
  outliers start: 12
  outliers final: 5
  residues processed: 86
  average time/residue: 0.0840
  time to fit residues: 9.5015
Evaluate side-chains
  72 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  295 ILE
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
H  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.055568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.039217 restraints weight = 39776.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 5.42
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7500  Z= 0.141
  Angle     :  0.625  11.879  10156  Z= 0.312
  Chirality :  0.041   0.193   1173
  Planarity :  0.004   0.045   1326
  Dihedral  :  4.475  41.433   1008
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.22 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.64 (0.29), residues: 933
  helix:  1.51 (0.20), residues: 710
  sheet:  None (None), residues: 0
  loop : -0.10 (0.46), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 105 
 TYR   0.006   0.001   TYR H 544 
 PHE   0.020   0.001   PHE H  36 
 TRP   0.009   0.001   TRP H 283 
 HIS   0.003   0.001   HIS H 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7499)
  covalent geometry    : angle       0.62512 (10153)
  hydrogen bonds       : bond        0.04062 (  468)
  hydrogen bonds       : angle       3.88728 ( 1383)
  link_TRANS           : bond        0.00006 (    1)
  link_TRANS           : angle       0.08537 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  268 MET cc_start: 0.8760 (mmm) cc_final: 0.8428 (mtp)
REVERT: I    1 MET cc_start: 0.4810 (ppp) cc_final: 0.4279 (ppp)
REVERT: I   20 LYS cc_start: 0.9482 (mmmm) cc_final: 0.9149 (mmmm)
REVERT: I   47 MET cc_start: 0.9654 (tpt) cc_final: 0.9237 (tpp)
  outliers start: 18
  outliers final: 8
  residues processed: 82
  average time/residue: 0.0856
  time to fit residues: 9.1829
Evaluate side-chains
  71 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  295 ILE
Chi-restraints excluded: chain H residue  375 ILE
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  815 VAL
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0070
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.1604

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

Flipped N/Q/H residues before XYZ refinement:
H 590 ASN
** I  46 GLN ** 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 = 0.3415 r_free = 0.3415 target = 0.055602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.039325 restraints weight = 39539.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 5.38
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7500  Z= 0.124
  Angle     :  0.652  11.718  10156  Z= 0.313
  Chirality :  0.041   0.196   1173
  Planarity :  0.004   0.042   1326
  Dihedral  :  4.358  40.431   1008
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.46 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.91 (0.29), residues: 933
  helix:  1.68 (0.20), residues: 710
  sheet:  None (None), residues: 0
  loop :  0.07 (0.47), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  39 
 TYR   0.016   0.001   TYR H 248 
 PHE   0.015   0.001   PHE H  36 
 TRP   0.008   0.001   TRP H 283 
 HIS   0.001   0.000   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7499)
  covalent geometry    : angle       0.65165 (10153)
  hydrogen bonds       : bond        0.03772 (  468)
  hydrogen bonds       : angle       3.76629 ( 1383)
  link_TRANS           : bond        0.00013 (    1)
  link_TRANS           : angle       0.09024 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  864 TRP cc_start: 0.9521 (OUTLIER) cc_final: 0.9247 (t-100)
REVERT: I    1 MET cc_start: 0.4959 (ppp) cc_final: 0.4395 (ppp)
REVERT: I   20 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9171 (mmmm)
REVERT: I   47 MET cc_start: 0.9698 (tpt) cc_final: 0.9355 (tpp)
  outliers start: 13
  outliers final: 7
  residues processed: 80
  average time/residue: 0.1083
  time to fit residues: 11.2774
Evaluate side-chains
  70 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  295 ILE
Chi-restraints excluded: chain H residue  375 ILE
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  815 VAL
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 35 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
H 401 GLN
H 508 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.056346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.040044 restraints weight = 38842.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 5.41
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7500  Z= 0.115
  Angle     :  0.666  12.139  10156  Z= 0.318
  Chirality :  0.041   0.273   1173
  Planarity :  0.004   0.041   1326
  Dihedral  :  4.273  39.455   1008
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.07 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.86 (0.29), residues: 933
  helix:  1.65 (0.21), residues: 717
  sheet:  None (None), residues: 0
  loop : -0.02 (0.46), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  39 
 TYR   0.008   0.001   TYR H 248 
 PHE   0.019   0.001   PHE J  19 
 TRP   0.006   0.001   TRP H 283 
 HIS   0.001   0.000   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7499)
  covalent geometry    : angle       0.66576 (10153)
  hydrogen bonds       : bond        0.03431 (  468)
  hydrogen bonds       : angle       3.69790 ( 1383)
  link_TRANS           : bond        0.00019 (    1)
  link_TRANS           : angle       0.09034 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  864 TRP cc_start: 0.9516 (OUTLIER) cc_final: 0.9182 (t-100)
REVERT: I    1 MET cc_start: 0.5095 (ppp) cc_final: 0.4828 (ppp)
REVERT: I   27 MET cc_start: 0.9418 (mmm) cc_final: 0.9085 (mmp)
REVERT: I   30 ARG cc_start: 0.9044 (mtm-85) cc_final: 0.8580 (mtt-85)
REVERT: I   40 LYS cc_start: 0.9728 (tppp) cc_final: 0.9279 (tptp)
REVERT: I   44 ASP cc_start: 0.8744 (p0) cc_final: 0.8426 (p0)
REVERT: I   47 MET cc_start: 0.9651 (tpt) cc_final: 0.9194 (tpp)
  outliers start: 12
  outliers final: 7
  residues processed: 79
  average time/residue: 0.1055
  time to fit residues: 10.8625
Evaluate side-chains
  67 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  375 ILE
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  506 ILE
Chi-restraints excluded: chain H residue  815 VAL
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** I  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.056006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.040073 restraints weight = 38753.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 5.35
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7500  Z= 0.113
  Angle     :  0.682  14.331  10156  Z= 0.320
  Chirality :  0.042   0.299   1173
  Planarity :  0.004   0.041   1326
  Dihedral  :  4.217  38.845   1008
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.07 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.87 (0.29), residues: 933
  helix:  1.69 (0.21), residues: 714
  sheet:  None (None), residues: 0
  loop : -0.12 (0.46), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  39 
 TYR   0.007   0.001   TYR H 251 
 PHE   0.013   0.001   PHE H  36 
 TRP   0.005   0.001   TRP H  80 
 HIS   0.001   0.000   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7499)
  covalent geometry    : angle       0.68240 (10153)
  hydrogen bonds       : bond        0.03349 (  468)
  hydrogen bonds       : angle       3.69082 ( 1383)
  link_TRANS           : bond        0.00017 (    1)
  link_TRANS           : angle       0.08610 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  864 TRP cc_start: 0.9513 (OUTLIER) cc_final: 0.9154 (t-100)
REVERT: I    1 MET cc_start: 0.5150 (ppp) cc_final: 0.4888 (ppp)
REVERT: I   47 MET cc_start: 0.9584 (tpt) cc_final: 0.9110 (tpp)
  outliers start: 13
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0984
  time to fit residues: 10.0060
Evaluate side-chains
  67 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  375 ILE
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  506 ILE
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 46 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** I  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.056350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.039986 restraints weight = 39213.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 5.45
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7500  Z= 0.114
  Angle     :  0.696  14.169  10156  Z= 0.328
  Chirality :  0.042   0.306   1173
  Planarity :  0.004   0.040   1326
  Dihedral  :  4.192  38.256   1008
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.94 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.89 (0.29), residues: 933
  helix:  1.70 (0.21), residues: 715
  sheet:  None (None), residues: 0
  loop : -0.09 (0.46), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  39 
 TYR   0.006   0.001   TYR H 544 
 PHE   0.022   0.001   PHE H 209 
 TRP   0.005   0.001   TRP H 283 
 HIS   0.001   0.000   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7499)
  covalent geometry    : angle       0.69601 (10153)
  hydrogen bonds       : bond        0.03302 (  468)
  hydrogen bonds       : angle       3.70321 ( 1383)
  link_TRANS           : bond        0.00019 (    1)
  link_TRANS           : angle       0.08722 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  864 TRP cc_start: 0.9517 (OUTLIER) cc_final: 0.9167 (t-100)
REVERT: I    1 MET cc_start: 0.4996 (ppp) cc_final: 0.4735 (ppp)
REVERT: I   47 MET cc_start: 0.9602 (tpt) cc_final: 0.9134 (tpp)
  outliers start: 10
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1172
  time to fit residues: 11.1630
Evaluate side-chains
  68 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  375 ILE
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  506 ILE
Chi-restraints excluded: chain H residue  535 ILE
Chi-restraints excluded: chain H residue  815 VAL
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** I  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.056057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.040606 restraints weight = 38597.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 5.26
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7500  Z= 0.113
  Angle     :  0.697  15.294  10156  Z= 0.325
  Chirality :  0.042   0.322   1173
  Planarity :  0.004   0.051   1326
  Dihedral  :  4.134  37.841   1008
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.43 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.92 (0.29), residues: 933
  helix:  1.71 (0.21), residues: 717
  sheet:  None (None), residues: 0
  loop : -0.08 (0.46), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG H 852 
 TYR   0.006   0.001   TYR H 544 
 PHE   0.015   0.001   PHE J  19 
 TRP   0.006   0.001   TRP H 283 
 HIS   0.001   0.000   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7499)
  covalent geometry    : angle       0.69702 (10153)
  hydrogen bonds       : bond        0.03236 (  468)
  hydrogen bonds       : angle       3.66451 ( 1383)
  link_TRANS           : bond        0.00021 (    1)
  link_TRANS           : angle       0.08635 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  864 TRP cc_start: 0.9511 (OUTLIER) cc_final: 0.9144 (t-100)
REVERT: I    1 MET cc_start: 0.5035 (ppp) cc_final: 0.4782 (ppp)
REVERT: I   18 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8545 (mmtp)
REVERT: I   47 MET cc_start: 0.9574 (tpt) cc_final: 0.9096 (tpp)
  outliers start: 9
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0985
  time to fit residues: 9.1920
Evaluate side-chains
  72 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  375 ILE
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  506 ILE
Chi-restraints excluded: chain H residue  535 ILE
Chi-restraints excluded: chain H residue  815 VAL
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0370
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.0060

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

Flipped N/Q/H residues before XYZ refinement:
H 589 GLN
** I  46 GLN ** 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 = 0.3427 r_free = 0.3427 target = 0.055935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.040477 restraints weight = 38779.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 5.23
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.4103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7500  Z= 0.122
  Angle     :  0.730  15.253  10156  Z= 0.342
  Chirality :  0.042   0.332   1173
  Planarity :  0.004   0.042   1326
  Dihedral  :  4.132  37.648   1008
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.17 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.91 (0.29), residues: 933
  helix:  1.69 (0.21), residues: 717
  sheet:  None (None), residues: 0
  loop : -0.02 (0.46), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H 852 
 TYR   0.013   0.001   TYR H 156 
 PHE   0.023   0.001   PHE H 209 
 TRP   0.006   0.001   TRP H 380 
 HIS   0.001   0.000   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7499)
  covalent geometry    : angle       0.73006 (10153)
  hydrogen bonds       : bond        0.03346 (  468)
  hydrogen bonds       : angle       3.79715 ( 1383)
  link_TRANS           : bond        0.00020 (    1)
  link_TRANS           : angle       0.08627 (    3)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  864 TRP cc_start: 0.9514 (OUTLIER) cc_final: 0.9153 (t-100)
REVERT: I    1 MET cc_start: 0.5078 (ppp) cc_final: 0.4819 (ppp)
REVERT: I   47 MET cc_start: 0.9589 (tpt) cc_final: 0.9107 (tpp)
  outliers start: 9
  outliers final: 8
  residues processed: 71
  average time/residue: 0.1020
  time to fit residues: 9.8148
Evaluate side-chains
  69 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  375 ILE
Chi-restraints excluded: chain H residue  497 TYR
Chi-restraints excluded: chain H residue  506 ILE
Chi-restraints excluded: chain H residue  535 ILE
Chi-restraints excluded: chain H residue  815 VAL
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  864 TRP
Chi-restraints excluded: chain I residue    9 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 86 optimal weight:    0.4980
   chunk 8 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 71 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0570
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.9502

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

Flipped N/Q/H residues before XYZ refinement:
I  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.055830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.040422 restraints weight = 38773.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 5.24
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7500  Z= 0.120
  Angle     :  0.743  15.080  10156  Z= 0.346
  Chirality :  0.043   0.335   1173
  Planarity :  0.004   0.039   1326
  Dihedral  :  4.090  37.059   1008
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.30 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.91 (0.30), residues: 933
  helix:  1.67 (0.21), residues: 724
  sheet:  None (None), residues: 0
  loop : -0.00 (0.48), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H 852 
 TYR   0.009   0.001   TYR H 156 
 PHE   0.020   0.001   PHE H 209 
 TRP   0.006   0.001   TRP H 380 
 HIS   0.001   0.000   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7499)
  covalent geometry    : angle       0.74300 (10153)
  hydrogen bonds       : bond        0.03288 (  468)
  hydrogen bonds       : angle       3.82895 ( 1383)
  link_TRANS           : bond        0.00021 (    1)
  link_TRANS           : angle       0.08741 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1609.40 seconds
wall clock time: 28 minutes 21.43 seconds (1701.43 seconds total)