Starting phenix.real_space_refine
on Wed Feb  4 00:53:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m30_63594/02_2026/9m30_63594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m30_63594/02_2026/9m30_63594.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m30_63594/02_2026/9m30_63594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m30_63594/02_2026/9m30_63594.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m30_63594/02_2026/9m30_63594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m30_63594/02_2026/9m30_63594.cif"
  }
  resolution = 3.05
  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=   0.020
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: 6
    Type Number    sf(0)   Gaussians
     P      50      5.49       5
     Mg      1      5.21       5
     S      23      5.16       5
     C    4955      2.51       5
     N    1379      2.21       5
     O    1619      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  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: 8027
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6941
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 844, 6932
          Classifications: {'peptide': 844}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 26, 'TRANS': 817}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 844, 6932
          Classifications: {'peptide': 844}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 26, 'TRANS': 817}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 7070
    Chain: "B"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 1085
          Classifications: {'RNA': 51}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 1, 'rna3p_pur': 23, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 7, 'rna3p': 43}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ALYS A   5 " occ=0.70
      ... (16 atoms not shown)
      pdb=" NZ BLYS A   5 " occ=0.30
  Time building chain proxies: 2.68, per 1000 atoms: 0.33
  Number of scatterers: 8027
  At special positions: 0
  Unit cell: (88.32, 94.76, 107.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      23     16.00
     P      50     15.00
     Mg      1     11.99
     O    1619      8.00
     N    1379      7.00
     C    4955      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
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 477.8 milliseconds
  

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1630

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 4 sheets defined
      63.4% alpha, 4.1% beta
      4 base pairs and 28 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 15
    Processing helix  chain 'A' and resid 96 through 105
    Processing helix  chain 'A' and resid 113 through 123
    Processing helix  chain 'A' and resid 125 through 143
    Processing helix  chain 'A' and resid 166 through 173
      removed outlier: 4.238A  pdb=" N   ARG A 170 " --> pdb=" O   TYR A 166 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 185
      removed outlier: 3.946A  pdb=" N   ASN A 181 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 191
      removed outlier: 3.792A  pdb=" N   LEU A 189 " --> pdb=" O   LYS A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 222
      removed outlier: 3.510A  pdb=" N   ILE A 207 " --> pdb=" O   TYR A 203 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A 222 " --> pdb=" O   ALA A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 267
      removed outlier: 3.641A  pdb=" N   VAL A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 273 through 284
    Processing helix  chain 'A' and resid 288 through 301
    Processing helix  chain 'A' and resid 311 through 320
      removed outlier: 3.790A  pdb=" N   LEU A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE A 318 " --> pdb=" O   LYS A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 353
    Processing helix  chain 'A' and resid 355 through 368
      removed outlier: 3.660A  pdb=" N   LYS A 359 " --> pdb=" O   HIS A 355 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU A 360 " --> pdb=" O   ALA A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 399
      removed outlier: 3.679A  pdb=" N   LYS A 375 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU A 376 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER A 388 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   ALA A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ASP A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LYS A 395 " --> pdb=" O   GLY A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 412
      removed outlier: 3.637A  pdb=" N   LYS A 411 " --> pdb=" O   ARG A 407 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A 412 " --> pdb=" O   ASP A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 442
    Processing helix  chain 'A' and resid 445 through 473
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 4.491A  pdb=" N   ASP A 485 " --> pdb=" O   PRO A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 506
      removed outlier: 3.990A  pdb=" N   TYR A 494 " --> pdb=" O   THR A 490 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A 504 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 527
      removed outlier: 3.716A  pdb=" N   LEU A 527 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 545
    Processing helix  chain 'A' and resid 558 through 568
    Processing helix  chain 'A' and resid 571 through 581
    Processing helix  chain 'A' and resid 585 through 591
      removed outlier: 4.042A  pdb=" N   THR A 588 " --> pdb=" O   LYS A 585 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LEU A 589 " --> pdb=" O   THR A 586 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A 590 " --> pdb=" O   ARG A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 603
      removed outlier: 3.770A  pdb=" N   GLY A 602 " --> pdb=" O   PHE A 598 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ILE A 603 " --> pdb=" O   VAL A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 615
      removed outlier: 3.544A  pdb=" N   ARG A 610 " --> pdb=" O   THR A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 639
      removed outlier: 3.505A  pdb=" N   VAL A 632 " --> pdb=" O   ALA A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 647
      removed outlier: 4.364A  pdb=" N   ASP A 647 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 712
      removed outlier: 3.528A  pdb=" N   LYS A 669 " --> pdb=" O   ASP A 665 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   MET A 683 " --> pdb=" O   TYR A 679 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG A 696 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   TYR A 697 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ALA A 700 " --> pdb=" O   ARG A 696 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE A 709 " --> pdb=" O   GLU A 705 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU A 710 " --> pdb=" O   ARG A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 731
      removed outlier: 3.605A  pdb=" N   THR A 729 " --> pdb=" O   SER A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 734
      No H-bonds generated for 'chain 'A' and resid 732 through 734'
    Processing helix  chain 'A' and resid 751 through 761
      removed outlier: 3.715A  pdb=" N   GLN A 761 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 778
    Processing helix  chain 'A' and resid 778 through 783
      removed outlier: 3.702A  pdb=" N   ARG A 782 " --> pdb=" O   ILE A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 813
      removed outlier: 3.603A  pdb=" N   LEU A 800 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 834
    Processing helix  chain 'A' and resid 845 through 849
      removed outlier: 3.602A  pdb=" N   PHE A 848 " --> pdb=" O   CYS A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 860
    Processing helix  chain 'A' and resid 860 through 865
      removed outlier: 4.524A  pdb=" N   ASP A 865 " --> pdb=" O   ASN A 861 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22
      removed outlier: 8.681A  pdb=" N   LEU A  16 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   PHE A  31 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU A  18 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR A  29 " --> pdb=" O   GLU A  18 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   SER A  30 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   LEU A  39 " --> pdb=" O   SER A  30 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 64
      removed outlier: 4.928A  pdb=" N   ASN A  60 " --> pdb=" O   GLN A  71 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLN A  71 " --> pdb=" O   ASN A  60 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 197
    Processing sheet with id=AA4, first strand: chain 'A' and resid 717 through 718

    352 hydrogen bonds defined for protein.
    1017 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      18 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      28 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2274
        1.34 -     1.45: 1576
        1.45 -     1.57: 4317
        1.57 -     1.69: 100
        1.69 -     1.81: 38
  Bond restraints: 8305
  Sorted by residual:
  bond pdb=" O5'   C B  -1 "
       pdb=" C5'   C B  -1 "
    ideal  model  delta    sigma   weight residual
    1.420  1.446 -0.026 1.50e-02 4.44e+03 2.99e+00
  bond pdb=" O5'   G B   1 "
       pdb=" C5'   G B   1 "
    ideal  model  delta    sigma   weight residual
    1.420  1.446 -0.026 1.50e-02 4.44e+03 2.96e+00
  bond pdb=" C   ILE A 846 "
       pdb=" N   PRO A 847 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.034 2.34e-02 1.83e+03 2.06e+00
  bond pdb=" C1'   G B   1 "
       pdb=" N9    G B   1 "
    ideal  model  delta    sigma   weight residual
    1.475  1.454  0.021 1.50e-02 4.44e+03 2.01e+00
  bond pdb=" P     C B  -1 "
       pdb=" OP2   C B  -1 "
    ideal  model  delta    sigma   weight residual
    1.485  1.507 -0.022 2.00e-02 2.50e+03 1.21e+00
  ... (remaining 8300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 11258
        1.60 -     3.20: 160
        3.20 -     4.80: 25
        4.80 -     6.40: 8
        6.40 -     8.00: 1
  Bond angle restraints: 11452
  Sorted by residual:
  angle pdb=" C3'   C B  -1 "
        pdb=" O3'   C B  -1 "
        pdb=" P     G B   1 "
      ideal   model   delta    sigma   weight residual
     120.20  112.20    8.00 1.50e+00 4.44e-01 2.84e+01
  angle pdb=" C4'   G B   1 "
        pdb=" C3'   G B   1 "
        pdb=" C2'   G B   1 "
      ideal   model   delta    sigma   weight residual
     102.60   99.18    3.42 1.00e+00 1.00e+00 1.17e+01
  angle pdb=" C   VAL A 851 "
        pdb=" N   VAL A 852 "
        pdb=" CA  VAL A 852 "
      ideal   model   delta    sigma   weight residual
     120.33  122.96   -2.63 8.00e-01 1.56e+00 1.08e+01
  angle pdb=" C   GLN A 172 "
        pdb=" N   THR A 173 "
        pdb=" CA  THR A 173 "
      ideal   model   delta    sigma   weight residual
     121.54  127.60   -6.06 1.91e+00 2.74e-01 1.01e+01
  angle pdb=" C3'   A B  -2 "
        pdb=" O3'   A B  -2 "
        pdb=" P     C B  -1 "
      ideal   model   delta    sigma   weight residual
     120.20  116.13    4.07 1.50e+00 4.44e-01 7.36e+00
  ... (remaining 11447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.59: 4552
       21.59 -    43.18: 387
       43.18 -    64.77: 98
       64.77 -    86.36: 24
       86.36 -   107.95: 3
  Dihedral angle restraints: 5064
    sinusoidal: 2543
      harmonic: 2521
  Sorted by residual:
  dihedral pdb=" CG  ARG A 316 "
           pdb=" CD  ARG A 316 "
           pdb=" NE  ARG A 316 "
           pdb=" CZ  ARG A 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.60   44.60     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG A 579 "
           pdb=" CD  ARG A 579 "
           pdb=" NE  ARG A 579 "
           pdb=" CZ  ARG A 579 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.24  -43.24     2      1.50e+01 4.44e-03 1.00e+01
  dihedral pdb=" O5'   G B -12 "
           pdb=" C5'   G B -12 "
           pdb=" C4'   G B -12 "
           pdb=" C3'   G B -12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.00 -126.13  -58.87     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 5061 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1221
       0.069 -    0.138: 80
       0.138 -    0.207: 4
       0.207 -    0.276: 0
       0.276 -    0.345: 2
  Chirality restraints: 1307
  Sorted by residual:
  chirality pdb=" P     C B  -1 "
            pdb=" OP1   C B  -1 "
            pdb=" OP2   C B  -1 "
            pdb=" O5'   C B  -1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.75   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" P     G B   1 "
            pdb=" OP1   G B   1 "
            pdb=" OP2   G B   1 "
            pdb=" O5'   G B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.72   -0.31 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" C3'   C B  -1 "
            pdb=" C4'   C B  -1 "
            pdb=" O3'   C B  -1 "
            pdb=" C2'   C B  -1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.66    0.18 2.00e-01 2.50e+01 8.48e-01
  ... (remaining 1304 not shown)

  Planarity restraints: 1264
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  48 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.19e+00
        pdb=" N   PRO A  49 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A  49 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  49 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 480 "    0.033 5.00e-02 4.00e+02   4.95e-02 3.92e+00
        pdb=" N   PRO A 481 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 481 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 481 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 119 "   -0.013 2.00e-02 2.50e+03   1.05e-02 2.21e+00
        pdb=" CG  TYR A 119 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 119 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 119 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 119 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 119 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 119 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 119 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1261 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2260
        2.81 -     3.34: 6842
        3.34 -     3.86: 12012
        3.86 -     4.38: 14667
        4.38 -     4.90: 24688
  Nonbonded interactions: 60469
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 306 "
            pdb=" O2'   C B   2 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   SER A 368 "
            pdb=" OG  SER A 368 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" ND2 ASN A 276 "
            pdb=" OH  TYR A 296 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" NZ  LYS A 744 "
            pdb=" OP1   C B -26 "
     model   vdw
     2.364 3.120
  nonbonded pdb=" O   SER A 639 "
            pdb=" OG  SER A 639 "
     model   vdw
     2.368 3.040
  ... (remaining 60464 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=0.01 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:             2.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.190
  Find NCS groups from input model:        0.040
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
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   0.035   8305  Z= 0.144
  Angle     :  0.500   8.000  11452  Z= 0.277
  Chirality :  0.039   0.345   1307
  Planarity :  0.004   0.051   1264
  Dihedral  : 16.883 107.950   3434
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.39 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.07 (0.27), residues: 840
  helix: -0.16 (0.22), residues: 493
  sheet: -0.64 (1.69), residues: 11
  loop : -1.44 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 384 
 TYR   0.026   0.001   TYR A 119 
 PHE   0.025   0.001   PHE A 420 
 TRP   0.009   0.001   TRP A 752 
 HIS   0.007   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8305)
  covalent geometry    : angle       0.50008 (11452)
  hydrogen bonds       : bond        0.30039 (  361)
  hydrogen bonds       : angle       6.51112 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  615 CYS cc_start: 0.8085 (m) cc_final: 0.7877 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1234
  time to fit residues: 23.1696
Evaluate side-chains
  145 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.102198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.085447 restraints weight = 18934.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.46
r_work: 0.2810 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2809 r_free = 0.2809    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2809
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8305  Z= 0.213
  Angle     :  0.608   7.259  11452  Z= 0.321
  Chirality :  0.041   0.152   1307
  Planarity :  0.005   0.047   1264
  Dihedral  : 16.128 110.684   1682
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.63 %
    Favored  : 92.46 %
  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: -0.03 (0.29), residues: 840
  helix:  0.93 (0.24), residues: 507
  sheet:  0.60 (1.15), residues: 21
  loop : -1.65 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 384 
 TYR   0.023   0.002   TYR A 119 
 PHE   0.026   0.002   PHE A 420 
 TRP   0.012   0.002   TRP A 752 
 HIS   0.009   0.002   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 8305)
  covalent geometry    : angle       0.60791 (11452)
  hydrogen bonds       : bond        0.08994 (  361)
  hydrogen bonds       : angle       4.26819 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  186 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7592 (ttpp)
REVERT: A  317 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7464 (mm-30)
  outliers start: 6
  outliers final: 6
  residues processed: 135
  average time/residue: 0.1188
  time to fit residues: 19.9032
Evaluate side-chains
  139 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  421 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  835 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0170
   chunk 39 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.104281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.086433 restraints weight = 29144.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.05
r_work: 0.2792 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8305  Z= 0.157
  Angle     :  0.537   6.883  11452  Z= 0.283
  Chirality :  0.039   0.145   1307
  Planarity :  0.004   0.048   1264
  Dihedral  : 15.981 110.120   1682
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.19 %
    Favored  : 90.38 %
  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:  0.25 (0.29), residues: 840
  helix:  1.22 (0.24), residues: 508
  sheet:  0.79 (1.16), residues: 21
  loop : -1.69 (0.32), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 384 
 TYR   0.018   0.001   TYR A 119 
 PHE   0.024   0.002   PHE A 420 
 TRP   0.014   0.002   TRP A 752 
 HIS   0.006   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8305)
  covalent geometry    : angle       0.53745 (11452)
  hydrogen bonds       : bond        0.07213 (  361)
  hydrogen bonds       : angle       3.92648 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.263 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 135
  average time/residue: 0.1264
  time to fit residues: 21.2380
Evaluate side-chains
  140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  421 GLU
Chi-restraints excluded: chain A residue  705 GLU
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  835 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 61 optimal weight:    0.0670
   chunk 67 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0050
   chunk 84 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0980
   chunk 2 optimal weight:    0.5980
   chunk 49 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.2532

-------------------------------------------------------------------------------
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 = 0.3282 r_free = 0.3282 target = 0.106350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.087686 restraints weight = 36088.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 3.52
r_work: 0.2815 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8305  Z= 0.115
  Angle     :  0.495   5.813  11452  Z= 0.259
  Chirality :  0.036   0.148   1307
  Planarity :  0.004   0.049   1264
  Dihedral  : 15.807 110.276   1682
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.71 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.53 (0.29), residues: 840
  helix:  1.43 (0.24), residues: 510
  sheet:  0.81 (1.15), residues: 21
  loop : -1.56 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 384 
 TYR   0.010   0.001   TYR A 119 
 PHE   0.023   0.001   PHE A 420 
 TRP   0.013   0.001   TRP A 752 
 HIS   0.003   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 8305)
  covalent geometry    : angle       0.49546 (11452)
  hydrogen bonds       : bond        0.05610 (  361)
  hydrogen bonds       : angle       3.67200 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  601 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8089 (tp30)
  outliers start: 10
  outliers final: 5
  residues processed: 135
  average time/residue: 0.1189
  time to fit residues: 19.9768
Evaluate side-chains
  133 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  421 GLU
Chi-restraints excluded: chain A residue  755 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0070
   chunk 39 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 53 optimal weight:    0.1980
   chunk 62 optimal weight:    0.3980
   chunk 49 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.3598

-------------------------------------------------------------------------------
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 = 0.3271 r_free = 0.3271 target = 0.105578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.088490 restraints weight = 20654.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.61
r_work: 0.2854 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8305  Z= 0.128
  Angle     :  0.501   8.869  11452  Z= 0.262
  Chirality :  0.038   0.243   1307
  Planarity :  0.004   0.048   1264
  Dihedral  : 15.737 110.746   1682
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.92 %
    Favored  : 88.04 %
  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:  0.66 (0.29), residues: 840
  helix:  1.56 (0.24), residues: 510
  sheet:  0.91 (1.16), residues: 21
  loop : -1.58 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 384 
 TYR   0.012   0.001   TYR A 119 
 PHE   0.024   0.001   PHE A 420 
 TRP   0.011   0.001   TRP A 752 
 HIS   0.004   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8305)
  covalent geometry    : angle       0.50050 (11452)
  hydrogen bonds       : bond        0.05878 (  361)
  hydrogen bonds       : angle       3.63864 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  494 TYR cc_start: 0.8030 (m-10) cc_final: 0.7674 (m-10)
REVERT: A  601 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8026 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 133
  average time/residue: 0.1103
  time to fit residues: 18.4800
Evaluate side-chains
  136 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  755 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    0.2980
   chunk 62 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 44 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.105913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.087645 restraints weight = 33363.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 3.24
r_work: 0.2794 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8305  Z= 0.149
  Angle     :  0.511   7.795  11452  Z= 0.268
  Chirality :  0.038   0.205   1307
  Planarity :  0.004   0.047   1264
  Dihedral  : 15.732 110.242   1682
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.27 %
    Favored  : 88.04 %
  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:  0.65 (0.29), residues: 840
  helix:  1.59 (0.24), residues: 508
  sheet:  0.97 (1.18), residues: 21
  loop : -1.64 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 384 
 TYR   0.015   0.001   TYR A 119 
 PHE   0.022   0.001   PHE A 420 
 TRP   0.011   0.001   TRP A 752 
 HIS   0.005   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8305)
  covalent geometry    : angle       0.51067 (11452)
  hydrogen bonds       : bond        0.06277 (  361)
  hydrogen bonds       : angle       3.68968 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  494 TYR cc_start: 0.8146 (m-10) cc_final: 0.7750 (m-10)
REVERT: A  601 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8137 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 135
  average time/residue: 0.1025
  time to fit residues: 17.4297
Evaluate side-chains
  137 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  835 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3259 r_free = 0.3259 target = 0.104568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.087430 restraints weight = 24768.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.69
r_work: 0.2825 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8305  Z= 0.201
  Angle     :  0.566  11.456  11452  Z= 0.294
  Chirality :  0.041   0.196   1307
  Planarity :  0.004   0.046   1264
  Dihedral  : 15.752 109.857   1682
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.66 %
    Favored  : 87.91 %
  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:  0.46 (0.29), residues: 840
  helix:  1.44 (0.24), residues: 508
  sheet:  1.00 (1.20), residues: 21
  loop : -1.74 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 384 
 TYR   0.020   0.002   TYR A 119 
 PHE   0.025   0.002   PHE A 420 
 TRP   0.010   0.001   TRP A 752 
 HIS   0.007   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 8305)
  covalent geometry    : angle       0.56640 (11452)
  hydrogen bonds       : bond        0.07367 (  361)
  hydrogen bonds       : angle       3.84639 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.244 
Fit side-chains
  outliers start: 10
  outliers final: 10
  residues processed: 135
  average time/residue: 0.1185
  time to fit residues: 19.8870
Evaluate side-chains
  140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  835 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 45 optimal weight:    0.2980
   chunk 22 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3283 r_free = 0.3283 target = 0.106152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.089515 restraints weight = 20972.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 2.47
r_work: 0.2883 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8305  Z= 0.146
  Angle     :  0.523  10.223  11452  Z= 0.272
  Chirality :  0.038   0.184   1307
  Planarity :  0.004   0.047   1264
  Dihedral  : 15.722 110.309   1682
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.53 %
    Favored  : 87.91 %
  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:  0.58 (0.29), residues: 840
  helix:  1.54 (0.24), residues: 507
  sheet:  0.95 (1.19), residues: 21
  loop : -1.67 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 384 
 TYR   0.014   0.001   TYR A 119 
 PHE   0.025   0.001   PHE A 420 
 TRP   0.012   0.001   TRP A 752 
 HIS   0.005   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8305)
  covalent geometry    : angle       0.52325 (11452)
  hydrogen bonds       : bond        0.06358 (  361)
  hydrogen bonds       : angle       3.73839 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  186 LYS cc_start: 0.8432 (ptmt) cc_final: 0.8224 (ptmt)
  outliers start: 11
  outliers final: 11
  residues processed: 137
  average time/residue: 0.1224
  time to fit residues: 21.0208
Evaluate side-chains
  142 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  735 LYS
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  835 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.103956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.086204 restraints weight = 29195.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.99
r_work: 0.2811 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8305  Z= 0.193
  Angle     :  0.562  10.374  11452  Z= 0.292
  Chirality :  0.040   0.177   1307
  Planarity :  0.004   0.046   1264
  Dihedral  : 15.681 109.900   1682
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.92 %
    Favored  : 87.65 %
  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:  0.50 (0.29), residues: 840
  helix:  1.53 (0.24), residues: 502
  sheet:  0.88 (1.20), residues: 21
  loop : -1.75 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 384 
 TYR   0.019   0.001   TYR A 119 
 PHE   0.026   0.002   PHE A 420 
 TRP   0.011   0.001   TRP A 752 
 HIS   0.007   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8305)
  covalent geometry    : angle       0.56232 (11452)
  hydrogen bonds       : bond        0.07176 (  361)
  hydrogen bonds       : angle       3.85241 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  186 LYS cc_start: 0.8430 (ptmt) cc_final: 0.8180 (ptmt)
REVERT: A  494 TYR cc_start: 0.8203 (m-10) cc_final: 0.7798 (m-10)
  outliers start: 10
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1103
  time to fit residues: 19.2546
Evaluate side-chains
  144 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  835 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0070
   chunk 50 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0980
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0050
   overall best weight:    0.2812

-------------------------------------------------------------------------------
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 = 0.3311 r_free = 0.3311 target = 0.108058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.091052 restraints weight = 23460.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.63
r_work: 0.2877 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8305  Z= 0.118
  Angle     :  0.507  10.501  11452  Z= 0.262
  Chirality :  0.037   0.162   1307
  Planarity :  0.004   0.049   1264
  Dihedral  : 15.613 110.409   1682
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.31 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.69 (0.30), residues: 840
  helix:  1.58 (0.24), residues: 511
  sheet:  0.98 (1.19), residues: 21
  loop : -1.57 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 384 
 TYR   0.016   0.001   TYR A 642 
 PHE   0.026   0.001   PHE A 420 
 TRP   0.013   0.001   TRP A 752 
 HIS   0.006   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8305)
  covalent geometry    : angle       0.50739 (11452)
  hydrogen bonds       : bond        0.05575 (  361)
  hydrogen bonds       : angle       3.67446 ( 1035)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  185 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7907 (tpp80)
  outliers start: 8
  outliers final: 8
  residues processed: 135
  average time/residue: 0.1213
  time to fit residues: 20.4889
Evaluate side-chains
  139 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  585 LYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  755 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0670
   chunk 59 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0670
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.5056

-------------------------------------------------------------------------------
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 = 0.3276 r_free = 0.3276 target = 0.105709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.087800 restraints weight = 29211.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 3.02
r_work: 0.2838 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8305  Z= 0.149
  Angle     :  0.530  11.055  11452  Z= 0.274
  Chirality :  0.038   0.164   1307
  Planarity :  0.004   0.046   1264
  Dihedral  : 15.587 111.291   1682
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.18 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.64 (0.29), residues: 840
  helix:  1.58 (0.24), residues: 508
  sheet:  0.93 (1.18), residues: 21
  loop : -1.64 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 384 
 TYR   0.015   0.001   TYR A 642 
 PHE   0.025   0.001   PHE A 420 
 TRP   0.011   0.001   TRP A 752 
 HIS   0.005   0.001   HIS A 742 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8305)
  covalent geometry    : angle       0.53015 (11452)
  hydrogen bonds       : bond        0.06255 (  361)
  hydrogen bonds       : angle       3.73332 ( 1035)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1879.46 seconds
wall clock time: 32 minutes 51.27 seconds (1971.27 seconds total)