Starting phenix.real_space_refine
on Wed Jan 14 07:48:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sgh_40455/01_2026/8sgh_40455_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sgh_40455/01_2026/8sgh_40455.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sgh_40455/01_2026/8sgh_40455_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sgh_40455/01_2026/8sgh_40455_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sgh_40455/01_2026/8sgh_40455.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sgh_40455/01_2026/8sgh_40455.map"
  }
  resolution = 3.17
  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=   0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4371      2.51       5
     N    1141      2.21       5
     O    1267      1.98       5
     H    6836      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13667
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 13491
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 844, 13467
          Classifications: {'peptide': 844}
          Link IDs: {'PTRANS': 48, 'TRANS': 795}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 844, 13467
          Classifications: {'peptide': 844}
          Link IDs: {'PTRANS': 48, 'TRANS': 795}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 13583
    Chain: "B"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 176
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 3, 'TRANS': 8}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 213 " occ=0.52
      ... (46 atoms not shown)
      pdb="HH22BARG A 213 " occ=0.48
  Time building chain proxies: 3.99, per 1000 atoms: 0.29
  Number of scatterers: 13667
  At special positions: 0
  Unit cell: (104.58, 119.52, 83.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     O    1267      8.00
     N    1141      7.00
     C    4371      6.00
     H    6836      1.00
    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: 1.33
  Conformation dependent library (CDL) restraints added in 588.8 milliseconds
  

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1648

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 0 sheets defined
      86.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 30
    Processing helix  chain 'A' and resid 34 through 49
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 69 through 88
    Processing helix  chain 'A' and resid 89 through 91
      No H-bonds generated for 'chain 'A' and resid 89 through 91'
    Processing helix  chain 'A' and resid 92 through 106
    Processing helix  chain 'A' and resid 111 through 129
    Processing helix  chain 'A' and resid 130 through 134
    Processing helix  chain 'A' and resid 136 through 146
      removed outlier: 4.026A  pdb=" N   ASP A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 167
      removed outlier: 3.585A  pdb=" N   CYS A 153 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 173
    Processing helix  chain 'A' and resid 179 through 190
      Proline residue:  A 185  - end of helix
    Processing helix  chain 'A' and resid 191 through 193
      No H-bonds generated for 'chain 'A' and resid 191 through 193'
    Processing helix  chain 'A' and resid 195 through 208
      removed outlier: 3.754A  pdb=" N   GLN A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 219
    Processing helix  chain 'A' and resid 220 through 231
    Processing helix  chain 'A' and resid 236 through 254
    Processing helix  chain 'A' and resid 254 through 259
      removed outlier: 3.669A  pdb=" N   LEU A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 274
    Processing helix  chain 'A' and resid 277 through 294
      removed outlier: 3.558A  pdb=" N   PHE A 287 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TRP A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN A 294 " --> pdb=" O   THR A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
    Processing helix  chain 'A' and resid 304 through 316
      Proline residue:  A 310  - end of helix
    Processing helix  chain 'A' and resid 319 through 326
    Processing helix  chain 'A' and resid 372 through 380
      removed outlier: 3.667A  pdb=" N   ASP A 380 " --> pdb=" O   ASP A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 399
    Processing helix  chain 'A' and resid 402 through 414
      Proline residue:  A 408  - end of helix
      removed outlier: 3.543A  pdb=" N   GLU A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 432
    Processing helix  chain 'A' and resid 432 through 441
      removed outlier: 6.231A  pdb=" N   GLN A 438 " --> pdb=" O   GLU A 434 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 455
      Proline residue:  A 449  - end of helix
    Processing helix  chain 'A' and resid 459 through 473
    Processing helix  chain 'A' and resid 473 through 480
      removed outlier: 3.590A  pdb=" N   GLN A 480 " --> pdb=" O   TRP A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 498
      removed outlier: 3.747A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 520
    Processing helix  chain 'A' and resid 521 through 525
      Proline residue:  A 525  - end of helix
    Processing helix  chain 'A' and resid 526 through 541
      removed outlier: 3.800A  pdb=" N   SER A 539 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 540 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 561
      removed outlier: 3.825A  pdb=" N   LEU A 547 " --> pdb=" O   HIS A 543 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   ILE A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 565
    Processing helix  chain 'A' and resid 566 through 584
      Proline residue:  A 575  - end of helix
    Processing helix  chain 'A' and resid 590 through 606
      removed outlier: 3.901A  pdb=" N   LEU A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   SER A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 611
      Proline residue:  A 611  - end of helix
    Processing helix  chain 'A' and resid 612 through 637
      removed outlier: 3.981A  pdb=" N   VAL A 616 " --> pdb=" O   TYR A 612 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL A 624 " --> pdb=" O   CYS A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 664
    Processing helix  chain 'A' and resid 667 through 672
    Processing helix  chain 'A' and resid 675 through 686
    Processing helix  chain 'A' and resid 688 through 705
    Processing helix  chain 'A' and resid 706 through 711
      removed outlier: 3.683A  pdb=" N   VAL A 710 " --> pdb=" O   CYS A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 726
      Proline residue:  A 719  - end of helix
      removed outlier: 3.949A  pdb=" N   ASN A 726 " --> pdb=" O   GLY A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 748
    Processing helix  chain 'A' and resid 749 through 752
      removed outlier: 3.878A  pdb=" N   GLN A 752 " --> pdb=" O   ILE A 749 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 749 through 752'
    Processing helix  chain 'A' and resid 753 through 767
      removed outlier: 4.257A  pdb=" N   MET A 757 " --> pdb=" O   PRO A 753 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 758 " --> pdb=" O   TYR A 754 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   HIS A 760 " --> pdb=" O   PRO A 756 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   GLN A 761 " --> pdb=" O   MET A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 790
    Processing helix  chain 'A' and resid 790 through 795
      removed outlier: 4.089A  pdb=" N   VAL A 794 " --> pdb=" O   CYS A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 810
      removed outlier: 5.172A  pdb=" N   ARG A 803 " --> pdb=" O   GLN A 799 " (cutoff:3.500A)
      Proline residue:  A 804  - end of helix
    Processing helix  chain 'A' and resid 815 through 832
    Processing helix  chain 'A' and resid 833 through 838
      removed outlier: 3.674A  pdb=" N   ILE A 837 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   GLN A 838 " --> pdb=" O   GLY A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 839 through 849
    Processing helix  chain 'A' and resid 854 through 869
    Processing helix  chain 'A' and resid 876 through 882
    Processing helix  chain 'A' and resid 885 through 895

    458 hydrogen bonds defined for protein.
    1356 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: 3.14

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 6810
        1.03 -     1.23: 28
        1.23 -     1.42: 2805
        1.42 -     1.62: 4091
        1.62 -     1.82: 78
  Bond restraints: 13812
  Sorted by residual:
  bond pdb=" CG1 ILE A 714 "
       pdb=" CD1 ILE A 714 "
    ideal  model  delta    sigma   weight residual
    1.513  1.424  0.089 3.90e-02 6.57e+02 5.25e+00
  bond pdb=" N   MET B 204 "
       pdb=" CA  MET B 204 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.90e-02 2.77e+03 3.51e+00
  bond pdb=" CA  ILE A 441 "
       pdb=" CB  ILE A 441 "
    ideal  model  delta    sigma   weight residual
    1.537  1.546 -0.009 5.00e-03 4.00e+04 3.05e+00
  bond pdb=" CG  GLN A 752 "
       pdb=" HG2 GLN A 752 "
    ideal  model  delta    sigma   weight residual
    0.970  1.001 -0.031 2.00e-02 2.50e+03 2.40e+00
  bond pdb=" N   MET B 204 "
       pdb=" H   MET B 204 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.19e+00
  ... (remaining 13807 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 24627
        1.85 -     3.70: 398
        3.70 -     5.54: 52
        5.54 -     7.39: 6
        7.39 -     9.24: 2
  Bond angle restraints: 25085
  Sorted by residual:
  angle pdb=" CB  MET B 204 "
        pdb=" CG  MET B 204 "
        pdb=" SD  MET B 204 "
      ideal   model   delta    sigma   weight residual
     112.70  121.94   -9.24 3.00e+00 1.11e-01 9.49e+00
  angle pdb=" N   GLN A 752 "
        pdb=" CA  GLN A 752 "
        pdb=" C   GLN A 752 "
      ideal   model   delta    sigma   weight residual
     109.81  116.37   -6.56 2.21e+00 2.05e-01 8.81e+00
  angle pdb=" N   ILE A 182 "
        pdb=" CA  ILE A 182 "
        pdb=" C   ILE A 182 "
      ideal   model   delta    sigma   weight residual
     112.96  110.27    2.69 1.00e+00 1.00e+00 7.24e+00
  angle pdb=" N   GLN A 752 "
        pdb=" CA  GLN A 752 "
        pdb=" CB  GLN A 752 "
      ideal   model   delta    sigma   weight residual
     110.37  106.08    4.29 1.78e+00 3.16e-01 5.81e+00
  angle pdb=" C   ASP A 174 "
        pdb=" N   VAL A 175 "
        pdb=" CA  VAL A 175 "
      ideal   model   delta    sigma   weight residual
     120.69  123.91   -3.22 1.46e+00 4.69e-01 4.87e+00
  ... (remaining 25080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 5915
       17.38 -    34.75: 387
       34.75 -    52.13: 139
       52.13 -    69.51: 54
       69.51 -    86.88: 7
  Dihedral angle restraints: 6502
    sinusoidal: 3599
      harmonic: 2903
  Sorted by residual:
  dihedral pdb=" CD AARG A 213 "
           pdb=" NE AARG A 213 "
           pdb=" CZ AARG A 213 "
           pdb=" NH1AARG A 213 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -75.63   75.63     1      1.00e+01 1.00e-02 7.22e+01
  dihedral pdb=" CA  PHE A 729 "
           pdb=" C   PHE A 729 "
           pdb=" N   ILE A 730 "
           pdb=" CA  ILE A 730 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.94  -27.06     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  ARG A 813 "
           pdb=" C   ARG A 813 "
           pdb=" N   ASP A 814 "
           pdb=" CA  ASP A 814 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.47   23.53     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 6499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 899
       0.054 -    0.108: 174
       0.108 -    0.161: 8
       0.161 -    0.215: 1
       0.215 -    0.269: 1
  Chirality restraints: 1083
  Sorted by residual:
  chirality pdb=" CB  ILE A  79 "
            pdb=" CA  ILE A  79 "
            pdb=" CG1 ILE A  79 "
            pdb=" CG2 ILE A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CG  LEU A  58 "
            pdb=" CB  LEU A  58 "
            pdb=" CD1 LEU A  58 "
            pdb=" CD2 LEU A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.90e-01
  chirality pdb=" CA  PRO A 753 "
            pdb=" N   PRO A 753 "
            pdb=" C   PRO A 753 "
            pdb=" CB  PRO A 753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.82e-01
  ... (remaining 1080 not shown)

  Planarity restraints: 2026
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD AARG A 213 "   -0.975 9.50e-02 1.11e+02   3.26e-01 1.18e+02
        pdb=" NE AARG A 213 "    0.068 2.00e-02 2.50e+03
        pdb=" CZ AARG A 213 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1AARG A 213 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH2AARG A 213 "   -0.005 2.00e-02 2.50e+03
        pdb="HH11AARG A 213 "    0.002 2.00e-02 2.50e+03
        pdb="HH12AARG A 213 "    0.008 2.00e-02 2.50e+03
        pdb="HH21AARG A 213 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22AARG A 213 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 259 "    0.037 5.00e-02 4.00e+02   5.54e-02 4.90e+00
        pdb=" N   PRO A 260 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 260 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 260 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 891 "    0.185 9.50e-02 1.11e+02   6.18e-02 4.11e+00
        pdb=" NE  ARG A 891 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 891 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 891 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 891 "    0.002 2.00e-02 2.50e+03
        pdb="HH11 ARG A 891 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG A 891 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 891 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 891 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2023 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 718
        2.19 -     2.79: 28412
        2.79 -     3.39: 40504
        3.39 -     4.00: 49731
        4.00 -     4.60: 79054
  Nonbonded interactions: 198419
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 734 "
            pdb="HD21 ASN A 778 "
     model   vdw
     1.586 2.450
  nonbonded pdb=" O   LEU A 144 "
            pdb=" HG  SER A 147 "
     model   vdw
     1.624 2.450
  nonbonded pdb="HH11 ARG A 692 "
            pdb=" OD1 ASN A 724 "
     model   vdw
     1.700 2.450
  nonbonded pdb=" OD1 ASP A  16 "
            pdb=" H   GLY A  19 "
     model   vdw
     1.711 2.450
  nonbonded pdb=" OE1 GLU A 278 "
            pdb=" H   GLU A 278 "
     model   vdw
     1.724 2.450
  ... (remaining 198414 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=0.48 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:             16.740
  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:             0.090
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.040
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
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   0.089   6976  Z= 0.158
  Angle     :  0.715   9.240   9473  Z= 0.370
  Chirality :  0.041   0.269   1083
  Planarity :  0.015   0.437   1224
  Dihedral  : 13.655  86.883   2633
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  7.01 %
    Favored  : 92.73 %
  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: -0.17 (0.28), residues: 851
  helix: -0.10 (0.19), residues: 643
  sheet:  None (None), residues: 0
  loop :  0.42 (0.47), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 254 
 TYR   0.016   0.002   TYR A 550 
 PHE   0.018   0.002   PHE A 868 
 TRP   0.028   0.003   TRP A 581 
 HIS   0.006   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6976)
  covalent geometry    : angle       0.71542 ( 9473)
  hydrogen bonds       : bond        0.10951 (  458)
  hydrogen bonds       : angle       5.66341 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  40 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.9595 (mt) cc_final: 0.9303 (tt)
  outliers start: 2
  outliers final: 1
  residues processed: 40
  average time/residue: 0.1263
  time to fit residues: 7.9896
Evaluate side-chains
  39 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0020
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.9794

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

Flipped N/Q/H residues before XYZ refinement:
A 505 GLN
A 545 ASN
A 726 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.083811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.055215 restraints weight = 107248.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 4.64
r_work: 0.2980 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6976  Z= 0.134
  Angle     :  0.605   5.745   9473  Z= 0.311
  Chirality :  0.037   0.150   1083
  Planarity :  0.006   0.099   1224
  Dihedral  :  5.254  46.135    911
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  7.40 %
    Favored  : 92.21 %
  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:  0.97 (0.29), residues: 851
  helix:  0.71 (0.20), residues: 651
  sheet:  None (None), residues: 0
  loop :  0.89 (0.49), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 768 
 TYR   0.012   0.001   TYR A 526 
 PHE   0.021   0.001   PHE A 868 
 TRP   0.022   0.002   TRP A 581 
 HIS   0.003   0.001   HIS A 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6976)
  covalent geometry    : angle       0.60544 ( 9473)
  hydrogen bonds       : bond        0.04508 (  458)
  hydrogen bonds       : angle       4.53382 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  43 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.9586 (mt) cc_final: 0.9355 (tt)
  outliers start: 3
  outliers final: 1
  residues processed: 43
  average time/residue: 0.1087
  time to fit residues: 7.5406
Evaluate side-chains
  37 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0010
   chunk 28 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.083775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.055325 restraints weight = 99217.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 4.52
r_work: 0.3003 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6976  Z= 0.107
  Angle     :  0.547   5.096   9473  Z= 0.277
  Chirality :  0.036   0.132   1083
  Planarity :  0.004   0.043   1224
  Dihedral  :  4.538  26.041    909
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  7.53 %
    Favored  : 92.21 %
  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:  1.66 (0.30), residues: 851
  helix:  1.20 (0.21), residues: 651
  sheet:  None (None), residues: 0
  loop :  1.15 (0.49), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 692 
 TYR   0.009   0.001   TYR A 526 
 PHE   0.021   0.001   PHE A 868 
 TRP   0.017   0.001   TRP A 581 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6976)
  covalent geometry    : angle       0.54705 ( 9473)
  hydrogen bonds       : bond        0.03756 (  458)
  hydrogen bonds       : angle       4.15826 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  38 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.9557 (mt) cc_final: 0.9325 (tt)
REVERT: A  747 MET cc_start: 0.8472 (ttm) cc_final: 0.8057 (ttm)
REVERT: A  751 MET cc_start: 0.9401 (ttp) cc_final: 0.9181 (ttp)
REVERT: A  797 MET cc_start: 0.7321 (mmm) cc_final: 0.7120 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 38
  average time/residue: 0.1247
  time to fit residues: 7.6369
Evaluate side-chains
  37 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  157 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 84 optimal weight:    0.0980
   chunk 7 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 74 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:    0.2980
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.083665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.055687 restraints weight = 76634.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 4.02
r_work: 0.3026 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3014
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6976  Z= 0.098
  Angle     :  0.523   5.858   9473  Z= 0.262
  Chirality :  0.035   0.116   1083
  Planarity :  0.004   0.038   1224
  Dihedral  :  4.339  25.869    909
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  7.27 %
    Favored  : 92.21 %
  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:  2.02 (0.30), residues: 851
  helix:  1.50 (0.21), residues: 657
  sheet:  None (None), residues: 0
  loop :  1.12 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 692 
 TYR   0.008   0.001   TYR A 526 
 PHE   0.019   0.001   PHE A 868 
 TRP   0.014   0.001   TRP A 581 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 6976)
  covalent geometry    : angle       0.52253 ( 9473)
  hydrogen bonds       : bond        0.03353 (  458)
  hydrogen bonds       : angle       3.98267 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  41 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.9552 (mt) cc_final: 0.9334 (tt)
REVERT: A  747 MET cc_start: 0.8425 (ttm) cc_final: 0.8018 (ttm)
REVERT: A  751 MET cc_start: 0.9382 (ttp) cc_final: 0.9160 (ttp)
REVERT: B  204 MET cc_start: 0.6486 (tmm) cc_final: 0.5827 (tmm)
  outliers start: 4
  outliers final: 1
  residues processed: 41
  average time/residue: 0.1173
  time to fit residues: 7.7168
Evaluate side-chains
  35 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 13 optimal weight:    0.3980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 HIS ** 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 = 0.3849 r_free = 0.3849 target = 0.083410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.055132 restraints weight = 82261.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 4.19
r_work: 0.3011 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6976  Z= 0.109
  Angle     :  0.514   5.237   9473  Z= 0.258
  Chirality :  0.035   0.106   1083
  Planarity :  0.004   0.052   1224
  Dihedral  :  4.208  25.896    909
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  7.27 %
    Favored  : 92.08 %
  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:  2.23 (0.30), residues: 851
  helix:  1.66 (0.21), residues: 670
  sheet:  None (None), residues: 0
  loop :  1.08 (0.50), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 768 
 TYR   0.010   0.001   TYR A 526 
 PHE   0.019   0.001   PHE A 868 
 TRP   0.012   0.001   TRP A 581 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6976)
  covalent geometry    : angle       0.51399 ( 9473)
  hydrogen bonds       : bond        0.03328 (  458)
  hydrogen bonds       : angle       3.91881 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  42 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.9539 (mt) cc_final: 0.9337 (tt)
REVERT: A  747 MET cc_start: 0.8438 (ttm) cc_final: 0.8034 (ttm)
REVERT: B  204 MET cc_start: 0.6440 (tmm) cc_final: 0.5885 (tmm)
  outliers start: 5
  outliers final: 3
  residues processed: 42
  average time/residue: 0.1311
  time to fit residues: 8.8868
Evaluate side-chains
  39 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  531 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 36 optimal weight:    0.1980
   chunk 70 optimal weight:    0.4980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.083807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.055423 restraints weight = 92965.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 4.39
r_work: 0.3018 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   6976  Z= 0.091
  Angle     :  0.498   5.444   9473  Z= 0.247
  Chirality :  0.034   0.107   1083
  Planarity :  0.004   0.038   1224
  Dihedral  :  4.070  25.619    909
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  6.75 %
    Favored  : 92.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.46 (0.30), residues: 851
  helix:  1.86 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop :  1.07 (0.49), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 692 
 TYR   0.007   0.001   TYR A 318 
 PHE   0.019   0.001   PHE A 868 
 TRP   0.012   0.001   TRP A 581 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 6976)
  covalent geometry    : angle       0.49818 ( 9473)
  hydrogen bonds       : bond        0.03057 (  458)
  hydrogen bonds       : angle       3.77391 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  42 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  747 MET cc_start: 0.8450 (ttm) cc_final: 0.8062 (ttm)
REVERT: B  204 MET cc_start: 0.6415 (tmm) cc_final: 0.5922 (tmm)
  outliers start: 6
  outliers final: 4
  residues processed: 41
  average time/residue: 0.1242
  time to fit residues: 8.2010
Evaluate side-chains
  38 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  797 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 HIS ** 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 = 0.3852 r_free = 0.3852 target = 0.083493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.055119 restraints weight = 98522.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 4.47
r_work: 0.3006 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6976  Z= 0.103
  Angle     :  0.501   5.240   9473  Z= 0.250
  Chirality :  0.034   0.107   1083
  Planarity :  0.004   0.040   1224
  Dihedral  :  4.022  25.829    909
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  7.27 %
    Favored  : 92.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.50 (0.30), residues: 851
  helix:  1.88 (0.21), residues: 663
  sheet:  None (None), residues: 0
  loop :  1.10 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 768 
 TYR   0.010   0.001   TYR A  51 
 PHE   0.018   0.001   PHE A 868 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6976)
  covalent geometry    : angle       0.50078 ( 9473)
  hydrogen bonds       : bond        0.03079 (  458)
  hydrogen bonds       : angle       3.79137 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  37 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  747 MET cc_start: 0.8450 (ttm) cc_final: 0.8073 (ttm)
REVERT: B  204 MET cc_start: 0.6424 (tmm) cc_final: 0.5967 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 37
  average time/residue: 0.1327
  time to fit residues: 7.8590
Evaluate side-chains
  36 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   75 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 76 optimal weight:   20.0000
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.081938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.053313 restraints weight = 95552.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 4.47
r_work: 0.2954 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6976  Z= 0.187
  Angle     :  0.548   5.570   9473  Z= 0.280
  Chirality :  0.036   0.114   1083
  Planarity :  0.004   0.037   1224
  Dihedral  :  4.119  25.826    909
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  7.14 %
    Favored  : 92.21 %
  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:  2.25 (0.30), residues: 851
  helix:  1.73 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.88 (0.49), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.015   0.001   TYR A 473 
 PHE   0.017   0.001   PHE A 868 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.003   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 6976)
  covalent geometry    : angle       0.54768 ( 9473)
  hydrogen bonds       : bond        0.03583 (  458)
  hydrogen bonds       : angle       4.02761 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  40 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  747 MET cc_start: 0.8495 (ttm) cc_final: 0.8108 (ttm)
REVERT: B  204 MET cc_start: 0.6516 (tmm) cc_final: 0.6093 (tmm)
  outliers start: 5
  outliers final: 4
  residues processed: 40
  average time/residue: 0.1249
  time to fit residues: 7.8669
Evaluate side-chains
  39 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  157 PHE
Chi-restraints excluded: chain A residue  531 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 42 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 48 optimal weight:    0.2980
   chunk 68 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0070
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   overall best weight:    1.0002

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 HIS ** 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 = 0.3838 r_free = 0.3838 target = 0.082727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.053915 restraints weight = 106692.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 4.70
r_work: 0.2966 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6976  Z= 0.112
  Angle     :  0.509   5.468   9473  Z= 0.254
  Chirality :  0.035   0.125   1083
  Planarity :  0.004   0.037   1224
  Dihedral  :  4.035  25.723    909
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  7.40 %
    Favored  : 92.21 %
  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:  2.47 (0.30), residues: 851
  helix:  1.88 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.97 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 399 
 TYR   0.007   0.001   TYR A 318 
 PHE   0.018   0.001   PHE A 868 
 TRP   0.012   0.001   TRP A 581 
 HIS   0.002   0.001   HIS A 709 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6976)
  covalent geometry    : angle       0.50948 ( 9473)
  hydrogen bonds       : bond        0.03239 (  458)
  hydrogen bonds       : angle       3.83668 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  38 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  747 MET cc_start: 0.8490 (ttm) cc_final: 0.8108 (ttm)
REVERT: B  204 MET cc_start: 0.6516 (tmm) cc_final: 0.6099 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 0.1275
  time to fit residues: 7.7218
Evaluate side-chains
  37 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   75 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0870
   chunk 75 optimal weight:    9.9990
   chunk 13 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 HIS ** 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 = 0.3862 r_free = 0.3862 target = 0.083686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.055550 restraints weight = 88332.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 4.30
r_work: 0.3013 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6976  Z= 0.092
  Angle     :  0.493   6.345   9473  Z= 0.243
  Chirality :  0.034   0.115   1083
  Planarity :  0.004   0.032   1224
  Dihedral  :  3.944  25.486    909
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  7.40 %
    Favored  : 92.21 %
  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:  2.69 (0.30), residues: 851
  helix:  2.05 (0.21), residues: 663
  sheet:  None (None), residues: 0
  loop :  0.97 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 399 
 TYR   0.007   0.001   TYR A 318 
 PHE   0.017   0.001   PHE A 868 
 TRP   0.012   0.001   TRP A 581 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 6976)
  covalent geometry    : angle       0.49345 ( 9473)
  hydrogen bonds       : bond        0.02962 (  458)
  hydrogen bonds       : angle       3.68623 ( 1356)

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  372 is missing expected H atoms. Skipping.
Residue THR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue SER  379 is missing expected H atoms. Skipping.
Evaluate side-chains
  38 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 MET cc_start: 0.6443 (tmm) cc_final: 0.6031 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 0.1340
  time to fit residues: 8.1516
Evaluate side-chains
  37 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   75 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0980
   chunk 73 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 709 HIS ** 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 = 0.3856 r_free = 0.3856 target = 0.083593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.055345 restraints weight = 89848.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 4.32
r_work: 0.3015 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3013
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3013
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6976  Z= 0.091
  Angle     :  0.492   5.564   9473  Z= 0.242
  Chirality :  0.034   0.117   1083
  Planarity :  0.004   0.030   1224
  Dihedral  :  3.902  25.648    909
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  7.66 %
    Favored  : 92.08 %
  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:  2.72 (0.30), residues: 851
  helix:  2.08 (0.21), residues: 663
  sheet:  None (None), residues: 0
  loop :  0.99 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 768 
 TYR   0.009   0.001   TYR A  51 
 PHE   0.017   0.001   PHE A 868 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 6976)
  covalent geometry    : angle       0.49180 ( 9473)
  hydrogen bonds       : bond        0.02923 (  458)
  hydrogen bonds       : angle       3.67205 ( 1356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4531.60 seconds
wall clock time: 77 minutes 31.19 seconds (4651.19 seconds total)