Starting phenix.real_space_refine
on Tue Mar  3 13:24:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oua_20200/03_2026/6oua_20200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oua_20200/03_2026/6oua_20200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oua_20200/03_2026/6oua_20200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oua_20200/03_2026/6oua_20200.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oua_20200/03_2026/6oua_20200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oua_20200/03_2026/6oua_20200.map"
  }
  resolution = 4.18
  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: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    3340      2.51       5
     N     885      2.21       5
     O     958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5208
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "I"
      Number of atoms: 3105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3105
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 12, 'TRANS': 369}
    Chain: "H"
      Number of atoms: 1100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1100
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "K"
      Number of atoms: 1003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1003
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
  Time building chain proxies: 1.06, per 1000 atoms: 0.20
  Number of scatterers: 5208
  At special positions: 0
  Unit cell: (111.35, 88.4, 77.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O     958      8.00
     N     885      7.00
     C    3340      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: 0.28
  Conformation dependent library (CDL) restraints added in 296.3 milliseconds
  

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1240

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 0 sheets defined
      62.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'I' and resid 342 through 348
      removed outlier: 4.690A  pdb=" N   ASN I 348 " --> pdb=" O   ILE I 344 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 354 through 368
      removed outlier: 3.809A  pdb=" N   GLU I 358 " --> pdb=" O   SER I 354 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE I 361 " --> pdb=" O   TYR I 357 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE I 368 " --> pdb=" O   LEU I 364 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 374 through 377
      removed outlier: 4.248A  pdb=" N   GLU I 377 " --> pdb=" O   THR I 374 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 374 through 377'
    Processing helix  chain 'I' and resid 378 through 386
    Processing helix  chain 'I' and resid 389 through 397
      removed outlier: 5.069A  pdb=" N   ARG I 395 " --> pdb=" O   LYS I 391 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE I 396 " --> pdb=" O   LEU I 392 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ILE I 397 " --> pdb=" O   SER I 393 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 412 through 420
    Processing helix  chain 'I' and resid 432 through 448
      removed outlier: 3.922A  pdb=" N   VAL I 437 " --> pdb=" O   ARG I 433 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   LYS I 438 " --> pdb=" O   GLU I 434 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   TRP I 446 " --> pdb=" O   SER I 442 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR I 448 " --> pdb=" O   PHE I 444 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 458 through 475
      removed outlier: 4.032A  pdb=" N   THR I 470 " --> pdb=" O   LEU I 466 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN I 471 " --> pdb=" O   GLN I 467 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ASP I 475 " --> pdb=" O   ASN I 471 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 478 through 494
      removed outlier: 3.944A  pdb=" N   THR I 484 " --> pdb=" O   ALA I 480 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   HIS I 487 " --> pdb=" O   LEU I 483 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ASP I 488 " --> pdb=" O   THR I 484 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 508 through 525
      removed outlier: 4.190A  pdb=" N   LEU I 519 " --> pdb=" O   SER I 515 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN I 525 " --> pdb=" O   GLN I 521 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 531 through 535
    Processing helix  chain 'I' and resid 550 through 565
      removed outlier: 3.908A  pdb=" N   LEU I 554 " --> pdb=" O   ASP I 550 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU I 561 " --> pdb=" O   ALA I 557 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 578 through 593
      removed outlier: 4.246A  pdb=" N   ASN I 590 " --> pdb=" O   MET I 586 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 608 through 613
    Processing helix  chain 'I' and resid 614 through 618
      removed outlier: 3.821A  pdb=" N   ASN I 617 " --> pdb=" O   ILE I 614 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU I 618 " --> pdb=" O   LEU I 615 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 614 through 618'
    Processing helix  chain 'I' and resid 625 through 630
      removed outlier: 3.868A  pdb=" N   LYS I 629 " --> pdb=" O   PHE I 625 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   PHE I 630 " --> pdb=" O   LYS I 626 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 625 through 630'
    Processing helix  chain 'I' and resid 641 through 653
      removed outlier: 3.955A  pdb=" N   ARG I 649 " --> pdb=" O   ILE I 645 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 668 through 675
    Processing helix  chain 'I' and resid 692 through 697
    Processing helix  chain 'I' and resid 697 through 705
      removed outlier: 4.891A  pdb=" N   HIS I 703 " --> pdb=" O   LYS I 699 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER I 705 " --> pdb=" O   LEU I 701 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 9 through 39
      removed outlier: 3.669A  pdb=" N   ILE H  28 " --> pdb=" O   ARG H  24 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ASP H  31 " --> pdb=" O   LEU H  27 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   TYR H  34 " --> pdb=" O   LEU H  30 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU H  35 " --> pdb=" O   ASP H  31 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   HIS H  39 " --> pdb=" O   LEU H  35 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 49 through 66
      removed outlier: 4.148A  pdb=" N   ARG H  56 " --> pdb=" O   LEU H  52 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   HIS H  57 " --> pdb=" O   LEU H  53 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE H  61 " --> pdb=" O   HIS H  57 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR H  66 " --> pdb=" O   ASN H  62 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 90
    Processing helix  chain 'H' and resid 102 through 129
      removed outlier: 3.802A  pdb=" N   SER H 108 " --> pdb=" O   LEU H 104 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLN H 113 " --> pdb=" O   SER H 109 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ARG H 118 " --> pdb=" O   LEU H 114 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLU H 120 " --> pdb=" O   GLU H 116 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   ARG H 121 " --> pdb=" O   SER H 117 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU H 123 " --> pdb=" O   ALA H 119 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 130 through 132
      No H-bonds generated for 'chain 'H' and resid 130 through 132'
    Processing helix  chain 'K' and resid 6 through 32
      removed outlier: 4.036A  pdb=" N   LYS K  13 " --> pdb=" O   ASP K   9 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLN K  18 " --> pdb=" O   ASN K  14 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 34 through 38
      removed outlier: 3.693A  pdb=" N   THR K  37 " --> pdb=" O   ASP K  34 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS K  38 " --> pdb=" O   GLU K  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 34 through 38'
    Processing helix  chain 'K' and resid 49 through 57
      removed outlier: 3.515A  pdb=" N   THR K  54 " --> pdb=" O   SER K  50 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   GLU K  55 " --> pdb=" O   GLU K  51 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU K  56 " --> pdb=" O   VAL K  52 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU K  57 " --> pdb=" O   PHE K  53 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 71 through 75
      removed outlier: 3.554A  pdb=" N   LEU K  74 " --> pdb=" O   GLY K  71 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 80 through 107
      removed outlier: 4.432A  pdb=" N   SER K  91 " --> pdb=" O   SER K  87 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LEU K 105 " --> pdb=" O   LYS K 101 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU K 106 " --> pdb=" O   ALA K 102 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 109 through 128
      removed outlier: 3.595A  pdb=" N   ASP K 113 " --> pdb=" O   ASN K 109 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LYS K 115 " --> pdb=" O   ASN K 111 " (cutoff:3.500A)

    218 hydrogen bonds defined for protein.
    645 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: 0.61

  Time building geometry restraints manager: 0.40 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: 1546
        1.34 -     1.45: 867
        1.45 -     1.57: 2850
        1.57 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 5305
  Sorted by residual:
  bond pdb=" CA  PHE I 630 "
       pdb=" CB  PHE I 630 "
    ideal  model  delta    sigma   weight residual
    1.524  1.480  0.044 1.33e-02 5.65e+03 1.08e+01
  bond pdb=" CB  GLU H  16 "
       pdb=" CG  GLU H  16 "
    ideal  model  delta    sigma   weight residual
    1.520  1.444  0.076 3.00e-02 1.11e+03 6.49e+00
  bond pdb=" C   LYS K  46 "
       pdb=" N   PRO K  47 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.053 2.34e-02 1.83e+03 5.04e+00
  bond pdb=" N   ASP I 351 "
       pdb=" CA  ASP I 351 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.028 1.29e-02 6.01e+03 4.76e+00
  bond pdb=" CB  LEU I 466 "
       pdb=" CG  LEU I 466 "
    ideal  model  delta    sigma   weight residual
    1.530  1.490  0.040 2.00e-02 2.50e+03 4.02e+00
  ... (remaining 5300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.18: 6900
        3.18 -     6.35: 206
        6.35 -     9.53: 46
        9.53 -    12.71: 6
       12.71 -    15.88: 1
  Bond angle restraints: 7159
  Sorted by residual:
  angle pdb=" C   CYS I 401 "
        pdb=" N   ASN I 402 "
        pdb=" CA  ASN I 402 "
      ideal   model   delta    sigma   weight residual
     121.54  130.86   -9.32 1.91e+00 2.74e-01 2.38e+01
  angle pdb=" C   ASP I 389 "
        pdb=" N   ASN I 390 "
        pdb=" CA  ASN I 390 "
      ideal   model   delta    sigma   weight residual
     121.54  130.30   -8.76 1.91e+00 2.74e-01 2.11e+01
  angle pdb=" CA  LEU H  90 "
        pdb=" CB  LEU H  90 "
        pdb=" CG  LEU H  90 "
      ideal   model   delta    sigma   weight residual
     116.30  132.18  -15.88 3.50e+00 8.16e-02 2.06e+01
  angle pdb=" CA  ILE I 620 "
        pdb=" CB  ILE I 620 "
        pdb=" CG2 ILE I 620 "
      ideal   model   delta    sigma   weight residual
     110.50  118.10   -7.60 1.70e+00 3.46e-01 2.00e+01
  angle pdb=" C   HIS H  41 "
        pdb=" N   ALA H  42 "
        pdb=" CA  ALA H  42 "
      ideal   model   delta    sigma   weight residual
     121.54  130.01   -8.47 1.91e+00 2.74e-01 1.97e+01
  ... (remaining 7154 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.45: 2859
       15.45 -    30.90: 297
       30.90 -    46.36: 71
       46.36 -    61.81: 14
       61.81 -    77.26: 6
  Dihedral angle restraints: 3247
    sinusoidal: 1354
      harmonic: 1893
  Sorted by residual:
  dihedral pdb=" CA  ILE I 636 "
           pdb=" C   ILE I 636 "
           pdb=" N   PRO I 637 "
           pdb=" CA  PRO I 637 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.27  -60.73     0      5.00e+00 4.00e-02 1.48e+02
  dihedral pdb=" CA  ASP K  68 "
           pdb=" C   ASP K  68 "
           pdb=" N   PRO K  69 "
           pdb=" CA  PRO K  69 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.87   27.13     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  TYR I 340 "
           pdb=" C   TYR I 340 "
           pdb=" N   SER I 341 "
           pdb=" CA  SER I 341 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.12   25.88     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 3244 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 679
       0.088 -    0.177: 125
       0.177 -    0.265: 17
       0.265 -    0.353: 2
       0.353 -    0.442: 1
  Chirality restraints: 824
  Sorted by residual:
  chirality pdb=" CB  ILE K  36 "
            pdb=" CA  ILE K  36 "
            pdb=" CG1 ILE K  36 "
            pdb=" CG2 ILE K  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.44 2.00e-01 2.50e+01 4.88e+00
  chirality pdb=" CB  ILE I 636 "
            pdb=" CA  ILE I 636 "
            pdb=" CG1 ILE I 636 "
            pdb=" CG2 ILE I 636 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.98   -0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CB  ILE H  44 "
            pdb=" CA  ILE H  44 "
            pdb=" CG1 ILE H  44 "
            pdb=" CG2 ILE H  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 821 not shown)

  Planarity restraints: 898
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE I 636 "    0.060 5.00e-02 4.00e+02   9.20e-02 1.36e+01
        pdb=" N   PRO I 637 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO I 637 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO I 637 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP K  68 "    0.044 5.00e-02 4.00e+02   6.54e-02 6.85e+00
        pdb=" N   PRO K  69 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO K  69 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO K  69 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP I 550 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO I 551 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO I 551 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO I 551 "    0.035 5.00e-02 4.00e+02
  ... (remaining 895 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1512
        2.82 -     3.34: 4911
        3.34 -     3.86: 7947
        3.86 -     4.38: 8702
        4.38 -     4.90: 14301
  Nonbonded interactions: 37373
  Sorted by model distance:
  nonbonded pdb=" O   LEU I 552 "
            pdb=" OG  SER I 555 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" NH2 ARG H 118 "
            pdb=" OE1 GLN K 107 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" OD1 ASP I 549 "
            pdb=" OG1 THR I 634 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OD2 ASP H  31 "
            pdb=" NH2 ARG H  56 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" NH2 ARG H  71 "
            pdb=" OD2 ASP K  68 "
     model   vdw
     2.331 3.120
  ... (remaining 37368 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.010
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
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      :  0.008   0.076   5305  Z= 0.336
  Angle     :  1.373  15.883   7159  Z= 0.694
  Chirality :  0.071   0.442    824
  Planarity :  0.008   0.092    898
  Dihedral  : 13.972  77.258   2007
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 17.43 %
    Favored  : 82.25 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 10.42 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -5.89 (0.23), residues: 631
  helix: -3.43 (0.17), residues: 371
  sheet:  None (None), residues: 0
  loop : -4.59 (0.31), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I 697 
 TYR   0.022   0.003   TYR I 464 
 PHE   0.033   0.003   PHE I 604 
 TRP   0.025   0.004   TRP I 446 
 HIS   0.007   0.002   HIS I 678 

Details of bonding type rmsd
  covalent geometry    : bond        0.00762 ( 5305)
  covalent geometry    : angle       1.37299 ( 7159)
  hydrogen bonds       : bond        0.15207 (  218)
  hydrogen bonds       : angle       6.75744 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  367 CYS cc_start: 0.8447 (p) cc_final: 0.8057 (p)
REVERT: I  668 GLU cc_start: 0.8605 (pp20) cc_final: 0.8396 (pp20)
REVERT: I  677 HIS cc_start: 0.8516 (t70) cc_final: 0.8258 (t-90)
REVERT: H   34 TYR cc_start: 0.8464 (t80) cc_final: 0.8257 (t80)
REVERT: H   99 GLU cc_start: 0.7937 (pm20) cc_final: 0.7598 (mt-10)
REVERT: H  100 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7817 (tm)
REVERT: K   38 LYS cc_start: 0.8380 (pttp) cc_final: 0.8048 (mttm)
REVERT: K   77 ASN cc_start: 0.8172 (t0) cc_final: 0.7665 (t0)
  outliers start: 14
  outliers final: 4
  residues processed: 147
  average time/residue: 0.0761
  time to fit residues: 14.1255
Evaluate side-chains
  103 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
I 371 GLN
I 501 ASN
I 581 GLN
I 666 ASN
H  13 GLN
H  58 GLN
** H  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 107 GLN
H 111 HIS
K 107 GLN
K 123 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.139582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.118007 restraints weight = 9491.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.121100 restraints weight = 5912.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.123223 restraints weight = 4154.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124713 restraints weight = 3212.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.125510 restraints weight = 2668.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5305  Z= 0.146
  Angle     :  0.778   7.173   7159  Z= 0.404
  Chirality :  0.048   0.225    824
  Planarity :  0.006   0.100    898
  Dihedral  :  6.866  51.837    682
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.15 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.87 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -4.38 (0.28), residues: 631
  helix: -2.02 (0.23), residues: 376
  sheet:  None (None), residues: 0
  loop : -4.31 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 119 
 TYR   0.013   0.002   TYR I 584 
 PHE   0.022   0.002   PHE I 604 
 TRP   0.010   0.001   TRP I 472 
 HIS   0.002   0.001   HIS H  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5305)
  covalent geometry    : angle       0.77777 ( 7159)
  hydrogen bonds       : bond        0.04335 (  218)
  hydrogen bonds       : angle       4.73823 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  434 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7991 (mp0)
REVERT: I  668 GLU cc_start: 0.8746 (pp20) cc_final: 0.8497 (pp20)
REVERT: I  677 HIS cc_start: 0.8145 (t70) cc_final: 0.7674 (t-90)
REVERT: H   37 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7350 (mtt180)
REVERT: H   99 GLU cc_start: 0.7813 (pm20) cc_final: 0.7342 (mt-10)
REVERT: K   35 GLU cc_start: 0.8612 (tp30) cc_final: 0.7721 (tp30)
REVERT: K   77 ASN cc_start: 0.8124 (t0) cc_final: 0.7661 (t0)
REVERT: K   93 MET cc_start: 0.7293 (mmp) cc_final: 0.6742 (ttm)
REVERT: K  103 MET cc_start: 0.7366 (mmp) cc_final: 0.6464 (tmm)
REVERT: K  128 MET cc_start: 0.6235 (mpp) cc_final: 0.5508 (ptp)
  outliers start: 2
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0723
  time to fit residues: 14.0545
Evaluate side-chains
  102 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
I 338 HIS
** H  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 122 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.146938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.127056 restraints weight = 8728.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.130274 restraints weight = 5344.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.132514 restraints weight = 3677.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.133983 restraints weight = 2777.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.135124 restraints weight = 2271.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5305  Z= 0.138
  Angle     :  0.750  10.365   7159  Z= 0.382
  Chirality :  0.047   0.304    824
  Planarity :  0.005   0.096    898
  Dihedral  :  6.322  49.045    682
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.84 %
    Favored  : 87.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -3.64 (0.31), residues: 631
  helix: -1.37 (0.25), residues: 388
  sheet:  None (None), residues: 0
  loop : -4.20 (0.35), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 118 
 TYR   0.021   0.002   TYR I 619 
 PHE   0.018   0.001   PHE I 604 
 TRP   0.012   0.001   TRP K  89 
 HIS   0.001   0.000   HIS H  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5305)
  covalent geometry    : angle       0.74989 ( 7159)
  hydrogen bonds       : bond        0.03776 (  218)
  hydrogen bonds       : angle       4.45287 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  434 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7946 (mp0)
REVERT: I  668 GLU cc_start: 0.8690 (pp20) cc_final: 0.8433 (pp20)
REVERT: H   37 ARG cc_start: 0.7983 (ttm170) cc_final: 0.7119 (mtt180)
REVERT: H   52 LEU cc_start: 0.8708 (mm) cc_final: 0.8271 (tp)
REVERT: H   78 ASN cc_start: 0.6072 (m-40) cc_final: 0.5865 (m-40)
REVERT: H   80 ASN cc_start: 0.6948 (t0) cc_final: 0.6627 (t0)
REVERT: H   99 GLU cc_start: 0.7678 (pm20) cc_final: 0.7444 (mt-10)
REVERT: K   21 ASN cc_start: 0.6973 (m-40) cc_final: 0.6695 (m110)
REVERT: K   25 PHE cc_start: 0.8237 (m-80) cc_final: 0.8031 (m-80)
REVERT: K   61 MET cc_start: 0.8254 (ptp) cc_final: 0.8003 (ptp)
REVERT: K   77 ASN cc_start: 0.8067 (t0) cc_final: 0.7551 (t0)
REVERT: K   93 MET cc_start: 0.7308 (mmp) cc_final: 0.6591 (ttm)
REVERT: K  103 MET cc_start: 0.7539 (mmp) cc_final: 0.6739 (tmm)
REVERT: K  128 MET cc_start: 0.5780 (mpp) cc_final: 0.5389 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0756
  time to fit residues: 12.9205
Evaluate side-chains
  100 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
I 501 ASN
H  58 GLN
K 122 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.154422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.136314 restraints weight = 9839.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.138640 restraints weight = 6701.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.140260 restraints weight = 5072.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.141428 restraints weight = 4153.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.141752 restraints weight = 3585.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5305  Z= 0.165
  Angle     :  0.768   7.761   7159  Z= 0.393
  Chirality :  0.050   0.243    824
  Planarity :  0.005   0.092    898
  Dihedral  :  6.201  47.884    682
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.90 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -3.16 (0.32), residues: 631
  helix: -0.93 (0.26), residues: 379
  sheet:  None (None), residues: 0
  loop : -4.03 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 118 
 TYR   0.016   0.002   TYR H  34 
 PHE   0.016   0.002   PHE K  72 
 TRP   0.007   0.001   TRP I 686 
 HIS   0.004   0.001   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5305)
  covalent geometry    : angle       0.76762 ( 7159)
  hydrogen bonds       : bond        0.04017 (  218)
  hydrogen bonds       : angle       4.38770 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: I  668 GLU cc_start: 0.8581 (pp20) cc_final: 0.8286 (pp20)
REVERT: I  677 HIS cc_start: 0.7770 (t-90) cc_final: 0.7493 (t-90)
REVERT: H   52 LEU cc_start: 0.8894 (mm) cc_final: 0.8453 (tp)
REVERT: H   80 ASN cc_start: 0.6872 (t0) cc_final: 0.6599 (t0)
REVERT: H   99 GLU cc_start: 0.7637 (pm20) cc_final: 0.7377 (mt-10)
REVERT: K   21 ASN cc_start: 0.6963 (m-40) cc_final: 0.6699 (m110)
REVERT: K   77 ASN cc_start: 0.8199 (t0) cc_final: 0.7626 (t0)
REVERT: K  103 MET cc_start: 0.7600 (mmp) cc_final: 0.6838 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0743
  time to fit residues: 12.2185
Evaluate side-chains
  97 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
I 487 HIS
** K  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.144965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.124684 restraints weight = 8884.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.127750 restraints weight = 5501.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.129971 restraints weight = 3848.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.131507 restraints weight = 2956.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.132633 restraints weight = 2433.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5305  Z= 0.138
  Angle     :  0.739   8.680   7159  Z= 0.372
  Chirality :  0.047   0.236    824
  Planarity :  0.005   0.091    898
  Dihedral  :  5.934  49.824    682
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.84 %
    Favored  : 87.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -2.78 (0.33), residues: 631
  helix: -0.59 (0.27), residues: 379
  sheet:  None (None), residues: 0
  loop : -3.94 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  32 
 TYR   0.015   0.001   TYR I 711 
 PHE   0.020   0.002   PHE K  25 
 TRP   0.005   0.001   TRP I 686 
 HIS   0.002   0.001   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5305)
  covalent geometry    : angle       0.73881 ( 7159)
  hydrogen bonds       : bond        0.03560 (  218)
  hydrogen bonds       : angle       4.16722 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  668 GLU cc_start: 0.8671 (pp20) cc_final: 0.8311 (pp20)
REVERT: I  677 HIS cc_start: 0.7860 (t-90) cc_final: 0.7587 (t-170)
REVERT: I  699 LYS cc_start: 0.6777 (mmpt) cc_final: 0.5569 (tptt)
REVERT: H   52 LEU cc_start: 0.8773 (mm) cc_final: 0.8464 (tp)
REVERT: H   80 ASN cc_start: 0.6862 (t0) cc_final: 0.6621 (t0)
REVERT: H   99 GLU cc_start: 0.7633 (pm20) cc_final: 0.7432 (mt-10)
REVERT: K   21 ASN cc_start: 0.6905 (m-40) cc_final: 0.6592 (m110)
REVERT: K   77 ASN cc_start: 0.8146 (t0) cc_final: 0.7605 (t0)
REVERT: K   93 MET cc_start: 0.7443 (mmp) cc_final: 0.6692 (ttm)
REVERT: K  103 MET cc_start: 0.7591 (mmp) cc_final: 0.6777 (tmm)
REVERT: K  128 MET cc_start: 0.7221 (mmm) cc_final: 0.5969 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0722
  time to fit residues: 12.3271
Evaluate side-chains
  104 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
I 581 GLN
** K  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.156537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.138281 restraints weight = 9830.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.140695 restraints weight = 6574.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.142451 restraints weight = 4922.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.143621 restraints weight = 3976.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.144352 restraints weight = 3413.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5305  Z= 0.147
  Angle     :  0.753  12.333   7159  Z= 0.380
  Chirality :  0.049   0.344    824
  Planarity :  0.005   0.094    898
  Dihedral  :  5.931  49.732    682
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.95 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -2.65 (0.33), residues: 631
  helix: -0.47 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -3.93 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  32 
 TYR   0.014   0.001   TYR H  34 
 PHE   0.019   0.001   PHE K  25 
 TRP   0.005   0.001   TRP I 686 
 HIS   0.002   0.001   HIS H  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5305)
  covalent geometry    : angle       0.75330 ( 7159)
  hydrogen bonds       : bond        0.03700 (  218)
  hydrogen bonds       : angle       4.17540 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  367 CYS cc_start: 0.8439 (p) cc_final: 0.8008 (p)
REVERT: I  532 ILE cc_start: 0.8129 (mp) cc_final: 0.7821 (mt)
REVERT: I  677 HIS cc_start: 0.7769 (t-90) cc_final: 0.7513 (t-170)
REVERT: I  699 LYS cc_start: 0.6874 (mmpt) cc_final: 0.5651 (tptt)
REVERT: H   80 ASN cc_start: 0.6731 (t0) cc_final: 0.6520 (t0)
REVERT: H   99 GLU cc_start: 0.7513 (pm20) cc_final: 0.7229 (mt-10)
REVERT: K   21 ASN cc_start: 0.6877 (m-40) cc_final: 0.6518 (m110)
REVERT: K   77 ASN cc_start: 0.8209 (t0) cc_final: 0.7598 (t0)
REVERT: K  103 MET cc_start: 0.7600 (mmp) cc_final: 0.6881 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0732
  time to fit residues: 12.2648
Evaluate side-chains
  107 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0020
   chunk 9 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0370
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.4066

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.163043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.145135 restraints weight = 9579.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.147522 restraints weight = 6348.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.149205 restraints weight = 4736.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.150383 restraints weight = 3828.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.151123 restraints weight = 3274.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5305  Z= 0.127
  Angle     :  0.741  11.108   7159  Z= 0.369
  Chirality :  0.047   0.315    824
  Planarity :  0.005   0.092    898
  Dihedral  :  5.729  49.030    682
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.73 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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 (0.33), residues: 631
  helix: -0.32 (0.27), residues: 377
  sheet:  None (None), residues: 0
  loop : -3.80 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 118 
 TYR   0.011   0.001   TYR H  34 
 PHE   0.018   0.001   PHE K  25 
 TRP   0.004   0.001   TRP I 472 
 HIS   0.002   0.000   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5305)
  covalent geometry    : angle       0.74085 ( 7159)
  hydrogen bonds       : bond        0.03325 (  218)
  hydrogen bonds       : angle       4.06793 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  677 HIS cc_start: 0.7576 (t-90) cc_final: 0.7368 (t-170)
REVERT: I  699 LYS cc_start: 0.6889 (mmpt) cc_final: 0.5650 (tptt)
REVERT: H   99 GLU cc_start: 0.7406 (pm20) cc_final: 0.7049 (mt-10)
REVERT: K   21 ASN cc_start: 0.6786 (m-40) cc_final: 0.6467 (m110)
REVERT: K   99 ASP cc_start: 0.7242 (m-30) cc_final: 0.7005 (t70)
REVERT: K  103 MET cc_start: 0.7327 (mmp) cc_final: 0.6856 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0713
  time to fit residues: 11.6574
Evaluate side-chains
  103 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0970
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0010
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7786

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

Flipped N/Q/H residues before XYZ refinement:
I 581 GLN
I 595 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.160754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.142556 restraints weight = 9652.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.145035 restraints weight = 6470.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.146782 restraints weight = 4823.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.147865 restraints weight = 3887.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.148785 restraints weight = 3359.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5305  Z= 0.135
  Angle     :  0.745  11.101   7159  Z= 0.371
  Chirality :  0.048   0.303    824
  Planarity :  0.004   0.089    898
  Dihedral  :  5.632  46.817    682
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.79 %
    Favored  : 86.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -2.29 (0.34), residues: 631
  helix: -0.15 (0.27), residues: 378
  sheet:  None (None), residues: 0
  loop : -3.79 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  32 
 TYR   0.019   0.001   TYR I 340 
 PHE   0.017   0.001   PHE K  25 
 TRP   0.004   0.001   TRP K  89 
 HIS   0.003   0.000   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 5305)
  covalent geometry    : angle       0.74549 ( 7159)
  hydrogen bonds       : bond        0.03423 (  218)
  hydrogen bonds       : angle       4.04398 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: I  677 HIS cc_start: 0.7596 (t-90) cc_final: 0.7378 (t-170)
REVERT: I  699 LYS cc_start: 0.6824 (mmpt) cc_final: 0.5613 (tptt)
REVERT: H   99 GLU cc_start: 0.7514 (pm20) cc_final: 0.7184 (mt-10)
REVERT: K   21 ASN cc_start: 0.6761 (m-40) cc_final: 0.6450 (m110)
REVERT: K  103 MET cc_start: 0.7573 (mmp) cc_final: 0.6883 (tmm)
REVERT: K  128 MET cc_start: 0.6493 (mmm) cc_final: 0.6157 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0745
  time to fit residues: 12.0273
Evaluate side-chains
  104 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 13 optimal weight:    0.1980
   chunk 14 optimal weight:    0.0870
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  57 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.161091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.143480 restraints weight = 9689.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.145830 restraints weight = 6593.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.147367 restraints weight = 4968.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.148608 restraints weight = 4060.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.149333 restraints weight = 3481.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5305  Z= 0.128
  Angle     :  0.744  11.669   7159  Z= 0.367
  Chirality :  0.048   0.291    824
  Planarity :  0.004   0.089    898
  Dihedral  :  5.628  47.046    682
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.31 %
    Favored  : 86.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -2.07 (0.34), residues: 631
  helix:  0.02 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -3.60 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 118 
 TYR   0.018   0.001   TYR I 340 
 PHE   0.018   0.001   PHE K  25 
 TRP   0.005   0.001   TRP I 686 
 HIS   0.001   0.000   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5305)
  covalent geometry    : angle       0.74449 ( 7159)
  hydrogen bonds       : bond        0.03240 (  218)
  hydrogen bonds       : angle       4.04043 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: I  367 CYS cc_start: 0.8293 (p) cc_final: 0.7858 (p)
REVERT: I  677 HIS cc_start: 0.7533 (t-90) cc_final: 0.7330 (t-170)
REVERT: I  699 LYS cc_start: 0.6833 (mmpt) cc_final: 0.5666 (tptt)
REVERT: H   99 GLU cc_start: 0.7444 (pm20) cc_final: 0.7079 (mt-10)
REVERT: K   21 ASN cc_start: 0.6700 (m-40) cc_final: 0.6412 (m110)
REVERT: K  103 MET cc_start: 0.7368 (mmp) cc_final: 0.6882 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0714
  time to fit residues: 11.9022
Evaluate side-chains
  105 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
I 581 GLN
H  14 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.148157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.130109 restraints weight = 9048.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.132580 restraints weight = 5975.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134444 restraints weight = 4411.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.135747 restraints weight = 3508.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.136579 restraints weight = 2961.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.4705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5305  Z= 0.139
  Angle     :  0.780  11.805   7159  Z= 0.387
  Chirality :  0.049   0.290    824
  Planarity :  0.005   0.086    898
  Dihedral  :  5.652  46.126    682
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.47 %
    Favored  : 86.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -2.05 (0.34), residues: 631
  helix:  0.05 (0.28), residues: 370
  sheet:  None (None), residues: 0
  loop : -3.60 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  66 
 TYR   0.018   0.001   TYR I 340 
 PHE   0.018   0.002   PHE K  25 
 TRP   0.005   0.001   TRP I 446 
 HIS   0.001   0.000   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5305)
  covalent geometry    : angle       0.78012 ( 7159)
  hydrogen bonds       : bond        0.03492 (  218)
  hydrogen bonds       : angle       4.12768 (  645)

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

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

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1262 Ramachandran restraints generated.
    631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: I  367 CYS cc_start: 0.8220 (p) cc_final: 0.7829 (p)
REVERT: I  677 HIS cc_start: 0.7663 (t-90) cc_final: 0.7419 (t-90)
REVERT: I  699 LYS cc_start: 0.6823 (mmpt) cc_final: 0.5597 (tptt)
REVERT: H   99 GLU cc_start: 0.7471 (pm20) cc_final: 0.7103 (mt-10)
REVERT: K   21 ASN cc_start: 0.6723 (m-40) cc_final: 0.6450 (m110)
REVERT: K   59 LYS cc_start: 0.8432 (pttp) cc_final: 0.8152 (mptt)
REVERT: K  103 MET cc_start: 0.7659 (mmp) cc_final: 0.6927 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0754
  time to fit residues: 11.6704
Evaluate side-chains
  103 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 37 optimal weight:    0.0670
   chunk 16 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0010
   chunk 38 optimal weight:    0.0010
   chunk 62 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0030
   overall best weight:    0.4142

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

Flipped N/Q/H residues before XYZ refinement:
** I 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  77 ASN ** 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 = 0.3905 r_free = 0.3905 target = 0.156145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.138523 restraints weight = 8779.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.141176 restraints weight = 5733.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.143147 restraints weight = 4130.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.144568 restraints weight = 3224.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.145063 restraints weight = 2661.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.4939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5305  Z= 0.131
  Angle     :  0.768  12.801   7159  Z= 0.378
  Chirality :  0.048   0.286    824
  Planarity :  0.005   0.085    898
  Dihedral  :  5.588  46.260    682
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.68 %
    Favored  : 87.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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: -1.88 (0.34), residues: 631
  helix:  0.22 (0.28), residues: 367
  sheet:  None (None), residues: 0
  loop : -3.56 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  66 
 TYR   0.017   0.001   TYR I 340 
 PHE   0.019   0.001   PHE K  25 
 TRP   0.004   0.001   TRP I 686 
 HIS   0.003   0.000   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 5305)
  covalent geometry    : angle       0.76840 ( 7159)
  hydrogen bonds       : bond        0.03172 (  218)
  hydrogen bonds       : angle       4.14177 (  645)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 929.67 seconds
wall clock time: 16 minutes 44.87 seconds (1004.87 seconds total)