Starting phenix.real_space_refine
on Thu Jul  2 17:06:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9x46_66531/07_2026/9x46_66531.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9x46_66531/07_2026/9x46_66531.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9x46_66531/07_2026/9x46_66531.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9x46_66531/07_2026/9x46_66531.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9x46_66531/07_2026/9x46_66531.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9x46_66531/07_2026/9x46_66531.map"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      40      5.16       5
     C    5840      2.51       5
     N    1528      2.21       5
     O    1658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9069
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4514
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 20, 'TRANS': 551}
    Chain: "B"
      Number of atoms: 4527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4527
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 13, 'TRANS': 556}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.71, per 1000 atoms: 0.19
  Number of scatterers: 9069
  At special positions: 0
  Unit cell: (72.24, 99.072, 136.224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      40     16.00
     P       2     15.00
     Mg      1     11.99
     O    1658      8.00
     N    1528      7.00
     C    5840      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: 0.87
  Conformation dependent library (CDL) restraints added in 219.0 milliseconds
  

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2154

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      71.6% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 8
      removed outlier: 3.990A  pdb=" N   LEU A   5 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A   6 " --> pdb=" O   ALA A   3 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TYR A   7 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 47
      Proline residue:  A  19  - end of helix
      Proline residue:  A  33  - end of helix
      removed outlier: 4.199A  pdb=" N   ILE A  44 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      Proline residue:  A  45  - end of helix
    Processing helix  chain 'A' and resid 48 through 98
    Processing helix  chain 'A' and resid 100 through 108
    Processing helix  chain 'A' and resid 108 through 133
      removed outlier: 4.345A  pdb=" N   ASP A 119 " --> pdb=" O   ARG A 115 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 152
      removed outlier: 3.653A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 201
      removed outlier: 3.724A  pdb=" N   PHE A 159 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      Proline residue:  A 179  - end of helix
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 210 through 237
      removed outlier: 3.730A  pdb=" N   ILE A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 264
    Processing helix  chain 'A' and resid 268 through 281
    Processing helix  chain 'A' and resid 282 through 311
    Processing helix  chain 'A' and resid 372 through 381
    Processing helix  chain 'A' and resid 402 through 409
    Processing helix  chain 'A' and resid 424 through 429
    Processing helix  chain 'A' and resid 437 through 448
      removed outlier: 3.615A  pdb=" N   ALA A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 456
      removed outlier: 3.503A  pdb=" N   VAL A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 456 " --> pdb=" O   ASP A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 462
      removed outlier: 4.422A  pdb=" N   ASP A 462 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 459 through 462'
    Processing helix  chain 'A' and resid 473 through 487
    Processing helix  chain 'A' and resid 503 through 518
    Processing helix  chain 'A' and resid 529 through 534
      removed outlier: 3.809A  pdb=" N   LYS A 534 " --> pdb=" O   ASN A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 559
    Processing helix  chain 'A' and resid 560 through 572
    Processing helix  chain 'B' and resid 9 through 18
    Processing helix  chain 'B' and resid 20 through 52
      Proline residue:  B  42  - end of helix
      removed outlier: 3.544A  pdb=" N   VAL B  52 " --> pdb=" O   ALA B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 108
      Proline residue:  B  83  - end of helix
    Processing helix  chain 'B' and resid 109 through 116
    Processing helix  chain 'B' and resid 117 through 161
      removed outlier: 4.272A  pdb=" N   ASP B 128 " --> pdb=" O   ARG B 124 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   SER B 129 " --> pdb=" O   VAL B 125 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   PHE B 144 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   VAL B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 210
      Proline residue:  B 173  - end of helix
    Processing helix  chain 'B' and resid 210 through 217
    Processing helix  chain 'B' and resid 221 through 247
    Processing helix  chain 'B' and resid 247 through 273
    Processing helix  chain 'B' and resid 278 through 321
      removed outlier: 3.510A  pdb=" N   VAL B 289 " --> pdb=" O   PHE B 285 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   THR B 290 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLN B 291 " --> pdb=" O   ASN B 287 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LYS B 294 " --> pdb=" O   THR B 290 " (cutoff:3.500A)
      Proline residue:  B 295  - end of helix
      removed outlier: 4.663A  pdb=" N   SER B 304 " --> pdb=" O   SER B 300 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLU B 305 " --> pdb=" O   SER B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 389
    Processing helix  chain 'B' and resid 410 through 417
    Processing helix  chain 'B' and resid 431 through 437
    Processing helix  chain 'B' and resid 444 through 455
      removed outlier: 3.595A  pdb=" N   VAL B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 464
      removed outlier: 3.672A  pdb=" N   ILE B 461 " --> pdb=" O   ALA B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 477
    Processing helix  chain 'B' and resid 480 through 496
      removed outlier: 3.500A  pdb=" N   ILE B 492 " --> pdb=" O   THR B 488 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ASN B 495 " --> pdb=" O   ARG B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 526
      removed outlier: 3.520A  pdb=" N   GLU B 514 " --> pdb=" O   ASP B 510 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B 515 " --> pdb=" O   THR B 511 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS B 526 " --> pdb=" O   ALA B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 542
    Processing helix  chain 'B' and resid 559 through 567
      removed outlier: 3.639A  pdb=" N   LYS B 567 " --> pdb=" O   LEU B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 576
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.543A  pdb=" N   THR A 392 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340
      removed outlier: 7.380A  pdb=" N   PHE A 340 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   GLN A 351 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 410 through 413
      removed outlier: 6.149A  pdb=" N   ALA A 411 " --> pdb=" O   ILE A 494 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   ASP A 496 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL A 413 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   LEU A 363 " --> pdb=" O   ILE A 525 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   SER A 527 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ILE A 365 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 422 through 423
    Processing sheet with id=AA5, first strand: chain 'A' and resid 542 through 543
    Processing sheet with id=AA6, first strand: chain 'B' and resid 358 through 361
      removed outlier: 5.773A  pdb=" N   VAL B 347 " --> pdb=" O   ASP B 360 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   HIS B 346 " --> pdb=" O   GLN B 398 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   GLN B 398 " --> pdb=" O   HIS B 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 418 through 421
      removed outlier: 3.905A  pdb=" N   ASP B 503 " --> pdb=" O   VAL B 421 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ASN B 550 " --> pdb=" O   ILE B 554 " (cutoff:3.500A)
      removed outlier: 5.191A  pdb=" N   ILE B 554 " --> pdb=" O   ASN B 550 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 400 through 401

    628 hydrogen bonds defined for protein.
    1848 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2925
        1.34 -     1.46: 1805
        1.46 -     1.58: 4419
        1.58 -     1.69: 3
        1.69 -     1.81: 77
  Bond restraints: 9229
  Sorted by residual:
  bond pdb=" C4  ADP A 701 "
       pdb=" C5  ADP A 701 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 9.85e-01
  bond pdb=" CG  LEU A 279 "
       pdb=" CD2 LEU A 279 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.19e-01
  bond pdb=" CB  VAL A  69 "
       pdb=" CG1 VAL A  69 "
    ideal  model  delta    sigma   weight residual
    1.521  1.497  0.024 3.30e-02 9.18e+02 5.35e-01
  bond pdb=" CG  LEU A 275 "
       pdb=" CD1 LEU A 275 "
    ideal  model  delta    sigma   weight residual
    1.521  1.497  0.024 3.30e-02 9.18e+02 5.14e-01
  bond pdb=" C   ILE A 107 "
       pdb=" N   GLY A 108 "
    ideal  model  delta    sigma   weight residual
    1.322  1.331 -0.009 1.20e-02 6.94e+03 5.05e-01
  ... (remaining 9224 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 12371
        1.87 -     3.73: 109
        3.73 -     5.60: 24
        5.60 -     7.47: 1
        7.47 -     9.34: 1
  Bond angle restraints: 12506
  Sorted by residual:
  angle pdb=" CB  MET A 147 "
        pdb=" CG  MET A 147 "
        pdb=" SD  MET A 147 "
      ideal   model   delta    sigma   weight residual
     112.70  122.04   -9.34 3.00e+00 1.11e-01 9.69e+00
  angle pdb=" C   ASN B 495 "
        pdb=" N   VAL B 496 "
        pdb=" CA  VAL B 496 "
      ideal   model   delta    sigma   weight residual
     122.13  126.32   -4.19 1.85e+00 2.92e-01 5.13e+00
  angle pdb=" CA  VAL B 496 "
        pdb=" CB  VAL B 496 "
        pdb=" CG1 VAL B 496 "
      ideal   model   delta    sigma   weight residual
     110.40  113.67   -3.27 1.70e+00 3.46e-01 3.71e+00
  angle pdb=" O1B ADP A 701 "
        pdb=" PB  ADP A 701 "
        pdb=" O2B ADP A 701 "
      ideal   model   delta    sigma   weight residual
     119.90  114.13    5.77 3.00e+00 1.11e-01 3.70e+00
  angle pdb=" N   ILE B 365 "
        pdb=" CA  ILE B 365 "
        pdb=" C   ILE B 365 "
      ideal   model   delta    sigma   weight residual
     107.76  109.67   -1.91 1.01e+00 9.80e-01 3.59e+00
  ... (remaining 12501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 5020
       17.34 -    34.68: 452
       34.68 -    52.02: 79
       52.02 -    69.36: 11
       69.36 -    86.70: 8
  Dihedral angle restraints: 5570
    sinusoidal: 2239
      harmonic: 3331
  Sorted by residual:
  dihedral pdb=" CA  ASP A 446 "
           pdb=" C   ASP A 446 "
           pdb=" N   MET A 447 "
           pdb=" CA  MET A 447 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.41   19.59     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ILE B 532 "
           pdb=" C   ILE B 532 "
           pdb=" N   ILE B 533 "
           pdb=" CA  ILE B 533 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.57   18.43     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ILE A 380 "
           pdb=" C   ILE A 380 "
           pdb=" N   MET A 381 "
           pdb=" CA  MET A 381 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.78   17.22     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 5567 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 955
       0.030 -    0.060: 358
       0.060 -    0.090: 112
       0.090 -    0.119: 45
       0.119 -    0.149: 7
  Chirality restraints: 1477
  Sorted by residual:
  chirality pdb=" CB  VAL B 496 "
            pdb=" CA  VAL B 496 "
            pdb=" CG1 VAL B 496 "
            pdb=" CG2 VAL B 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.57e-01
  chirality pdb=" CA  ILE B 532 "
            pdb=" N   ILE B 532 "
            pdb=" C   ILE B 532 "
            pdb=" CB  ILE B 532 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CB  VAL B 302 "
            pdb=" CA  VAL B 302 "
            pdb=" CG1 VAL B 302 "
            pdb=" CG2 VAL B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 1474 not shown)

  Planarity restraints: 1571
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 294 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.94e+00
        pdb=" N   PRO B 295 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 295 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 295 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  39 "   -0.006 2.00e-02 2.50e+03   1.30e-02 1.68e+00
        pdb=" C   ILE A  39 "    0.022 2.00e-02 2.50e+03
        pdb=" O   ILE A  39 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   VAL A  40 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  41 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO B  42 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B  42 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  42 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1568 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 102
        2.66 -     3.22: 8823
        3.22 -     3.78: 14474
        3.78 -     4.34: 19217
        4.34 -     4.90: 32505
  Nonbonded interactions: 75121
  Sorted by model distance:
  nonbonded pdb=" O2B ADP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.095 2.170
  nonbonded pdb=" OE1 GLN A 415 "
            pdb="MG    MG A 702 "
     model   vdw
     2.133 2.170
  nonbonded pdb=" OG  SER A 374 "
            pdb="MG    MG A 702 "
     model   vdw
     2.134 2.170
  nonbonded pdb=" OG1 THR B  31 "
            pdb=" OH  TYR B  86 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   LEU A 116 "
            pdb=" OG1 THR A 120 "
     model   vdw
     2.246 3.040
  ... (remaining 75116 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.560
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
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   0.027   9229  Z= 0.124
  Angle     :  0.488   9.336  12506  Z= 0.249
  Chirality :  0.038   0.149   1477
  Planarity :  0.003   0.035   1571
  Dihedral  : 13.515  86.696   3416
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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:  1.88 (0.26), residues: 1138
  helix:  2.22 (0.19), residues: 779
  sheet: -1.90 (0.62), residues: 69
  loop : -0.64 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 512 
 TYR   0.013   0.001   TYR B 260 
 PHE   0.009   0.001   PHE B 227 
 TRP   0.006   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 9229)
  covalent geometry    : angle       0.48785 /  0.25 (12506)
  hydrogen bonds       : bond        0.13242 /  8.93 (  628)
  hydrogen bonds       : angle       4.86429 /  3.56 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.6720 (mmtt) cc_final: 0.6254 (ttpp)
REVERT: A   57 PHE cc_start: 0.7258 (t80) cc_final: 0.7005 (t80)
REVERT: A  271 MET cc_start: 0.7749 (mmp) cc_final: 0.7429 (mmp)
REVERT: A  439 GLN cc_start: 0.8304 (mp10) cc_final: 0.8048 (tp40)
REVERT: A  447 MET cc_start: 0.7528 (mtp) cc_final: 0.7144 (ttm)
REVERT: A  449 GLN cc_start: 0.7710 (mp10) cc_final: 0.7490 (mp10)
REVERT: A  472 PHE cc_start: 0.8657 (m-80) cc_final: 0.8411 (m-10)
REVERT: B   50 ASP cc_start: 0.7440 (m-30) cc_final: 0.6884 (m-30)
REVERT: B  165 MET cc_start: 0.7495 (tmm) cc_final: 0.6871 (tmm)
REVERT: B  325 ILE cc_start: 0.7631 (pt) cc_final: 0.7428 (pt)
REVERT: B  440 ASN cc_start: 0.8306 (t0) cc_final: 0.7751 (t0)
REVERT: B  495 ASN cc_start: 0.8108 (t0) cc_final: 0.6977 (p0)
REVERT: B  549 MET cc_start: 0.8321 (ptm) cc_final: 0.8106 (ptm)
REVERT: B  556 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7265 (mt-10)
REVERT: B  564 MET cc_start: 0.6748 (mmm) cc_final: 0.6379 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0771
  time to fit residues: 14.9104
Evaluate side-chains
  107 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.5980
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
A 560 ASN
A 572 GLN
B 188 GLN
B 226 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.147933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.115547 restraints weight = 12040.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.89
r_work: 0.3275 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9229  Z= 0.184
  Angle     :  0.558   6.313  12506  Z= 0.284
  Chirality :  0.041   0.170   1477
  Planarity :  0.004   0.036   1571
  Dihedral  :  3.960  32.227   1244
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  6.55 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.25), residues: 1138
  helix:  1.93 (0.18), residues: 787
  sheet: -1.95 (0.59), residues: 74
  loop : -0.77 (0.38), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 528 
 TYR   0.026   0.002   TYR A 568 
 PHE   0.015   0.001   PHE A 453 
 TRP   0.008   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 546 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.18 ( 9229)
  covalent geometry    : angle       0.55771 /  0.28 (12506)
  hydrogen bonds       : bond        0.04583 /  2.90 (  628)
  hydrogen bonds       : angle       4.12032 /  3.00 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7214 (ttpp)
REVERT: A  439 GLN cc_start: 0.8586 (mp10) cc_final: 0.8264 (tp40)
REVERT: A  472 PHE cc_start: 0.8823 (m-80) cc_final: 0.8509 (m-10)
REVERT: A  572 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6786 (mp10)
REVERT: B  165 MET cc_start: 0.8489 (tmm) cc_final: 0.8139 (tmm)
REVERT: B  305 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7739 (mt-10)
REVERT: B  325 ILE cc_start: 0.8496 (pt) cc_final: 0.8275 (pt)
REVERT: B  360 ASP cc_start: 0.7912 (m-30) cc_final: 0.7090 (t0)
REVERT: B  440 ASN cc_start: 0.8320 (t0) cc_final: 0.7974 (t0)
REVERT: B  495 ASN cc_start: 0.8361 (t0) cc_final: 0.7606 (p0)
REVERT: B  530 SER cc_start: 0.9049 (p) cc_final: 0.8797 (p)
REVERT: B  549 MET cc_start: 0.8497 (ptm) cc_final: 0.8147 (ptm)
  outliers start: 8
  outliers final: 5
  residues processed: 116
  average time/residue: 0.0690
  time to fit residues: 11.6972
Evaluate side-chains
  105 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0570
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 91 optimal weight:    0.4980
   chunk 71 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.4898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN
B 463 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.149823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.117296 restraints weight = 11887.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.89
r_work: 0.3301 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9229  Z= 0.123
  Angle     :  0.499   5.938  12506  Z= 0.255
  Chirality :  0.039   0.159   1477
  Planarity :  0.003   0.036   1571
  Dihedral  :  3.892  30.068   1244
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.96 %
    Favored  : 89.73 %
  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:  1.62 (0.25), residues: 1138
  helix:  2.01 (0.18), residues: 785
  sheet: -1.93 (0.57), residues: 74
  loop : -0.74 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 512 
 TYR   0.020   0.001   TYR A 568 
 PHE   0.012   0.001   PHE B 460 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.003   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 9229)
  covalent geometry    : angle       0.49918 /  0.26 (12506)
  hydrogen bonds       : bond        0.04196 /  2.64 (  628)
  hydrogen bonds       : angle       3.97354 /  2.90 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7136 (ttpp)
REVERT: A   34 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8721 (mmm)
REVERT: A  439 GLN cc_start: 0.8562 (mp10) cc_final: 0.8231 (tp40)
REVERT: A  472 PHE cc_start: 0.8802 (m-80) cc_final: 0.8449 (m-10)
REVERT: A  568 TYR cc_start: 0.8389 (t80) cc_final: 0.8139 (t80)
REVERT: A  572 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6632 (mp10)
REVERT: B  165 MET cc_start: 0.8476 (tmm) cc_final: 0.8131 (tmm)
REVERT: B  305 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7721 (mt-10)
REVERT: B  360 ASP cc_start: 0.7859 (m-30) cc_final: 0.7009 (t0)
REVERT: B  440 ASN cc_start: 0.8363 (t0) cc_final: 0.8036 (t0)
REVERT: B  495 ASN cc_start: 0.8369 (t0) cc_final: 0.7574 (p0)
REVERT: B  530 SER cc_start: 0.9013 (p) cc_final: 0.8765 (p)
REVERT: B  549 MET cc_start: 0.8316 (ptm) cc_final: 0.8100 (ptm)
  outliers start: 13
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0787
  time to fit residues: 12.4398
Evaluate side-chains
  112 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  507 GLU
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  420 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 GLN
B 188 GLN
B 226 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.148434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.116032 restraints weight = 12128.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.91
r_work: 0.3287 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9229  Z= 0.138
  Angle     :  0.499   5.961  12506  Z= 0.255
  Chirality :  0.039   0.162   1477
  Planarity :  0.003   0.036   1571
  Dihedral  :  3.887  29.550   1244
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  9.77 %
    Favored  : 88.22 %
  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:  1.61 (0.25), residues: 1138
  helix:  2.00 (0.18), residues: 782
  sheet: -1.96 (0.57), residues: 74
  loop : -0.72 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  47 
 TYR   0.013   0.001   TYR A 568 
 PHE   0.011   0.001   PHE B 460 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.002   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 ( 9229)
  covalent geometry    : angle       0.49925 /  0.25 (12506)
  hydrogen bonds       : bond        0.04124 /  2.59 (  628)
  hydrogen bonds       : angle       3.92947 /  2.87 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7608 (mmtt) cc_final: 0.7227 (ttpp)
REVERT: A  439 GLN cc_start: 0.8603 (mp10) cc_final: 0.8266 (tp40)
REVERT: A  447 MET cc_start: 0.7990 (mtp) cc_final: 0.7657 (ttm)
REVERT: A  572 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6743 (mp10)
REVERT: B  165 MET cc_start: 0.8520 (tmm) cc_final: 0.8160 (tmm)
REVERT: B  305 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7749 (mt-10)
REVERT: B  360 ASP cc_start: 0.7856 (m-30) cc_final: 0.7016 (t0)
REVERT: B  440 ASN cc_start: 0.8358 (t0) cc_final: 0.8130 (t0)
REVERT: B  495 ASN cc_start: 0.8366 (t0) cc_final: 0.7611 (p0)
REVERT: B  530 SER cc_start: 0.9024 (p) cc_final: 0.8794 (p)
  outliers start: 20
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0646
  time to fit residues: 10.9679
Evaluate side-chains
  112 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  420 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 103 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.148702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.116173 restraints weight = 11891.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.88
r_work: 0.3290 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9229  Z= 0.133
  Angle     :  0.503   6.191  12506  Z= 0.256
  Chirality :  0.039   0.178   1477
  Planarity :  0.003   0.036   1571
  Dihedral  :  3.864  28.861   1244
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 10.47 %
    Favored  : 87.61 %
  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:  1.63 (0.25), residues: 1138
  helix:  2.03 (0.18), residues: 782
  sheet: -1.99 (0.56), residues: 74
  loop : -0.71 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  47 
 TYR   0.010   0.001   TYR A 568 
 PHE   0.036   0.001   PHE B 459 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.003   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 9229)
  covalent geometry    : angle       0.50346 /  0.26 (12506)
  hydrogen bonds       : bond        0.04075 /  2.55 (  628)
  hydrogen bonds       : angle       3.90477 /  2.85 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7566 (mmtt) cc_final: 0.7150 (ttpp)
REVERT: A  439 GLN cc_start: 0.8603 (mp10) cc_final: 0.8258 (tp40)
REVERT: A  447 MET cc_start: 0.7933 (mtp) cc_final: 0.7680 (ttm)
REVERT: B  165 MET cc_start: 0.8527 (tmm) cc_final: 0.8178 (tmm)
REVERT: B  305 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7757 (mt-10)
REVERT: B  360 ASP cc_start: 0.7833 (m-30) cc_final: 0.6989 (t0)
REVERT: B  440 ASN cc_start: 0.8374 (t0) cc_final: 0.8139 (t0)
REVERT: B  495 ASN cc_start: 0.8320 (t0) cc_final: 0.7534 (p0)
  outliers start: 19
  outliers final: 13
  residues processed: 113
  average time/residue: 0.0696
  time to fit residues: 11.4322
Evaluate side-chains
  108 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  420 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0870
   chunk 70 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 64 optimal weight:    0.2980
   chunk 92 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.4758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 HIS
B 188 GLN
B 226 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.149557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.117315 restraints weight = 11978.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.88
r_work: 0.3302 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9229  Z= 0.120
  Angle     :  0.496   6.649  12506  Z= 0.253
  Chirality :  0.039   0.164   1477
  Planarity :  0.003   0.037   1571
  Dihedral  :  3.842  27.752   1244
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.68 %
    Favored  : 86.61 %
  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:  1.73 (0.25), residues: 1138
  helix:  2.11 (0.18), residues: 783
  sheet: -2.01 (0.56), residues: 74
  loop : -0.67 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  47 
 TYR   0.019   0.001   TYR A 568 
 PHE   0.010   0.001   PHE B 460 
 TRP   0.007   0.001   TRP B 196 
 HIS   0.003   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 9229)
  covalent geometry    : angle       0.49573 /  0.25 (12506)
  hydrogen bonds       : bond        0.03966 /  2.51 (  628)
  hydrogen bonds       : angle       3.85085 /  2.81 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7150 (ttpp)
REVERT: A   34 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8734 (mmm)
REVERT: A  439 GLN cc_start: 0.8562 (mp10) cc_final: 0.8252 (tp40)
REVERT: A  447 MET cc_start: 0.7945 (mtp) cc_final: 0.7718 (ttm)
REVERT: B  165 MET cc_start: 0.8476 (tmm) cc_final: 0.8205 (tmm)
REVERT: B  292 TYR cc_start: 0.8633 (t80) cc_final: 0.8420 (t80)
REVERT: B  305 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7762 (mt-10)
REVERT: B  360 ASP cc_start: 0.7843 (m-30) cc_final: 0.7126 (t0)
REVERT: B  440 ASN cc_start: 0.8332 (t0) cc_final: 0.8104 (t0)
REVERT: B  495 ASN cc_start: 0.8316 (t0) cc_final: 0.7543 (p0)
  outliers start: 17
  outliers final: 14
  residues processed: 114
  average time/residue: 0.0637
  time to fit residues: 10.8720
Evaluate side-chains
  112 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  571 HIS
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  420 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.147372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.114766 restraints weight = 11998.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.89
r_work: 0.3272 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9229  Z= 0.170
  Angle     :  0.532  10.955  12506  Z= 0.269
  Chirality :  0.040   0.172   1477
  Planarity :  0.003   0.036   1571
  Dihedral  :  3.888  28.716   1244
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.58 %
    Favored  : 86.51 %
  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:  1.63 (0.25), residues: 1138
  helix:  2.01 (0.18), residues: 783
  sheet: -2.10 (0.55), residues: 74
  loop : -0.64 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 132 
 TYR   0.029   0.001   TYR A 568 
 PHE   0.010   0.001   PHE B 285 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.012   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.17 ( 9229)
  covalent geometry    : angle       0.53201 /  0.27 (12506)
  hydrogen bonds       : bond        0.04151 /  2.62 (  628)
  hydrogen bonds       : angle       3.92874 /  2.87 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7215 (ttpp)
REVERT: A  439 GLN cc_start: 0.8602 (mp10) cc_final: 0.8271 (tp40)
REVERT: B  305 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7742 (mt-10)
REVERT: B  360 ASP cc_start: 0.7823 (m-30) cc_final: 0.7097 (t0)
REVERT: B  440 ASN cc_start: 0.8388 (t0) cc_final: 0.8163 (t0)
REVERT: B  463 GLN cc_start: 0.8570 (mp10) cc_final: 0.8195 (mp10)
REVERT: B  495 ASN cc_start: 0.8353 (t0) cc_final: 0.7565 (p0)
REVERT: B  563 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7029 (mm)
  outliers start: 19
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0580
  time to fit residues: 9.5383
Evaluate side-chains
  111 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  563 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0970
   chunk 17 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 HIS
B 226 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.148192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.115913 restraints weight = 11958.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.87
r_work: 0.3285 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9229  Z= 0.139
  Angle     :  0.517   5.965  12506  Z= 0.262
  Chirality :  0.040   0.167   1477
  Planarity :  0.003   0.037   1571
  Dihedral  :  3.885  28.171   1244
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.08 %
    Favored  : 86.00 %
  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:  1.68 (0.25), residues: 1138
  helix:  2.05 (0.18), residues: 782
  sheet: -2.15 (0.54), residues: 74
  loop : -0.60 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 132 
 TYR   0.024   0.001   TYR A 568 
 PHE   0.010   0.001   PHE B 460 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.003   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 9229)
  covalent geometry    : angle       0.51706 /  0.26 (12506)
  hydrogen bonds       : bond        0.04066 /  2.57 (  628)
  hydrogen bonds       : angle       3.88954 /  2.85 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7148 (ttpp)
REVERT: A  439 GLN cc_start: 0.8590 (mp10) cc_final: 0.8282 (tp40)
REVERT: B  305 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7743 (mt-10)
REVERT: B  440 ASN cc_start: 0.8341 (t0) cc_final: 0.8121 (t0)
REVERT: B  463 GLN cc_start: 0.8588 (mp10) cc_final: 0.8270 (mp10)
REVERT: B  495 ASN cc_start: 0.8297 (t0) cc_final: 0.7499 (p0)
REVERT: B  563 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7005 (mm)
  outliers start: 19
  outliers final: 15
  residues processed: 108
  average time/residue: 0.0665
  time to fit residues: 10.7022
Evaluate side-chains
  109 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  571 HIS
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  563 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 12 optimal weight:    0.1980
   chunk 47 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 HIS
B 226 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.148416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.116145 restraints weight = 11962.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.88
r_work: 0.3290 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9229  Z= 0.136
  Angle     :  0.511   5.971  12506  Z= 0.260
  Chirality :  0.039   0.167   1477
  Planarity :  0.003   0.037   1571
  Dihedral  :  3.894  28.106   1244
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.59 %
    Favored  : 85.60 %
  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:  1.67 (0.25), residues: 1138
  helix:  2.05 (0.18), residues: 783
  sheet: -2.17 (0.55), residues: 74
  loop : -0.64 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 132 
 TYR   0.017   0.001   TYR A 568 
 PHE   0.010   0.001   PHE B 460 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.003   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 9229)
  covalent geometry    : angle       0.51126 /  0.26 (12506)
  hydrogen bonds       : bond        0.04027 /  2.54 (  628)
  hydrogen bonds       : angle       3.88763 /  2.85 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7077 (ttpp)
REVERT: A  439 GLN cc_start: 0.8586 (mp10) cc_final: 0.8281 (tp40)
REVERT: B  305 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7734 (mt-10)
REVERT: B  440 ASN cc_start: 0.8340 (t0) cc_final: 0.8117 (t0)
REVERT: B  463 GLN cc_start: 0.8549 (mp10) cc_final: 0.8295 (mp10)
REVERT: B  495 ASN cc_start: 0.8316 (t0) cc_final: 0.7528 (p0)
REVERT: B  563 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6977 (mm)
  outliers start: 18
  outliers final: 14
  residues processed: 109
  average time/residue: 0.0624
  time to fit residues: 10.1745
Evaluate side-chains
  108 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  571 HIS
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  563 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 HIS
B 226 ASN

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 = 0.147595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.115247 restraints weight = 11884.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.87
r_work: 0.3280 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9229  Z= 0.155
  Angle     :  0.526   5.982  12506  Z= 0.268
  Chirality :  0.040   0.171   1477
  Planarity :  0.003   0.036   1571
  Dihedral  :  3.901  28.563   1244
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.99 %
    Favored  : 85.40 %
  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:  1.60 (0.25), residues: 1138
  helix:  2.02 (0.18), residues: 782
  sheet: -2.15 (0.55), residues: 74
  loop : -0.70 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 132 
 TYR   0.023   0.001   TYR A 568 
 PHE   0.010   0.001   PHE B 460 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.009   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 ( 9229)
  covalent geometry    : angle       0.52640 /  0.27 (12506)
  hydrogen bonds       : bond        0.04087 /  2.57 (  628)
  hydrogen bonds       : angle       3.90870 /  2.86 ( 1848)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   13 LYS cc_start: 0.7494 (mmtt) cc_final: 0.7104 (ttpp)
REVERT: A   54 MET cc_start: 0.8762 (ttm) cc_final: 0.8490 (mtp)
REVERT: A  390 SER cc_start: 0.8063 (t) cc_final: 0.7675 (m)
REVERT: A  439 GLN cc_start: 0.8588 (mp10) cc_final: 0.8270 (tp40)
REVERT: B  305 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7737 (mt-10)
REVERT: B  440 ASN cc_start: 0.8332 (t0) cc_final: 0.8108 (t0)
REVERT: B  463 GLN cc_start: 0.8605 (mp10) cc_final: 0.8349 (mp10)
REVERT: B  495 ASN cc_start: 0.8314 (t0) cc_final: 0.7538 (p0)
REVERT: B  563 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7021 (mm)
  outliers start: 16
  outliers final: 13
  residues processed: 108
  average time/residue: 0.0640
  time to fit residues: 10.3874
Evaluate side-chains
  110 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  571 HIS
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  563 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   chunk 89 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 81 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 HIS
B 226 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.148513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.116193 restraints weight = 11797.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.87
r_work: 0.3293 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9229  Z= 0.134
  Angle     :  0.519   6.579  12506  Z= 0.263
  Chirality :  0.039   0.170   1477
  Planarity :  0.003   0.037   1571
  Dihedral  :  3.905  28.060   1244
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.39 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.25), residues: 1138
  helix:  2.05 (0.18), residues: 782
  sheet: -2.10 (0.56), residues: 74
  loop : -0.71 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 132 
 TYR   0.020   0.001   TYR A 568 
 PHE   0.018   0.001   PHE A 453 
 TRP   0.008   0.001   TRP B 196 
 HIS   0.004   0.001   HIS A 571 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 ( 9229)
  covalent geometry    : angle       0.51925 /  0.26 (12506)
  hydrogen bonds       : bond        0.04019 /  2.54 (  628)
  hydrogen bonds       : angle       3.88150 /  2.84 ( 1848)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1795.41 seconds
wall clock time: 31 minutes 28.86 seconds (1888.86 seconds total)