Starting phenix.real_space_refine
on Fri Aug 22 16:43:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c6o_45253/08_2025/9c6o_45253.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c6o_45253/08_2025/9c6o_45253.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c6o_45253/08_2025/9c6o_45253.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c6o_45253/08_2025/9c6o_45253.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c6o_45253/08_2025/9c6o_45253.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c6o_45253/08_2025/9c6o_45253.cif"
  }
  resolution = 2.77
  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=   0.069
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      34      5.16       5
     C    3925      2.51       5
     N    1029      2.21       5
     O    1098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6086
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1350
          Classifications: {'peptide': 195}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 15, 'TRANS': 179}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 242
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 94
    Chain: "A"
      Number of atoms: 4571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 4571
          Classifications: {'peptide': 582}
          Incomplete info: {'truncation_to_alanine': 89}
          Link IDs: {'PTRANS': 23, 'TRANS': 558}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 263
          Unresolved non-hydrogen angles: 332
          Unresolved non-hydrogen dihedrals: 196
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 18, 'ASN:plan1': 9, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 183
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.35, per 1000 atoms: 0.22
  Number of scatterers: 6086
  At special positions: 0
  Unit cell: (89, 94, 105, 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      34     16.00
     O    1098      8.00
     N    1029      7.00
     C    3925      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 425 " - pdb=" SG  CYS B 478 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 503 " - pdb=" SG  CYS B 538 " distance=2.09
    Simple disulfide: pdb=" SG  CYS B 506 " - pdb=" SG  CYS B 520 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 359 " distance=2.12
    Simple disulfide: pdb=" SG  CYS A 528 " - pdb=" SG  CYS A 540 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A 297 "
      " NAG A 802 " - " ASN A  76 "
      " NAG A 803 " - " ASN A  85 "
      " NAG A 804 " - " ASN A 320 "
      " NAG A 805 " - " ASN A 327 "
      " NAG A 806 " - " ASN A 544 "
      " NAG B 700 " - " ASN B 550 "
      " NAG C   1 " - " ASN B 496 "
      " NAG D   1 " - " ASN A  54 "
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 246.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1474

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      58.2% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'B' and resid 386 through 390
    Processing helix  chain 'B' and resid 395 through 399
      removed outlier: 3.795A  pdb=" N   PHE B 399 " --> pdb=" O   PRO B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 415
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 463 through 468
    Processing helix  chain 'B' and resid 535 through 549
      removed outlier: 4.782A  pdb=" N   VAL B 541 " --> pdb=" O   SER B 537 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE B 547 " --> pdb=" O   LEU B 543 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLY B 549 " --> pdb=" O   GLY B 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 53
      removed outlier: 3.888A  pdb=" N   LYS A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 82
      removed outlier: 3.523A  pdb=" N   ILE A  80 " --> pdb=" O   ASN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 84
      No H-bonds generated for 'chain 'A' and resid 83 through 84'
    Processing helix  chain 'A' and resid 85 through 89
    Processing helix  chain 'A' and resid 91 through 103
    Processing helix  chain 'A' and resid 111 through 127
    Processing helix  chain 'A' and resid 145 through 153
    Processing helix  chain 'A' and resid 155 through 170
    Processing helix  chain 'A' and resid 174 through 192
    Processing helix  chain 'A' and resid 196 through 202
    Processing helix  chain 'A' and resid 203 through 206
    Processing helix  chain 'A' and resid 210 through 214
      removed outlier: 4.163A  pdb=" N   ALA A 214 " --> pdb=" O   GLU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 250
      removed outlier: 3.660A  pdb=" N   ASP A 222 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU A 230 " --> pdb=" O   ARG A 226 " (cutoff:3.500A)
      Proline residue:  A 233  - end of helix
      removed outlier: 3.662A  pdb=" N   ASP A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 265
      No H-bonds generated for 'chain 'A' and resid 263 through 265'
    Processing helix  chain 'A' and resid 273 through 275
      No H-bonds generated for 'chain 'A' and resid 273 through 275'
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 291 through 298
    Processing helix  chain 'A' and resid 301 through 317
    Processing helix  chain 'A' and resid 324 through 329
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.732A  pdb=" N   HIS A 371 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 391
    Processing helix  chain 'A' and resid 397 through 410
      removed outlier: 3.545A  pdb=" N   GLY A 403 " --> pdb=" O   HIS A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 419
    Processing helix  chain 'A' and resid 430 through 445
    Processing helix  chain 'A' and resid 447 through 464
    Processing helix  chain 'A' and resid 467 through 469
      No H-bonds generated for 'chain 'A' and resid 467 through 469'
    Processing helix  chain 'A' and resid 470 through 483
    Processing helix  chain 'A' and resid 497 through 500
    Processing helix  chain 'A' and resid 501 through 506
    Processing helix  chain 'A' and resid 511 through 531
    Processing helix  chain 'A' and resid 536 through 540
    Processing helix  chain 'A' and resid 545 through 557
      removed outlier: 3.760A  pdb=" N   MET A 555 " --> pdb=" O   LYS A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 573
      removed outlier: 3.721A  pdb=" N   ILE A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 586
    Processing helix  chain 'A' and resid 586 through 597
    Processing sheet with id=AA1, first strand: chain 'B' and resid 400 through 404
      removed outlier: 6.682A  pdb=" N   TYR B 483 " --> pdb=" O   VAL B 420 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   VAL B 420 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 518 through 525
      removed outlier: 4.436A  pdb=" N   GLY B 505 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   GLU B 523 " --> pdb=" O   CYS B 503 " (cutoff:3.500A)
      removed outlier: 9.680A  pdb=" N   CYS B 503 " --> pdb=" O   GLU B 523 " (cutoff:3.500A)
      removed outlier: 10.583A  pdb=" N   VAL B 525 " --> pdb=" O   THR B 501 " (cutoff:3.500A)
      removed outlier: 12.818A  pdb=" N   THR B 501 " --> pdb=" O   VAL B 525 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL B 574 " --> pdb=" O   THR B 501 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   CYS B 503 " --> pdb=" O   LYS B 572 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LYS B 572 " --> pdb=" O   CYS B 503 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132
      removed outlier: 6.024A  pdb=" N   GLN A 138 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261
      removed outlier: 6.188A  pdb=" N   LEU A 260 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 348

    332 hydrogen bonds defined for protein.
    930 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: 0.85

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 974
        1.30 -     1.43: 1738
        1.43 -     1.57: 3473
        1.57 -     1.70: 9
        1.70 -     1.83: 54
  Bond restraints: 6248
  Sorted by residual:
  bond pdb=" C   LYS A  93 "
       pdb=" O   LYS A  93 "
    ideal  model  delta    sigma   weight residual
    1.237  1.170  0.067 1.19e-02 7.06e+03 3.18e+01
  bond pdb=" N   ILE B 547 "
       pdb=" CA  ILE B 547 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 8.60e-03 1.35e+04 1.75e+01
  bond pdb=" NE  ARG A 338 "
       pdb=" CZ  ARG A 338 "
    ideal  model  delta    sigma   weight residual
    1.326  1.370 -0.044 1.10e-02 8.26e+03 1.60e+01
  bond pdb=" N   ARG A 587 "
       pdb=" CA  ARG A 587 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.04e-02 9.25e+03 1.38e+01
  bond pdb=" N   VAL B 528 "
       pdb=" CA  VAL B 528 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.22e-02 6.72e+03 9.78e+00
  ... (remaining 6243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 7578
        1.74 -     3.48: 773
        3.48 -     5.22: 90
        5.22 -     6.96: 55
        6.96 -     8.70: 13
  Bond angle restraints: 8509
  Sorted by residual:
  angle pdb=" C   ASN A 135 "
        pdb=" N   PRO A 136 "
        pdb=" CA  PRO A 136 "
      ideal   model   delta    sigma   weight residual
     119.82  128.11   -8.29 9.80e-01 1.04e+00 7.15e+01
  angle pdb=" C   VAL A 281 "
        pdb=" N   PRO A 282 "
        pdb=" CA  PRO A 282 "
      ideal   model   delta    sigma   weight residual
     119.24  127.94   -8.70 1.04e+00 9.25e-01 7.00e+01
  angle pdb=" C   ASN B 513 "
        pdb=" N   PRO B 514 "
        pdb=" CA  PRO B 514 "
      ideal   model   delta    sigma   weight residual
     119.82  127.52   -7.70 9.80e-01 1.04e+00 6.17e+01
  angle pdb=" C   LYS A 132 "
        pdb=" N   PRO A 133 "
        pdb=" CA  PRO A 133 "
      ideal   model   delta    sigma   weight residual
     119.56  127.20   -7.64 1.01e+00 9.80e-01 5.73e+01
  angle pdb=" C   SER A 255 "
        pdb=" N   PRO A 256 "
        pdb=" CA  PRO A 256 "
      ideal   model   delta    sigma   weight residual
     119.56  126.69   -7.13 1.02e+00 9.61e-01 4.88e+01
  ... (remaining 8504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.29: 3683
       21.29 -    42.59: 111
       42.59 -    63.88: 22
       63.88 -    85.17: 13
       85.17 -   106.47: 5
  Dihedral angle restraints: 3834
    sinusoidal: 1554
      harmonic: 2280
  Sorted by residual:
  dihedral pdb=" O4  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.76  106.47     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C3  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -58.27  105.89     1      3.00e+01 1.11e-03 1.36e+01
  dihedral pdb=" C6  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O4  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -163.34  -63.10 -100.24     1      3.00e+01 1.11e-03 1.26e+01
  ... (remaining 3831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.171: 898
       0.171 -    0.342: 49
       0.342 -    0.512: 3
       0.512 -    0.683: 0
       0.683 -    0.854: 1
  Chirality restraints: 951
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.54    0.14 2.00e-02 2.50e+03 4.93e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.49    0.09 2.00e-02 2.50e+03 2.19e+01
  chirality pdb=" C1  NAG A 804 "
            pdb=" ND2 ASN A 320 "
            pdb=" C2  NAG A 804 "
            pdb=" O5  NAG A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.55   -0.85 2.00e-01 2.50e+01 1.82e+01
  ... (remaining 948 not shown)

  Planarity restraints: 1087
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 806 "    0.115 2.00e-02 2.50e+03   9.78e-02 1.20e+02
        pdb=" C7  NAG A 806 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8  NAG A 806 "   -0.027 2.00e-02 2.50e+03
        pdb=" N2  NAG A 806 "   -0.157 2.00e-02 2.50e+03
        pdb=" O7  NAG A 806 "    0.093 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 320 "   -0.070 2.00e-02 2.50e+03   8.79e-02 9.65e+01
        pdb=" CG  ASN A 320 "    0.027 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 320 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 320 "    0.151 2.00e-02 2.50e+03
        pdb=" C1  NAG A 804 "   -0.100 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 327 "   -0.021 2.00e-02 2.50e+03   2.17e-02 5.91e+00
        pdb=" CG  ASN A 327 "    0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 327 "    0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 327 "    0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG A 805 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1084 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 2208
        2.88 -     3.38: 5586
        3.38 -     3.89: 10177
        3.89 -     4.39: 11961
        4.39 -     4.90: 19506
  Nonbonded interactions: 49438
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 563 "
            pdb=" NZ  LYS A 286 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" NZ  LYS B 509 "
            pdb=" OD2 ASP B 517 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" OG  SER B 537 "
            pdb=" O   VAL B 557 "
     model   vdw
     2.408 3.040
  nonbonded pdb=" NZ  LYS A  93 "
            pdb=" OE1 GLN A 386 "
     model   vdw
     2.430 3.120
  nonbonded pdb=" NZ  LYS B 427 "
            pdb=" O   SER B 474 "
     model   vdw
     2.499 3.120
  ... (remaining 49433 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:             2.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.580
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
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      :  0.012   0.089   6266  Z= 0.654
  Angle     :  1.286  24.209   8557  Z= 0.846
  Chirality :  0.085   0.854    951
  Planarity :  0.006   0.098   1078
  Dihedral  : 12.614 106.469   2342
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.23 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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 aren not related in a simple way.
  whole: -0.10 (0.27), residues: 763
  helix: -0.06 (0.23), residues: 395
  sheet:  0.67 (0.56), residues: 69
  loop : -0.01 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 159 
 TYR   0.026   0.004   TYR B 504 
 PHE   0.015   0.003   PHE A 325 
 TRP   0.030   0.004   TRP A 476 
 HIS   0.005   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.01127 ( 6248)
  covalent geometry    : angle       1.21814 ( 8509)
  SS BOND              : bond        0.04397 (    6)
  SS BOND              : angle       3.71837 (   12)
  hydrogen bonds       : bond        0.22306 (  332)
  hydrogen bonds       : angle       6.78582 (  930)
  link_BETA1-4         : bond        0.05398 (    3)
  link_BETA1-4         : angle       3.07642 (    9)
  link_NAG-ASN         : bond        0.05306 (    9)
  link_NAG-ASN         : angle       6.84032 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7491 (mtpt) cc_final: 0.6778 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.5710
  time to fit residues: 61.3626
Evaluate side-chains
  66 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A  99 GLN
A 395 ASN
A 440 GLN
A 491 HIS
A 532 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.172978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.135069 restraints weight = 5997.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.45
r_work: 0.3441 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.124   6266  Z= 0.188
  Angle     :  0.692  12.043   8557  Z= 0.357
  Chirality :  0.048   0.321    951
  Planarity :  0.005   0.033   1078
  Dihedral  :  6.838  59.881   1086
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.31 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.43 %
    Favored  : 89.09 %
  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 aren not related in a simple way.
  whole:  1.16 (0.28), residues: 763
  helix:  1.28 (0.25), residues: 387
  sheet:  0.57 (0.52), residues: 74
  loop :  0.32 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 202 
 TYR   0.024   0.002   TYR A 383 
 PHE   0.015   0.002   PHE A 306 
 TRP   0.020   0.002   TRP A 476 
 HIS   0.008   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 6248)
  covalent geometry    : angle       0.66224 ( 8509)
  SS BOND              : bond        0.00849 (    6)
  SS BOND              : angle       3.78344 (   12)
  hydrogen bonds       : bond        0.06623 (  332)
  hydrogen bonds       : angle       4.95519 (  930)
  link_BETA1-4         : bond        0.00395 (    3)
  link_BETA1-4         : angle       2.25964 (    9)
  link_NAG-ASN         : bond        0.00544 (    9)
  link_NAG-ASN         : angle       2.29778 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B  508 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6453 (p0)
REVERT: A  121 MET cc_start: 0.8730 (mtm) cc_final: 0.8491 (mtp)
REVERT: A  180 LYS cc_start: 0.7574 (mttt) cc_final: 0.7158 (mtmp)
  outliers start: 8
  outliers final: 2
  residues processed: 87
  average time/residue: 0.5284
  time to fit residues: 48.1232
Evaluate side-chains
  70 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  508 ASP
Chi-restraints excluded: chain A residue  554 LYS
Chi-restraints excluded: chain A residue  577 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 579 GLN
A  99 GLN
A 532 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.169657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.136463 restraints weight = 5971.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.36
r_work: 0.3397 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6266  Z= 0.174
  Angle     :  0.657   9.126   8557  Z= 0.334
  Chirality :  0.049   0.311    951
  Planarity :  0.005   0.035   1078
  Dihedral  :  5.417  41.006   1086
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.57 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.83 %
    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 aren not related in a simple way.
  whole:  1.20 (0.29), residues: 763
  helix:  1.41 (0.26), residues: 387
  sheet:  0.65 (0.55), residues: 74
  loop :  0.17 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 190 
 TYR   0.022   0.002   TYR A 383 
 PHE   0.016   0.002   PHE A 521 
 TRP   0.016   0.002   TRP A 476 
 HIS   0.009   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6248)
  covalent geometry    : angle       0.63065 ( 8509)
  SS BOND              : bond        0.00985 (    6)
  SS BOND              : angle       3.05558 (   12)
  hydrogen bonds       : bond        0.06496 (  332)
  hydrogen bonds       : angle       4.66835 (  930)
  link_BETA1-4         : bond        0.00692 (    3)
  link_BETA1-4         : angle       1.99512 (    9)
  link_NAG-ASN         : bond        0.01563 (    9)
  link_NAG-ASN         : angle       2.46847 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7520 (mp)
REVERT: A  569 GLU cc_start: 0.8258 (tt0) cc_final: 0.7999 (tt0)
  outliers start: 9
  outliers final: 3
  residues processed: 76
  average time/residue: 0.5201
  time to fit residues: 41.4480
Evaluate side-chains
  69 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 8 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 579 GLN
A 524 GLN
A 532 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.170166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.137002 restraints weight = 6023.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.39
r_work: 0.3403 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6266  Z= 0.144
  Angle     :  0.589   8.279   8557  Z= 0.301
  Chirality :  0.046   0.287    951
  Planarity :  0.004   0.034   1078
  Dihedral  :  4.662  37.843   1086
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.57 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.49 %
    Favored  : 84.84 %
  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 aren not related in a simple way.
  whole:  1.32 (0.29), residues: 763
  helix:  1.48 (0.26), residues: 390
  sheet:  0.76 (0.56), residues: 73
  loop :  0.24 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.020   0.001   TYR A 383 
 PHE   0.012   0.002   PHE A 521 
 TRP   0.015   0.001   TRP A 476 
 HIS   0.007   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6248)
  covalent geometry    : angle       0.56781 ( 8509)
  SS BOND              : bond        0.00540 (    6)
  SS BOND              : angle       2.61971 (   12)
  hydrogen bonds       : bond        0.05604 (  332)
  hydrogen bonds       : angle       4.55168 (  930)
  link_BETA1-4         : bond        0.00531 (    3)
  link_BETA1-4         : angle       1.74863 (    9)
  link_NAG-ASN         : bond        0.00762 (    9)
  link_NAG-ASN         : angle       2.10249 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6678 (mm-30)
REVERT: A  150 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.5789 (mpt)
REVERT: A  569 GLU cc_start: 0.8171 (tt0) cc_final: 0.7939 (tt0)
  outliers start: 9
  outliers final: 1
  residues processed: 84
  average time/residue: 0.4917
  time to fit residues: 43.3218
Evaluate side-chains
  73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  150 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0030
   chunk 58 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 48 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN
B 579 GLN
A 532 GLN

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 = 0.170566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.133405 restraints weight = 6074.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.43
r_work: 0.3353 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6266  Z= 0.128
  Angle     :  0.561   8.679   8557  Z= 0.285
  Chirality :  0.044   0.294    951
  Planarity :  0.004   0.035   1078
  Dihedral  :  4.392  30.599   1086
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.57 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.49 %
    Favored  : 84.29 %
  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 aren not related in a simple way.
  whole:  1.56 (0.30), residues: 763
  helix:  1.66 (0.26), residues: 391
  sheet:  0.84 (0.57), residues: 73
  loop :  0.39 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 338 
 TYR   0.017   0.001   TYR A 383 
 PHE   0.014   0.001   PHE A 521 
 TRP   0.013   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6248)
  covalent geometry    : angle       0.53960 ( 8509)
  SS BOND              : bond        0.00634 (    6)
  SS BOND              : angle       2.76067 (   12)
  hydrogen bonds       : bond        0.05276 (  332)
  hydrogen bonds       : angle       4.49996 (  930)
  link_BETA1-4         : bond        0.00569 (    3)
  link_BETA1-4         : angle       1.62407 (    9)
  link_NAG-ASN         : bond        0.00416 (    9)
  link_NAG-ASN         : angle       1.88830 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6440 (mm-30)
REVERT: A  150 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.5761 (mpt)
REVERT: A  196 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7574 (p0)
REVERT: A  569 GLU cc_start: 0.8160 (tt0) cc_final: 0.7914 (tt0)
  outliers start: 12
  outliers final: 3
  residues processed: 83
  average time/residue: 0.5008
  time to fit residues: 43.6265
Evaluate side-chains
  75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN
B 579 GLN
A 193 ASN
A 532 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.165275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.131303 restraints weight = 6081.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.49
r_work: 0.3343 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 2.56 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074   6266  Z= 0.245
  Angle     :  0.723  10.713   8557  Z= 0.370
  Chirality :  0.051   0.373    951
  Planarity :  0.006   0.041   1078
  Dihedral  :  4.930  27.831   1086
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.57 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.49 %
    Favored  : 83.55 %
  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 aren not related in a simple way.
  whole:  0.96 (0.30), residues: 763
  helix:  1.10 (0.25), residues: 387
  sheet:  0.85 (0.56), residues: 81
  loop :  0.11 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 587 
 TYR   0.023   0.002   TYR A 383 
 PHE   0.022   0.003   PHE A 521 
 TRP   0.019   0.002   TRP A 476 
 HIS   0.010   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 6248)
  covalent geometry    : angle       0.70067 ( 8509)
  SS BOND              : bond        0.00692 (    6)
  SS BOND              : angle       3.28710 (   12)
  hydrogen bonds       : bond        0.07499 (  332)
  hydrogen bonds       : angle       4.86824 (  930)
  link_BETA1-4         : bond        0.00528 (    3)
  link_BETA1-4         : angle       2.08128 (    9)
  link_NAG-ASN         : bond        0.00335 (    9)
  link_NAG-ASN         : angle       2.18836 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6818 (mtp85) cc_final: 0.6550 (mtp85)
REVERT: A   28 GLU cc_start: 0.7323 (pt0) cc_final: 0.7038 (pt0)
REVERT: A  150 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.5977 (mpt)
REVERT: A  187 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7307 (mt-10)
REVERT: A  225 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7944 (mm-30)
REVERT: A  569 GLU cc_start: 0.8214 (tt0) cc_final: 0.7981 (tt0)
  outliers start: 16
  outliers final: 6
  residues processed: 79
  average time/residue: 0.5562
  time to fit residues: 46.1028
Evaluate side-chains
  73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  399 HIS
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  489 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    0.0770
   chunk 22 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 75 optimal weight:    0.3980
   chunk 30 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.169699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.132208 restraints weight = 6093.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.46
r_work: 0.3336 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   6266  Z= 0.129
  Angle     :  0.582  12.916   8557  Z= 0.295
  Chirality :  0.044   0.340    951
  Planarity :  0.004   0.039   1078
  Dihedral  :  4.493  26.080   1086
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.31 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.16 %
    Favored  : 82.99 %
  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 aren not related in a simple way.
  whole:  1.47 (0.30), residues: 763
  helix:  1.52 (0.26), residues: 391
  sheet:  0.93 (0.57), residues: 78
  loop :  0.38 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 587 
 TYR   0.016   0.001   TYR A 383 
 PHE   0.011   0.001   PHE A 521 
 TRP   0.013   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6248)
  covalent geometry    : angle       0.55949 ( 8509)
  SS BOND              : bond        0.00660 (    6)
  SS BOND              : angle       3.07321 (   12)
  hydrogen bonds       : bond        0.05313 (  332)
  hydrogen bonds       : angle       4.56078 (  930)
  link_BETA1-4         : bond        0.00492 (    3)
  link_BETA1-4         : angle       1.67520 (    9)
  link_NAG-ASN         : bond        0.00371 (    9)
  link_NAG-ASN         : angle       1.88957 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6520 (mtp85) cc_final: 0.6263 (mtp85)
REVERT: B  508 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7019 (p0)
REVERT: A   38 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6422 (mm-30)
REVERT: A  150 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.5744 (mpt)
REVERT: A  569 GLU cc_start: 0.8116 (tt0) cc_final: 0.7872 (tt0)
  outliers start: 10
  outliers final: 3
  residues processed: 72
  average time/residue: 0.5019
  time to fit residues: 37.9681
Evaluate side-chains
  68 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  508 ASP
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    0.0980
   chunk 57 optimal weight:    0.0270
   chunk 62 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.181280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.149105 restraints weight = 5820.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.42
r_work: 0.3411 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   6266  Z= 0.129
  Angle     :  0.580  14.546   8557  Z= 0.293
  Chirality :  0.044   0.333    951
  Planarity :  0.004   0.037   1078
  Dihedral  :  4.325  27.645   1086
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.57 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.45 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.30), residues: 763
  helix:  1.64 (0.26), residues: 391
  sheet:  1.05 (0.58), residues: 78
  loop :  0.43 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 587 
 TYR   0.017   0.001   TYR A 383 
 PHE   0.015   0.001   PHE A 521 
 TRP   0.014   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6248)
  covalent geometry    : angle       0.55873 ( 8509)
  SS BOND              : bond        0.00628 (    6)
  SS BOND              : angle       3.02067 (   12)
  hydrogen bonds       : bond        0.05205 (  332)
  hydrogen bonds       : angle       4.46344 (  930)
  link_BETA1-4         : bond        0.00532 (    3)
  link_BETA1-4         : angle       1.60564 (    9)
  link_NAG-ASN         : bond        0.00354 (    9)
  link_NAG-ASN         : angle       1.83626 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6755 (mtp85) cc_final: 0.6536 (mtp85)
REVERT: A   36 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7373 (tp30)
REVERT: A   38 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6742 (mm-30)
REVERT: A  150 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.5829 (mpt)
REVERT: A  569 GLU cc_start: 0.8211 (tt0) cc_final: 0.8000 (tt0)
  outliers start: 6
  outliers final: 2
  residues processed: 70
  average time/residue: 0.4875
  time to fit residues: 35.8662
Evaluate side-chains
  70 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0070
   chunk 35 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.167345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.130596 restraints weight = 6149.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 1.42
r_work: 0.3319 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   6266  Z= 0.158
  Angle     :  0.617  13.474   8557  Z= 0.313
  Chirality :  0.045   0.339    951
  Planarity :  0.005   0.036   1078
  Dihedral  :  4.445  27.978   1086
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.57 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.27 %
    Favored  : 82.26 %
  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 aren not related in a simple way.
  whole:  1.51 (0.30), residues: 763
  helix:  1.55 (0.26), residues: 391
  sheet:  1.02 (0.57), residues: 78
  loop :  0.40 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 587 
 TYR   0.020   0.001   TYR A 383 
 PHE   0.018   0.002   PHE A 521 
 TRP   0.015   0.002   TRP A 476 
 HIS   0.007   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6248)
  covalent geometry    : angle       0.59571 ( 8509)
  SS BOND              : bond        0.00743 (    6)
  SS BOND              : angle       3.10105 (   12)
  hydrogen bonds       : bond        0.05815 (  332)
  hydrogen bonds       : angle       4.53513 (  930)
  link_BETA1-4         : bond        0.00551 (    3)
  link_BETA1-4         : angle       1.66243 (    9)
  link_NAG-ASN         : bond        0.00361 (    9)
  link_NAG-ASN         : angle       1.90662 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6607 (mtp85) cc_final: 0.6347 (mtp85)
REVERT: A   28 GLU cc_start: 0.7070 (pt0) cc_final: 0.6772 (pt0)
REVERT: A   38 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6495 (mm-30)
REVERT: A  150 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.5778 (mpt)
REVERT: A  569 GLU cc_start: 0.8191 (tt0) cc_final: 0.7958 (tt0)
  outliers start: 8
  outliers final: 4
  residues processed: 73
  average time/residue: 0.5423
  time to fit residues: 41.3579
Evaluate side-chains
  73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.168711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.131793 restraints weight = 6108.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.43
r_work: 0.3321 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6266  Z= 0.154
  Angle     :  0.622  16.186   8557  Z= 0.315
  Chirality :  0.045   0.341    951
  Planarity :  0.005   0.037   1078
  Dihedral  :  4.492  30.611   1086
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.70 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 16.82 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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 aren not related in a simple way.
  whole:  1.55 (0.30), residues: 763
  helix:  1.62 (0.26), residues: 385
  sheet:  0.96 (0.56), residues: 78
  loop :  0.42 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 587 
 TYR   0.019   0.001   TYR A 383 
 PHE   0.016   0.002   PHE A 521 
 TRP   0.015   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6248)
  covalent geometry    : angle       0.60172 ( 8509)
  SS BOND              : bond        0.00681 (    6)
  SS BOND              : angle       2.95993 (   12)
  hydrogen bonds       : bond        0.05757 (  332)
  hydrogen bonds       : angle       4.54127 (  930)
  link_BETA1-4         : bond        0.00483 (    3)
  link_BETA1-4         : angle       1.63391 (    9)
  link_NAG-ASN         : bond        0.00366 (    9)
  link_NAG-ASN         : angle       1.91350 (   27)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6524 (mtp85) cc_final: 0.6299 (mtp85)
REVERT: A   28 GLU cc_start: 0.7024 (pt0) cc_final: 0.6724 (pt0)
REVERT: A   36 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7366 (tp30)
REVERT: A   38 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6472 (mm-30)
REVERT: A  150 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.5763 (mpt)
REVERT: A  569 GLU cc_start: 0.8176 (tt0) cc_final: 0.7949 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 71
  average time/residue: 0.5198
  time to fit residues: 38.8317
Evaluate side-chains
  70 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.166289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.134673 restraints weight = 6070.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.50
r_work: 0.3327 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   6266  Z= 0.221
  Angle     :  0.708  16.583   8557  Z= 0.360
  Chirality :  0.050   0.378    951
  Planarity :  0.005   0.040   1078
  Dihedral  :  4.898  34.136   1086
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.23 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.27 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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 aren not related in a simple way.
  whole:  1.08 (0.30), residues: 763
  helix:  1.22 (0.26), residues: 388
  sheet:  0.80 (0.55), residues: 81
  loop :  0.15 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 167 
 TYR   0.021   0.002   TYR A 383 
 PHE   0.020   0.002   PHE A 521 
 TRP   0.015   0.002   TRP A 476 
 HIS   0.008   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 6248)
  covalent geometry    : angle       0.68708 ( 8509)
  SS BOND              : bond        0.00761 (    6)
  SS BOND              : angle       3.16543 (   12)
  hydrogen bonds       : bond        0.07002 (  332)
  hydrogen bonds       : angle       4.80266 (  930)
  link_BETA1-4         : bond        0.00482 (    3)
  link_BETA1-4         : angle       1.80741 (    9)
  link_NAG-ASN         : bond        0.00337 (    9)
  link_NAG-ASN         : angle       2.12623 (   27)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2257.74 seconds
wall clock time: 39 minutes 0.95 seconds (2340.95 seconds total)