Starting phenix.real_space_refine
on Tue Feb 11 17:21:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n0c_24103/02_2025/7n0c_24103.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n0c_24103/02_2025/7n0c_24103.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n0c_24103/02_2025/7n0c_24103.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n0c_24103/02_2025/7n0c_24103.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n0c_24103/02_2025/7n0c_24103.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n0c_24103/02_2025/7n0c_24103.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002 sd=   0.079
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: 7
    Type Number    sf(0)   Gaussians
     Zn      5      6.06       5
     P      49      5.49       5
     Mg      2      5.21       5
     S      52      5.16       5
     C    3685      2.51       5
     N    1033      2.21       5
     O    1262      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6088
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 955
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 7, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 4090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 4090
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 26, 'TRANS': 486}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 529
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 1, 'rna3p': 23}
    Chain: "D"
      Number of atoms: 506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 506
          Classifications: {'RNA': 24}
          Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 12}
          Link IDs: {'rna3p': 23}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Unusual residues: {' MG': 2, ' ZN': 3}
          Classifications: {'undetermined': 5, 'water': 1}
          Link IDs: {None: 5}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    520  SG  CYS A  74      40.023  24.791  92.919  1.00 51.61           S
  ATOM    546  SG  CYS A  77      36.858  25.756  93.856  1.00 51.71           S
  ATOM    651  SG  CYS A  90      37.756  22.498  94.187  1.00 57.18           S
  ATOM    854  SG  CYS A 117      52.155  10.429  99.974  1.00112.87           S
  ATOM    874  SG  CYS A 120      52.595  10.897 103.370  1.00118.76           S
  ATOM    935  SG  CYS A 128      55.207  11.780 101.062  1.00109.13           S
  ATOM    947  SG  CYS A 130      55.533   8.590 102.165  1.00128.22           S
  ATOM   2582  SG  CYS B 207      44.467  25.564  61.321  1.00 62.28           S
  ATOM   2602  SG  CYS B 210      45.850  26.017  57.879  1.00 73.07           S
  ATOM   2723  SG  CYS B 226      43.066  27.801  59.072  1.00 56.89           S
  ATOM   3023  SG  CYS B 261      24.861  55.828  57.812  1.00 65.13           S
  ATOM   3153  SG  CYS B 279      27.911  54.398  59.550  1.00 44.17           S
  ATOM   4543  SG  CYS B 452      49.557  45.528  11.477  1.00134.04           S
  ATOM   4657  SG  CYS B 477      45.734  45.992  12.975  1.00138.24           S
  ATOM   4699  SG  CYS B 484      48.139  43.581  13.594  1.00139.40           S

  Time building chain proxies: 4.60, per 1000 atoms: 0.76
  Number of scatterers: 6088
  At special positions: 0
  Unit cell: (70.488, 89.712, 144.18, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      5     29.99
     S      52     16.00
     P      49     15.00
     Mg      2     11.99
     O    1262      8.00
     N    1033      7.00
     C    3685      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: 1.73
  Conformation dependent library (CDL) restraints added in 734.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 201 "
        pdb="ZN    ZN A 201 " - pdb=" NE2 HIS A  83 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  77 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  90 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  74 "
      pdb="  ZN A 202 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 128 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 130 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 120 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 117 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" ND1 HIS B 229 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 226 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 210 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 207 "
      pdb="  ZN B 604 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 264 "
        pdb="ZN    ZN B 604 " - pdb=" NE2 HIS B 257 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 279 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 261 "
      pdb="  ZN B 605 "
        pdb="ZN    ZN B 605 " - pdb=" ND1 HIS B 487 "
        pdb="ZN    ZN B 605 " - pdb=" SG  CYS B 484 "
        pdb="ZN    ZN B 605 " - pdb=" SG  CYS B 477 "
        pdb="ZN    ZN B 605 " - pdb=" SG  CYS B 452 "
      Number of angles added : 17


  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1204

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      26.6% alpha, 12.1% beta
      23 base pairs and 33 stacking pairs defined.
    Time for finding SS restraints: 2.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 19
    Processing helix  chain 'A' and resid 22 through 33
    Processing helix  chain 'A' and resid 74 through 80
    Processing helix  chain 'A' and resid 85 through 89
      removed outlier: 4.249A  pdb=" N   PHE A  89 " --> pdb=" O   PRO A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 104
      No H-bonds generated for 'chain 'A' and resid 102 through 104'
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 4.067A  pdb=" N   LYS A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.595A  pdb=" N   VAL B  29 " --> pdb=" O   HIS B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 155
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 187 through 194
      removed outlier: 3.844A  pdb=" N   ALA B 191 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   THR B 193 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 248
      removed outlier: 3.850A  pdb=" N   GLY B 248 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 245 through 248'
    Processing helix  chain 'B' and resid 253 through 258
      removed outlier: 3.654A  pdb=" N   ASP B 258 " --> pdb=" O   GLN B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 274
    Processing helix  chain 'B' and resid 275 through 287
      removed outlier: 3.841A  pdb=" N   CYS B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 325
      removed outlier: 3.584A  pdb=" N   ASN B 306 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS B 318 " --> pdb=" O   HIS B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 374
    Processing helix  chain 'B' and resid 414 through 416
      No H-bonds generated for 'chain 'B' and resid 414 through 416'
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 3.931A  pdb=" N   VAL B 437 " --> pdb=" O   SER B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 480
      removed outlier: 3.589A  pdb=" N   GLY B 480 " --> pdb=" O   ARG B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 505
      removed outlier: 4.313A  pdb=" N   ASN B 489 " --> pdb=" O   ARG B 485 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   GLU B 490 " --> pdb=" O   HIS B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 523
      removed outlier: 3.754A  pdb=" N   ASN B 521 " --> pdb=" O   ASN B 518 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56
    Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55
      removed outlier: 4.365A  pdb=" N   TYR B 124 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118
      removed outlier: 5.519A  pdb=" N   CYS B  94 " --> pdb=" O   PRO B 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 225
      removed outlier: 3.726A  pdb=" N   THR B 223 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 365
      removed outlier: 7.020A  pdb=" N   LEU B 329 " --> pdb=" O   LYS B 349 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   TYR B 351 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   ASP B 331 " --> pdb=" O   TYR B 351 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL B 381 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 401
    Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412
    Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 447
      removed outlier: 5.938A  pdb=" N   TYR B 446 " --> pdb=" O   ILE B 474 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    125 hydrogen bonds defined for protein.
    324 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      53 hydrogen bonds
      106 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 860
        1.29 -     1.42: 2016
        1.42 -     1.56: 3298
        1.56 -     1.69: 97
        1.69 -     1.83: 68
  Bond restraints: 6339
  Sorted by residual:
  bond pdb=" C   PRO B 106 "
       pdb=" O   PRO B 106 "
    ideal  model  delta    sigma   weight residual
    1.233  1.151  0.082 1.06e-02 8.90e+03 6.06e+01
  bond pdb=" CA  PRO B 106 "
       pdb=" CB  PRO B 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.485  0.048 1.26e-02 6.30e+03 1.44e+01
  bond pdb=" N   LEU B 105 "
       pdb=" CA  LEU B 105 "
    ideal  model  delta    sigma   weight residual
    1.452  1.499 -0.047 1.41e-02 5.03e+03 1.12e+01
  bond pdb=" C   ASN B 104 "
       pdb=" O   ASN B 104 "
    ideal  model  delta    sigma   weight residual
    1.234  1.195  0.039 1.19e-02 7.06e+03 1.06e+01
  bond pdb=" C   LEU B 105 "
       pdb=" N   PRO B 106 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 1.11e-02 8.12e+03 9.49e+00
  ... (remaining 6334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 8233
        1.82 -     3.63: 502
        3.63 -     5.45: 81
        5.45 -     7.27: 19
        7.27 -     9.09: 6
  Bond angle restraints: 8841
  Sorted by residual:
  angle pdb=" CA  PRO B 106 "
        pdb=" C   PRO B 106 "
        pdb=" O   PRO B 106 "
      ideal   model   delta    sigma   weight residual
     120.97  111.88    9.09 1.17e+00 7.31e-01 6.03e+01
  angle pdb=" C   PRO B 106 "
        pdb=" CA  PRO B 106 "
        pdb=" CB  PRO B 106 "
      ideal   model   delta    sigma   weight residual
     111.11  103.39    7.72 1.17e+00 7.31e-01 4.35e+01
  angle pdb=" CA  PRO B 106 "
        pdb=" C   PRO B 106 "
        pdb=" N   LEU B 107 "
      ideal   model   delta    sigma   weight residual
     115.93  123.67   -7.74 1.26e+00 6.30e-01 3.78e+01
  angle pdb=" CA  LEU B 105 "
        pdb=" C   LEU B 105 "
        pdb=" N   PRO B 106 "
      ideal   model   delta    sigma   weight residual
     117.67  123.60   -5.93 1.01e+00 9.80e-01 3.45e+01
  angle pdb=" N   VAL B 167 "
        pdb=" CA  VAL B 167 "
        pdb=" C   VAL B 167 "
      ideal   model   delta    sigma   weight residual
     112.90  107.43    5.47 9.60e-01 1.09e+00 3.24e+01
  ... (remaining 8836 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.34: 3624
       34.34 -    68.68: 129
       68.68 -   103.02: 12
      103.02 -   137.36: 0
      137.36 -   171.70: 1
  Dihedral angle restraints: 3766
    sinusoidal: 1891
      harmonic: 1875
  Sorted by residual:
  dihedral pdb=" O4'   U T   6 "
           pdb=" C1'   U T   6 "
           pdb=" N1    U T   6 "
           pdb=" C2    U T   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   60.30  171.70     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" CA  HIS B 268 "
           pdb=" C   HIS B 268 "
           pdb=" N   VAL B 269 "
           pdb=" CA  VAL B 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.65   23.35     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  TYR B 237 "
           pdb=" C   TYR B 237 "
           pdb=" N   ASN B 238 "
           pdb=" CA  ASN B 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.88  -20.12     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 3763 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 671
       0.041 -    0.083: 237
       0.083 -    0.124: 74
       0.124 -    0.166: 21
       0.166 -    0.207: 12
  Chirality restraints: 1015
  Sorted by residual:
  chirality pdb=" CA  ASN B 478 "
            pdb=" N   ASN B 478 "
            pdb=" C   ASN B 478 "
            pdb=" CB  ASN B 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  CYS B 210 "
            pdb=" N   CYS B 210 "
            pdb=" C   CYS B 210 "
            pdb=" CB  CYS B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ASP B 415 "
            pdb=" N   ASP B 415 "
            pdb=" C   ASP B 415 "
            pdb=" CB  ASP B 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1012 not shown)

  Planarity restraints: 953
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 487 "   -0.060 2.00e-02 2.50e+03   4.49e-02 3.02e+01
        pdb=" CG  HIS B 487 "    0.061 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 487 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 487 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 487 "   -0.039 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 487 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 229 "   -0.053 2.00e-02 2.50e+03   4.01e-02 2.41e+01
        pdb=" CG  HIS B 229 "    0.054 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 229 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 229 "    0.028 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 229 "   -0.037 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 229 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A  83 "    0.044 2.00e-02 2.50e+03   3.24e-02 1.58e+01
        pdb=" CG  HIS A  83 "   -0.047 2.00e-02 2.50e+03
        pdb=" ND1 HIS A  83 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 HIS A  83 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 HIS A  83 "    0.028 2.00e-02 2.50e+03
        pdb=" NE2 HIS A  83 "    0.019 2.00e-02 2.50e+03
  ... (remaining 950 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 510
        2.72 -     3.27: 5827
        3.27 -     3.81: 10466
        3.81 -     4.36: 12799
        4.36 -     4.90: 20376
  Nonbonded interactions: 49978
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  90 "
            pdb="MG    MG B 602 "
     model   vdw
     2.180 2.170
  nonbonded pdb=" OD2 ASP B  90 "
            pdb="MG    MG B 601 "
     model   vdw
     2.216 2.170
  nonbonded pdb=" O   ILE B  80 "
            pdb=" OH  TYR B 296 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER B 171 "
            pdb=" O   TRP B 227 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OE1 GLU B 302 "
            pdb=" ND2 ASN B 422 "
     model   vdw
     2.257 3.120
  ... (remaining 49973 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:             1.370
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     21.700
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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      :  0.009   0.082   6339  Z= 0.571
  Angle     :  0.996   9.085   8841  Z= 0.611
  Chirality :  0.052   0.207   1015
  Planarity :  0.007   0.059    953
  Dihedral  : 16.673 171.703   2562
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.80 (0.27), residues: 638
  helix: -3.43 (0.29), residues: 142
  sheet: -2.66 (0.62), residues: 49
  loop : -2.34 (0.25), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 385 
 HIS   0.011   0.003   HIS B 257 
 PHE   0.040   0.003   PHE A  19 
 TYR   0.022   0.002   TYR A  76 
 ARG   0.005   0.001   ARG B 163 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7961 (mmtp)
REVERT: A   98 GLN cc_start: 0.8060 (mp-120) cc_final: 0.7752 (mm110)
REVERT: A  114 ASN cc_start: 0.8736 (m-40) cc_final: 0.8522 (m110)
REVERT: B   58 MET cc_start: 0.8765 (mtp) cc_final: 0.8335 (mtp)
REVERT: B  169 MET cc_start: 0.8659 (ttp) cc_final: 0.7961 (tmm)
REVERT: B  330 HIS cc_start: 0.7916 (m-70) cc_final: 0.6908 (m-70)
REVERT: B  499 ASN cc_start: 0.7843 (m-40) cc_final: 0.7558 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2182
  time to fit residues: 29.5258
Evaluate side-chains
  88 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0010
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** B  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  95 HIS
B 499 ASN
B 521 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.177998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.121724 restraints weight = 7259.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.85
r_work: 0.3072 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6339  Z= 0.193
  Angle     :  0.541   5.751   8841  Z= 0.284
  Chirality :  0.039   0.148   1015
  Planarity :  0.005   0.052    953
  Dihedral  : 16.332 172.709   1417
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.85 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.29), residues: 638
  helix: -1.96 (0.39), residues: 139
  sheet: -2.75 (0.60), residues: 48
  loop : -1.87 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 385 
 HIS   0.004   0.001   HIS B 283 
 PHE   0.013   0.001   PHE B 133 
 TYR   0.023   0.001   TYR B 370 
 ARG   0.005   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8349 (t) cc_final: 0.8131 (t)
REVERT: A   95 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7289 (mmtp)
REVERT: A   98 GLN cc_start: 0.8244 (mp-120) cc_final: 0.7825 (mm-40)
REVERT: A  114 ASN cc_start: 0.8778 (m-40) cc_final: 0.8409 (m110)
REVERT: B   58 MET cc_start: 0.8994 (mtp) cc_final: 0.8574 (mtp)
REVERT: B   61 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8792 (mtpp)
REVERT: B  169 MET cc_start: 0.8804 (ttp) cc_final: 0.8505 (tmm)
REVERT: B  330 HIS cc_start: 0.7439 (m-70) cc_final: 0.6317 (m170)
REVERT: B  368 TYR cc_start: 0.8059 (t80) cc_final: 0.7845 (t80)
REVERT: B  384 PHE cc_start: 0.8997 (m-80) cc_final: 0.8740 (m-80)
REVERT: B  391 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7610 (mtp180)
REVERT: B  395 ASN cc_start: 0.8455 (p0) cc_final: 0.8116 (p0)
REVERT: B  499 ASN cc_start: 0.7747 (m110) cc_final: 0.7461 (m-40)
  outliers start: 9
  outliers final: 5
  residues processed: 110
  average time/residue: 0.1872
  time to fit residues: 26.9644
Evaluate side-chains
  95 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  223 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 47 optimal weight:    0.0030
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 64 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0970
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
** B  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.179600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.124123 restraints weight = 7398.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.81
r_work: 0.3107 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6339  Z= 0.168
  Angle     :  0.500   5.880   8841  Z= 0.256
  Chirality :  0.038   0.147   1015
  Planarity :  0.004   0.058    953
  Dihedral  : 16.078 173.035   1417
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 11.03 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.31), residues: 638
  helix: -1.31 (0.42), residues: 148
  sheet: -2.30 (0.59), residues: 60
  loop : -1.50 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 520 
 HIS   0.003   0.001   HIS B 257 
 PHE   0.011   0.001   PHE B 133 
 TYR   0.010   0.001   TYR B 370 
 ARG   0.007   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8206 (t) cc_final: 0.7940 (t)
REVERT: A   40 ASN cc_start: 0.8902 (t0) cc_final: 0.8534 (t0)
REVERT: A   95 LYS cc_start: 0.7507 (mmtt) cc_final: 0.7195 (mmtp)
REVERT: A   98 GLN cc_start: 0.8435 (mp-120) cc_final: 0.8079 (mm-40)
REVERT: A  114 ASN cc_start: 0.8719 (m-40) cc_final: 0.8319 (m110)
REVERT: B   58 MET cc_start: 0.9037 (mtp) cc_final: 0.8633 (mtp)
REVERT: B   61 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8654 (mtpp)
REVERT: B  169 MET cc_start: 0.8783 (ttp) cc_final: 0.8511 (ptm)
REVERT: B  185 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8496 (mt)
REVERT: B  330 HIS cc_start: 0.7550 (m-70) cc_final: 0.6828 (m170)
REVERT: B  334 ASN cc_start: 0.8493 (t0) cc_final: 0.8251 (p0)
REVERT: B  384 PHE cc_start: 0.8948 (m-80) cc_final: 0.8733 (m-80)
REVERT: B  391 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7570 (mtp180)
REVERT: B  395 ASN cc_start: 0.8493 (p0) cc_final: 0.8055 (p0)
REVERT: B  398 VAL cc_start: 0.9088 (t) cc_final: 0.8704 (p)
REVERT: B  445 PHE cc_start: 0.8932 (p90) cc_final: 0.8616 (p90)
REVERT: B  499 ASN cc_start: 0.7702 (m110) cc_final: 0.7484 (m-40)
REVERT: B  512 LYS cc_start: 0.8636 (mmtm) cc_final: 0.8434 (mmtm)
  outliers start: 18
  outliers final: 12
  residues processed: 110
  average time/residue: 0.1729
  time to fit residues: 25.4620
Evaluate side-chains
  110 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  382 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 66 optimal weight:   20.0000
   chunk 58 optimal weight:    9.9990
   chunk 67 optimal weight:   10.0000
   chunk 47 optimal weight:    0.4980
   chunk 37 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** B  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.179828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.122614 restraints weight = 7538.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.75
r_work: 0.3105 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6339  Z= 0.168
  Angle     :  0.484   5.893   8841  Z= 0.249
  Chirality :  0.038   0.142   1015
  Planarity :  0.004   0.061    953
  Dihedral  : 15.956 173.262   1417
  Min Nonbonded Distance : 1.443

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 11.93 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.32), residues: 638
  helix: -0.95 (0.44), residues: 144
  sheet: -2.16 (0.60), residues: 62
  loop : -1.28 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 520 
 HIS   0.003   0.001   HIS B 257 
 PHE   0.017   0.001   PHE B 350 
 TYR   0.008   0.001   TYR B 370 
 ARG   0.004   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8093 (t) cc_final: 0.7816 (t)
REVERT: A   40 ASN cc_start: 0.8891 (t0) cc_final: 0.8568 (t0)
REVERT: A   95 LYS cc_start: 0.7495 (mmtt) cc_final: 0.7176 (mmtp)
REVERT: A   98 GLN cc_start: 0.8458 (mp-120) cc_final: 0.8157 (mm-40)
REVERT: A  114 ASN cc_start: 0.8735 (m-40) cc_final: 0.8334 (m110)
REVERT: B   58 MET cc_start: 0.9008 (mtp) cc_final: 0.8622 (mtp)
REVERT: B   61 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8498 (mtpp)
REVERT: B  169 MET cc_start: 0.8806 (ttp) cc_final: 0.8499 (ptm)
REVERT: B  185 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8444 (mt)
REVERT: B  315 MET cc_start: 0.8136 (tpp) cc_final: 0.7883 (tpp)
REVERT: B  330 HIS cc_start: 0.7636 (m-70) cc_final: 0.6642 (m-70)
REVERT: B  384 PHE cc_start: 0.8992 (m-80) cc_final: 0.8777 (m-80)
REVERT: B  391 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7665 (mtp180)
REVERT: B  395 ASN cc_start: 0.8528 (p0) cc_final: 0.8094 (p0)
REVERT: B  398 VAL cc_start: 0.9061 (t) cc_final: 0.8706 (p)
REVERT: B  445 PHE cc_start: 0.8872 (p90) cc_final: 0.8463 (p90)
REVERT: B  499 ASN cc_start: 0.7666 (m110) cc_final: 0.7453 (m-40)
  outliers start: 18
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1719
  time to fit residues: 24.8810
Evaluate side-chains
  110 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  382 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 25 optimal weight:    0.4980
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.188741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.134581 restraints weight = 7435.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.81
r_work: 0.3240 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6339  Z= 0.212
  Angle     :  0.489   5.247   8841  Z= 0.253
  Chirality :  0.039   0.141   1015
  Planarity :  0.004   0.061    953
  Dihedral  : 15.928 173.119   1417
  Min Nonbonded Distance : 1.069

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 12.48 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.32), residues: 638
  helix: -0.77 (0.46), residues: 143
  sheet: -2.08 (0.61), residues: 62
  loop : -1.20 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 520 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.014   0.001   PHE A  19 
 TYR   0.008   0.001   TYR B 420 
 ARG   0.002   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8252 (t) cc_final: 0.7979 (t)
REVERT: B   58 MET cc_start: 0.9018 (mtp) cc_final: 0.8475 (mtp)
REVERT: B   61 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8688 (mtpp)
REVERT: B  169 MET cc_start: 0.8757 (ttp) cc_final: 0.8448 (ptm)
REVERT: B  185 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8639 (mt)
REVERT: B  315 MET cc_start: 0.8145 (tpp) cc_final: 0.7921 (tpp)
REVERT: B  330 HIS cc_start: 0.7611 (m-70) cc_final: 0.6786 (m-70)
REVERT: B  391 ARG cc_start: 0.8343 (ttm170) cc_final: 0.7986 (mtp180)
REVERT: B  395 ASN cc_start: 0.8544 (p0) cc_final: 0.8148 (p0)
REVERT: B  398 VAL cc_start: 0.9088 (t) cc_final: 0.8798 (p)
REVERT: B  445 PHE cc_start: 0.8880 (p90) cc_final: 0.8534 (p90)
REVERT: B  499 ASN cc_start: 0.7890 (m110) cc_final: 0.7662 (m-40)
  outliers start: 21
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1714
  time to fit residues: 25.1213
Evaluate side-chains
  109 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  382 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0470
   chunk 60 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
** B  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.188916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.134839 restraints weight = 7420.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.66
r_work: 0.3259 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6339  Z= 0.205
  Angle     :  0.499   6.882   8841  Z= 0.256
  Chirality :  0.039   0.136   1015
  Planarity :  0.004   0.056    953
  Dihedral  : 15.894 173.119   1417
  Min Nonbonded Distance : 1.113

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 13.56 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.32), residues: 638
  helix: -0.70 (0.45), residues: 143
  sheet: -1.93 (0.60), residues: 62
  loop : -1.13 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 520 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.017   0.001   PHE B 350 
 TYR   0.007   0.001   TYR B 420 
 ARG   0.003   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8184 (t) cc_final: 0.7899 (t)
REVERT: B   58 MET cc_start: 0.9020 (mtp) cc_final: 0.8482 (mtp)
REVERT: B   61 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8632 (mtpp)
REVERT: B  169 MET cc_start: 0.8750 (ttp) cc_final: 0.8446 (ptm)
REVERT: B  185 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8660 (mt)
REVERT: B  330 HIS cc_start: 0.7480 (m-70) cc_final: 0.6901 (m170)
REVERT: B  336 LYS cc_start: 0.8341 (mttm) cc_final: 0.8044 (mtpp)
REVERT: B  391 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7994 (mtp180)
REVERT: B  395 ASN cc_start: 0.8606 (p0) cc_final: 0.8290 (p0)
REVERT: B  398 VAL cc_start: 0.9075 (t) cc_final: 0.8756 (p)
REVERT: B  444 PHE cc_start: 0.7299 (t80) cc_final: 0.6986 (t80)
REVERT: B  445 PHE cc_start: 0.8870 (p90) cc_final: 0.8564 (p90)
REVERT: B  499 ASN cc_start: 0.7926 (m110) cc_final: 0.7669 (m-40)
  outliers start: 22
  outliers final: 15
  residues processed: 107
  average time/residue: 0.1712
  time to fit residues: 24.6462
Evaluate side-chains
  107 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  348 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.189954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.134687 restraints weight = 7579.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.68
r_work: 0.3234 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6339  Z= 0.235
  Angle     :  0.507   5.837   8841  Z= 0.261
  Chirality :  0.039   0.145   1015
  Planarity :  0.004   0.058    953
  Dihedral  : 15.892 172.825   1417
  Min Nonbonded Distance : 1.099

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.01 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.32), residues: 638
  helix: -0.71 (0.45), residues: 143
  sheet: -1.96 (0.59), residues: 62
  loop : -1.09 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 520 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.016   0.001   PHE B 350 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.004   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8178 (t) cc_final: 0.7905 (t)
REVERT: B   58 MET cc_start: 0.9030 (mtp) cc_final: 0.8600 (mtp)
REVERT: B   61 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8604 (mtpp)
REVERT: B  169 MET cc_start: 0.8787 (ttp) cc_final: 0.8444 (ptm)
REVERT: B  185 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8622 (mt)
REVERT: B  330 HIS cc_start: 0.7557 (m-70) cc_final: 0.6937 (m-70)
REVERT: B  391 ARG cc_start: 0.8379 (ttm170) cc_final: 0.8025 (mtp180)
REVERT: B  395 ASN cc_start: 0.8586 (p0) cc_final: 0.8291 (p0)
REVERT: B  398 VAL cc_start: 0.9088 (t) cc_final: 0.8777 (p)
REVERT: B  442 LEU cc_start: 0.7871 (mm) cc_final: 0.7669 (mm)
REVERT: B  445 PHE cc_start: 0.8853 (p90) cc_final: 0.8537 (p90)
REVERT: B  499 ASN cc_start: 0.7865 (m110) cc_final: 0.7630 (m-40)
  outliers start: 20
  outliers final: 14
  residues processed: 107
  average time/residue: 0.1695
  time to fit residues: 24.4019
Evaluate side-chains
  110 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  348 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0570
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
B  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.192123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.135702 restraints weight = 7544.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.59
r_work: 0.3278 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6339  Z= 0.167
  Angle     :  0.479   5.894   8841  Z= 0.245
  Chirality :  0.038   0.152   1015
  Planarity :  0.004   0.048    953
  Dihedral  : 15.814 173.041   1417
  Min Nonbonded Distance : 1.129

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 15.91 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.32), residues: 638
  helix: -0.67 (0.45), residues: 143
  sheet: -1.90 (0.59), residues: 62
  loop : -1.00 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 520 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.018   0.001   PHE B 350 
 TYR   0.007   0.001   TYR B 420 
 ARG   0.004   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8101 (t) cc_final: 0.7808 (t)
REVERT: B   58 MET cc_start: 0.9016 (mtp) cc_final: 0.8473 (mtp)
REVERT: B   61 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8575 (mtpp)
REVERT: B  169 MET cc_start: 0.8758 (ttp) cc_final: 0.8453 (ptm)
REVERT: B  185 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8637 (mt)
REVERT: B  330 HIS cc_start: 0.7496 (m-70) cc_final: 0.7013 (m-70)
REVERT: B  391 ARG cc_start: 0.8386 (ttm170) cc_final: 0.8048 (mtp180)
REVERT: B  395 ASN cc_start: 0.8578 (p0) cc_final: 0.8345 (p0)
REVERT: B  398 VAL cc_start: 0.9082 (t) cc_final: 0.8795 (p)
REVERT: B  445 PHE cc_start: 0.8806 (p90) cc_final: 0.8463 (p90)
REVERT: B  499 ASN cc_start: 0.7829 (m110) cc_final: 0.7626 (m-40)
  outliers start: 18
  outliers final: 16
  residues processed: 101
  average time/residue: 0.1759
  time to fit residues: 23.6929
Evaluate side-chains
  106 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0270
   chunk 44 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.9844

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.188299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.132391 restraints weight = 7479.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.58
r_work: 0.3241 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6339  Z= 0.272
  Angle     :  0.532   9.893   8841  Z= 0.269
  Chirality :  0.040   0.148   1015
  Planarity :  0.004   0.026    953
  Dihedral  : 15.828 172.607   1417
  Min Nonbonded Distance : 1.095

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.73 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.32), residues: 638
  helix: -0.73 (0.45), residues: 143
  sheet: -2.03 (0.58), residues: 62
  loop : -1.01 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 520 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.017   0.001   PHE A  19 
 TYR   0.021   0.001   TYR A  96 
 ARG   0.006   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8192 (t) cc_final: 0.7938 (t)
REVERT: A   98 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7239 (mm-40)
REVERT: B   58 MET cc_start: 0.9056 (mtp) cc_final: 0.8541 (mtp)
REVERT: B   61 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8611 (mtpp)
REVERT: B  169 MET cc_start: 0.8790 (ttp) cc_final: 0.8447 (ptm)
REVERT: B  185 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8618 (mt)
REVERT: B  318 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8066 (tttm)
REVERT: B  330 HIS cc_start: 0.7605 (m-70) cc_final: 0.7070 (m-70)
REVERT: B  391 ARG cc_start: 0.8437 (ttm170) cc_final: 0.8126 (mtp180)
REVERT: B  395 ASN cc_start: 0.8607 (p0) cc_final: 0.8366 (p0)
REVERT: B  398 VAL cc_start: 0.9094 (t) cc_final: 0.8778 (p)
REVERT: B  445 PHE cc_start: 0.8834 (p90) cc_final: 0.8478 (p90)
REVERT: B  499 ASN cc_start: 0.7807 (m110) cc_final: 0.7606 (m-40)
  outliers start: 19
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1617
  time to fit residues: 23.1844
Evaluate side-chains
  109 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  348 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.190344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.132350 restraints weight = 7538.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.40
r_work: 0.3258 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6339  Z= 0.234
  Angle     :  0.522   8.963   8841  Z= 0.265
  Chirality :  0.039   0.143   1015
  Planarity :  0.003   0.026    953
  Dihedral  : 15.816 172.593   1417
  Min Nonbonded Distance : 1.090

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 16.09 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.32), residues: 638
  helix: -0.75 (0.43), residues: 148
  sheet: -2.09 (0.58), residues: 60
  loop : -0.99 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 520 
 HIS   0.004   0.001   HIS B 487 
 PHE   0.017   0.001   PHE B 350 
 TYR   0.017   0.001   TYR A  96 
 ARG   0.005   0.000   ARG A  78 

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 SER cc_start: 0.8155 (t) cc_final: 0.7906 (t)
REVERT: A   98 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7211 (mm-40)
REVERT: B   58 MET cc_start: 0.9031 (mtp) cc_final: 0.8613 (mtp)
REVERT: B   61 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8628 (mtpp)
REVERT: B  169 MET cc_start: 0.8795 (ttp) cc_final: 0.8423 (ptm)
REVERT: B  185 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8618 (mt)
REVERT: B  318 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8043 (tttm)
REVERT: B  330 HIS cc_start: 0.7514 (m-70) cc_final: 0.7145 (m-70)
REVERT: B  377 PHE cc_start: 0.6879 (m-80) cc_final: 0.6437 (m-80)
REVERT: B  391 ARG cc_start: 0.8409 (ttm170) cc_final: 0.8116 (mtp180)
REVERT: B  395 ASN cc_start: 0.8612 (p0) cc_final: 0.8377 (p0)
REVERT: B  398 VAL cc_start: 0.9093 (t) cc_final: 0.8775 (p)
REVERT: B  445 PHE cc_start: 0.8776 (p90) cc_final: 0.8399 (p90)
  outliers start: 18
  outliers final: 17
  residues processed: 102
  average time/residue: 0.1653
  time to fit residues: 22.7981
Evaluate side-chains
  110 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  195 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  348 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 29 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 499 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.175862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.120551 restraints weight = 7536.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.95
r_work: 0.3013 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   6339  Z= 0.384
  Angle     :  0.602  12.296   8841  Z= 0.307
  Chirality :  0.042   0.164   1015
  Planarity :  0.004   0.030    953
  Dihedral  : 15.900 171.897   1417
  Min Nonbonded Distance : 1.050

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 16.27 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.32), residues: 638
  helix: -0.99 (0.43), residues: 149
  sheet: -2.24 (0.54), residues: 70
  loop : -1.05 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 520 
 HIS   0.004   0.001   HIS B  95 
 PHE   0.023   0.002   PHE A  19 
 TYR   0.017   0.001   TYR A  96 
 ARG   0.006   0.001   ARG A  78 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3064.01 seconds
wall clock time: 55 minutes 14.04 seconds (3314.04 seconds total)