Starting phenix.real_space_refine
on Tue Feb 11 12:51:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vqd_43439/02_2025/8vqd_43439.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vqd_43439/02_2025/8vqd_43439.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vqd_43439/02_2025/8vqd_43439.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vqd_43439/02_2025/8vqd_43439.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vqd_43439/02_2025/8vqd_43439.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vqd_43439/02_2025/8vqd_43439.cif"
  }
  resolution = 2.61
  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=   0.000 sd=   0.016
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      47      5.16       5
     C    3564      2.51       5
     N     993      2.21       5
     O    1082      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 5686
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 502, 3873
          Classifications: {'peptide': 502}
          Link IDs: {'PTRANS': 28, 'TRANS': 473}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 977
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 808
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    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
  Time building chain proxies: 4.31, per 1000 atoms: 0.76
  Number of scatterers: 5686
  At special positions: 0
  Unit cell: (78.375, 93.225, 100.65, 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      47     16.00
     O    1082      8.00
     N     993      7.00
     C    3564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 204 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 199 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 235 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 244 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 268 " - pdb=" SG  CYS A 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 315 " - pdb=" SG  CYS A 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 338 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 367 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 475 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 531 " - pdb=" SG  CYS A 540 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04

  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 D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 259 "
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 826.8 milliseconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 16 sheets defined
      15.9% alpha, 26.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 51
      removed outlier: 3.516A  pdb=" N   GLN A  51 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 75
    Processing helix  chain 'A' and resid 107 through 110
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.757A  pdb=" N   ILE A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.837A  pdb=" N   GLN A 178 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 3.687A  pdb=" N   CYS A 212 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 351
    Processing helix  chain 'A' and resid 360 through 365
    Processing helix  chain 'A' and resid 377 through 383
      removed outlier: 3.975A  pdb=" N   PHE A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 402
      removed outlier: 3.679A  pdb=" N   GLU A 401 " --> pdb=" O   GLN A 398 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   THR A 402 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
    Processing helix  chain 'A' and resid 436 through 439
    Processing helix  chain 'A' and resid 481 through 486
      removed outlier: 3.528A  pdb=" N   LEU A 485 " --> pdb=" O   PRO A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 508
    Processing helix  chain 'A' and resid 515 through 519
      removed outlier: 3.913A  pdb=" N   GLY A 518 " --> pdb=" O   CYS A 515 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 31
      removed outlier: 3.931A  pdb=" N   GLY C  31 " --> pdb=" O   PHE C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'C' and resid 106 through 108
      No H-bonds generated for 'chain 'C' and resid 106 through 108'
    Processing helix  chain 'B' and resid 29 through 31
      No H-bonds generated for 'chain 'B' and resid 29 through 31'
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 4.008A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.571A  pdb=" N   CYS A  26 " --> pdb=" O   GLN A  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63
      removed outlier: 5.154A  pdb=" N   GLY A 152 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 244
      removed outlier: 5.137A  pdb=" N   ALA A 241 " --> pdb=" O   CYS A 255 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   CYS A 255 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLY A 243 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 260
    Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 291
    Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 312
      removed outlier: 6.553A  pdb=" N   SER A 305 " --> pdb=" O   CYS A 331 " (cutoff:3.500A)
      removed outlier: 8.348A  pdb=" N   LYS A 333 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 343
      removed outlier: 6.649A  pdb=" N   CYS A 342 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 376
      removed outlier: 6.274A  pdb=" N   LEU A 374 " --> pdb=" O   TYR A 411 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU A 410 " --> pdb=" O   THR A 444 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   GLN A 446 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE A 412 " --> pdb=" O   GLN A 446 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   TYR A 441 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   LEU A 467 " --> pdb=" O   TYR A 441 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A 443 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   HIS A 469 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU A 445 " --> pdb=" O   HIS A 469 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ALA A 466 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   THR A 496 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE A 468 " --> pdb=" O   THR A 496 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 534 through 536
    Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.515A  pdb=" N   ILE C  34 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   SER C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12
      removed outlier: 4.120A  pdb=" N   TYR C 118 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 102 through 104
    Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 7
    Processing sheet with id=AB6, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.487A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 106 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.487A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 106 " (cutoff:3.500A)

    148 hydrogen bonds defined for protein.
    318 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1520
        1.33 -     1.45: 1275
        1.45 -     1.58: 2968
        1.58 -     1.70: 0
        1.70 -     1.83: 54
  Bond restraints: 5817
  Sorted by residual:
  bond pdb=" C   LEU A 183 "
       pdb=" O   LEU A 183 "
    ideal  model  delta    sigma   weight residual
    1.233  1.206  0.027 1.26e-02 6.30e+03 4.73e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.25e+00
  bond pdb=" N   ASP A 185 "
       pdb=" CA  ASP A 185 "
    ideal  model  delta    sigma   weight residual
    1.456  1.480 -0.024 1.25e-02 6.40e+03 3.78e+00
  bond pdb=" N   THR A 182 "
       pdb=" CA  THR A 182 "
    ideal  model  delta    sigma   weight residual
    1.457  1.480 -0.023 1.29e-02 6.01e+03 3.09e+00
  bond pdb=" CB  ASN A 284 "
       pdb=" CG  ASN A 284 "
    ideal  model  delta    sigma   weight residual
    1.516  1.558 -0.042 2.50e-02 1.60e+03 2.86e+00
  ... (remaining 5812 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 7497
        1.68 -     3.36: 346
        3.36 -     5.03: 44
        5.03 -     6.71: 14
        6.71 -     8.39: 2
  Bond angle restraints: 7903
  Sorted by residual:
  angle pdb=" CA  MET A  45 "
        pdb=" CB  MET A  45 "
        pdb=" CG  MET A  45 "
      ideal   model   delta    sigma   weight residual
     114.10  121.29   -7.19 2.00e+00 2.50e-01 1.29e+01
  angle pdb=" CA  ASN A 284 "
        pdb=" CB  ASN A 284 "
        pdb=" CG  ASN A 284 "
      ideal   model   delta    sigma   weight residual
     112.60  116.08   -3.48 1.00e+00 1.00e+00 1.21e+01
  angle pdb=" CA  LYS C  43 "
        pdb=" CB  LYS C  43 "
        pdb=" CG  LYS C  43 "
      ideal   model   delta    sigma   weight residual
     114.10  120.33   -6.23 2.00e+00 2.50e-01 9.71e+00
  angle pdb=" N   MET A  45 "
        pdb=" CA  MET A  45 "
        pdb=" CB  MET A  45 "
      ideal   model   delta    sigma   weight residual
     110.12  114.68   -4.56 1.47e+00 4.63e-01 9.62e+00
  angle pdb=" CA  LEU A 183 "
        pdb=" C   LEU A 183 "
        pdb=" O   LEU A 183 "
      ideal   model   delta    sigma   weight residual
     120.92  117.70    3.22 1.04e+00 9.25e-01 9.57e+00
  ... (remaining 7898 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3072
       17.92 -    35.84: 310
       35.84 -    53.76: 104
       53.76 -    71.69: 22
       71.69 -    89.61: 13
  Dihedral angle restraints: 3521
    sinusoidal: 1422
      harmonic: 2099
  Sorted by residual:
  dihedral pdb=" CB  CYS A 162 "
           pdb=" SG  CYS A 162 "
           pdb=" SG  CYS A 192 "
           pdb=" CB  CYS A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -174.95   88.95     1      1.00e+01 1.00e-02 9.42e+01
  dihedral pdb=" CB  CYS A 511 "
           pdb=" SG  CYS A 511 "
           pdb=" SG  CYS A 520 "
           pdb=" CB  CYS A 520 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.46   75.46     1      1.00e+01 1.00e-02 7.19e+01
  dihedral pdb=" CB  CYS A 224 "
           pdb=" SG  CYS A 224 "
           pdb=" SG  CYS A 235 "
           pdb=" CB  CYS A 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.31   39.31     1      1.00e+01 1.00e-02 2.17e+01
  ... (remaining 3518 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 511
       0.041 -    0.083: 252
       0.083 -    0.124: 89
       0.124 -    0.166: 23
       0.166 -    0.207: 3
  Chirality restraints: 878
  Sorted by residual:
  chirality pdb=" CB  ILE B   2 "
            pdb=" CA  ILE B   2 "
            pdb=" CG1 ILE B   2 "
            pdb=" CG2 ILE B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  LEU A 183 "
            pdb=" N   LEU A 183 "
            pdb=" C   LEU A 183 "
            pdb=" CB  LEU A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CB  VAL A 399 "
            pdb=" CA  VAL A 399 "
            pdb=" CG1 VAL A 399 "
            pdb=" CG2 VAL A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 875 not shown)

  Planarity restraints: 1026
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  43 "    0.014 2.00e-02 2.50e+03   2.87e-02 8.21e+00
        pdb=" C   LEU A  43 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LEU A  43 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASP A  44 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  46 "    0.013 2.00e-02 2.50e+03   2.51e-02 6.31e+00
        pdb=" C   LEU A  46 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   LEU A  46 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ARG A  47 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 396 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.64e+00
        pdb=" C   GLN A 396 "    0.041 2.00e-02 2.50e+03
        pdb=" O   GLN A 396 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 397 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1023 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1312
        2.79 -     3.32: 4921
        3.32 -     3.85: 9796
        3.85 -     4.37: 11955
        4.37 -     4.90: 19990
  Nonbonded interactions: 47974
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 303 "
            pdb=" O   TYR C 107 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   THR A 273 "
            pdb=" OG1 THR A 273 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" OD2 ASP A 421 "
            pdb=" OG  SER A 423 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   SER C  85 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" OG1 THR A 216 "
            pdb=" NH1 ARG A 226 "
     model   vdw
     2.408 3.120
  ... (remaining 47969 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:             2.390
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.590
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:12.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
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      :  0.005   0.043   5817  Z= 0.318
  Angle     :  0.808   8.391   7903  Z= 0.449
  Chirality :  0.054   0.207    878
  Planarity :  0.006   0.046   1025
  Dihedral  : 16.761  89.606   2121
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 20.32 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.18 (0.30), residues: 726
  helix: -1.96 (0.88), residues: 26
  sheet: -0.06 (0.38), residues: 183
  loop :  0.41 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  29 
 HIS   0.007   0.001   HIS A 495 
 PHE   0.029   0.002   PHE C 128 
 TYR   0.029   0.002   TYR C  52 
 ARG   0.007   0.001   ARG A 354 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7784 (tm-30)
REVERT: B   17 ASP cc_start: 0.8264 (t0) cc_final: 0.7985 (t0)
REVERT: B   45 LYS cc_start: 0.8839 (ptmt) cc_final: 0.8593 (pttm)
  outliers start: 5
  outliers final: 2
  residues processed: 77
  average time/residue: 1.2906
  time to fit residues: 103.8992
Evaluate side-chains
  67 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.0170
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.2980
   chunk 56 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.8422

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
A 178 GLN
A 398 GLN
A 478 HIS
C  13 GLN
C  77 ASN
B   6 GLN
B  90 GLN
B 101 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.090837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.067593 restraints weight = 8602.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 2.65
r_work: 0.2679 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2522 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5817  Z= 0.269
  Angle     :  0.558   7.159   7903  Z= 0.293
  Chirality :  0.045   0.172    878
  Planarity :  0.004   0.034   1025
  Dihedral  :  5.102  50.610    840
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 17.42 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.53 (0.31), residues: 726
  helix: -1.52 (1.00), residues: 26
  sheet: -0.05 (0.40), residues: 169
  loop :  0.74 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  29 
 HIS   0.003   0.001   HIS C  35 
 PHE   0.018   0.001   PHE C  27 
 TYR   0.017   0.001   TYR C  33 
 ARG   0.004   0.000   ARG A 517 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 61
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8068 (tmm)
REVERT: A  286 GLU cc_start: 0.8856 (mt-10) cc_final: 0.7809 (tm-30)
REVERT: A  368 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8622 (mtpm)
REVERT: C   87 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7507 (mtt90)
REVERT: B   17 ASP cc_start: 0.8601 (t0) cc_final: 0.8120 (t0)
REVERT: B   42 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8472 (mtpp)
REVERT: B   45 LYS cc_start: 0.9125 (ptmt) cc_final: 0.8345 (pttm)
  outliers start: 27
  outliers final: 13
  residues processed: 78
  average time/residue: 1.2792
  time to fit residues: 104.4029
Evaluate side-chains
  78 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   42 LYS
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C  13 GLN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.090400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.067433 restraints weight = 9203.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.71
r_work: 0.2714 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2573 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5817  Z= 0.254
  Angle     :  0.531   7.985   7903  Z= 0.277
  Chirality :  0.044   0.177    878
  Planarity :  0.004   0.033   1025
  Dihedral  :  5.043  53.596    840
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.42 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.52 (0.31), residues: 726
  helix: -1.38 (0.98), residues: 26
  sheet: -0.15 (0.39), residues: 179
  loop :  0.78 (0.27), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  93 
 HIS   0.003   0.001   HIS C  35 
 PHE   0.010   0.001   PHE A 381 
 TYR   0.015   0.001   TYR C  33 
 ARG   0.004   0.000   ARG A 517 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7997 (tmm)
REVERT: A  183 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8304 (tt)
REVERT: A  368 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8499 (mtpm)
REVERT: C    6 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6565 (mt-10)
REVERT: C   86 LEU cc_start: 0.8859 (mp) cc_final: 0.8592 (mp)
REVERT: B   17 ASP cc_start: 0.8563 (t0) cc_final: 0.8170 (t0)
REVERT: B   42 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8328 (mtpp)
REVERT: B   45 LYS cc_start: 0.9005 (ptmt) cc_final: 0.8162 (pttm)
  outliers start: 22
  outliers final: 9
  residues processed: 72
  average time/residue: 1.3027
  time to fit residues: 98.1743
Evaluate side-chains
  70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   42 LYS
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.089129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.066121 restraints weight = 9302.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.72
r_work: 0.2682 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2538 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   5817  Z= 0.329
  Angle     :  0.549   8.743   7903  Z= 0.285
  Chirality :  0.045   0.155    878
  Planarity :  0.004   0.033   1025
  Dihedral  :  5.127  57.708    840
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 17.42 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.47 (0.31), residues: 726
  helix: -1.30 (0.99), residues: 26
  sheet: -0.32 (0.38), residues: 179
  loop :  0.79 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C  35 
 PHE   0.018   0.001   PHE C  27 
 TYR   0.015   0.001   TYR C  33 
 ARG   0.003   0.000   ARG A 330 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7908 (tmm)
REVERT: A  183 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8208 (tt)
REVERT: A  368 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8516 (mtpm)
REVERT: A  533 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8322 (mm-40)
REVERT: C    6 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6601 (mt-10)
REVERT: C   28 THR cc_start: 0.8409 (t) cc_final: 0.8171 (p)
REVERT: C   77 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8342 (t0)
REVERT: C  121 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7822 (pp30)
REVERT: B   17 ASP cc_start: 0.8531 (t0) cc_final: 0.8182 (t0)
REVERT: B   45 LYS cc_start: 0.8961 (ptmt) cc_final: 0.8089 (pttm)
  outliers start: 26
  outliers final: 9
  residues processed: 75
  average time/residue: 1.2573
  time to fit residues: 98.8902
Evaluate side-chains
  74 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain A residue  533 GLN
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   77 ASN
Chi-restraints excluded: chain C residue  121 GLN
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0770
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.9142

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.089680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.066782 restraints weight = 9130.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 2.69
r_work: 0.2687 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2542 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5817  Z= 0.281
  Angle     :  0.539   9.016   7903  Z= 0.279
  Chirality :  0.044   0.158    878
  Planarity :  0.004   0.032   1025
  Dihedral  :  5.083  59.511    840
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 19.52 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.43 (0.31), residues: 726
  helix: -1.15 (1.00), residues: 26
  sheet: -0.38 (0.38), residues: 179
  loop :  0.77 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C  35 
 PHE   0.009   0.001   PHE A 381 
 TYR   0.015   0.001   TYR C  33 
 ARG   0.004   0.000   ARG A 330 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7874 (tmm)
REVERT: A  183 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8174 (tt)
REVERT: A  286 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8443 (mm-30)
REVERT: A  368 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8517 (mtpm)
REVERT: C    6 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6561 (mt-10)
REVERT: C   28 THR cc_start: 0.8423 (t) cc_final: 0.8164 (p)
REVERT: C   77 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8339 (t0)
REVERT: B   17 ASP cc_start: 0.8544 (t0) cc_final: 0.8244 (t0)
REVERT: B   42 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8171 (mtpp)
REVERT: B   45 LYS cc_start: 0.8955 (ptmt) cc_final: 0.8074 (pttm)
  outliers start: 22
  outliers final: 8
  residues processed: 72
  average time/residue: 1.3282
  time to fit residues: 100.1154
Evaluate side-chains
  73 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   77 ASN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   42 LYS
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0570
   chunk 26 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0980
   chunk 49 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
C  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.090331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.067777 restraints weight = 9304.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 2.80
r_work: 0.2701 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5817  Z= 0.161
  Angle     :  0.508   9.150   7903  Z= 0.260
  Chirality :  0.042   0.141    878
  Planarity :  0.004   0.039   1025
  Dihedral  :  4.922  59.034    840
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.00 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.46 (0.31), residues: 726
  helix: -0.99 (1.02), residues: 26
  sheet: -0.35 (0.38), residues: 179
  loop :  0.78 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  29 
 HIS   0.002   0.000   HIS C  35 
 PHE   0.021   0.001   PHE C  27 
 TYR   0.014   0.001   TYR C  33 
 ARG   0.009   0.000   ARG A 517 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7775 (tmm)
REVERT: A  183 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8182 (tt)
REVERT: A  286 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8400 (mm-30)
REVERT: A  368 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8428 (mtpm)
REVERT: C   19 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7634 (tmm-80)
REVERT: B   17 ASP cc_start: 0.8546 (t0) cc_final: 0.8306 (t0)
REVERT: B   42 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8260 (mtpp)
REVERT: B   45 LYS cc_start: 0.8892 (ptmt) cc_final: 0.8011 (pttm)
REVERT: B   61 ARG cc_start: 0.8017 (ptp90) cc_final: 0.7737 (ptp-170)
  outliers start: 18
  outliers final: 6
  residues processed: 74
  average time/residue: 1.3315
  time to fit residues: 103.0338
Evaluate side-chains
  71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   19 ARG
Chi-restraints excluded: chain B residue   42 LYS
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0570
   chunk 32 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
C  13 GLN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.090424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.067517 restraints weight = 9161.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 2.71
r_work: 0.2715 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5817  Z= 0.212
  Angle     :  0.515   9.510   7903  Z= 0.263
  Chirality :  0.043   0.139    878
  Planarity :  0.004   0.036   1025
  Dihedral  :  4.862  59.161    840
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.48 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.51 (0.31), residues: 726
  helix: -0.92 (1.03), residues: 26
  sheet: -0.31 (0.38), residues: 179
  loop :  0.81 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 119 
 HIS   0.002   0.000   HIS C  35 
 PHE   0.008   0.001   PHE A 381 
 TYR   0.014   0.001   TYR C  33 
 ARG   0.010   0.000   ARG A 517 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7817 (tmm)
REVERT: A  183 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8259 (tt)
REVERT: A  286 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8475 (mm-30)
REVERT: A  368 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8540 (mtpm)
REVERT: B   42 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8267 (mtpp)
REVERT: B   45 LYS cc_start: 0.8987 (ptmt) cc_final: 0.8136 (pttm)
  outliers start: 19
  outliers final: 7
  residues processed: 75
  average time/residue: 1.3387
  time to fit residues: 105.9282
Evaluate side-chains
  70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain B residue   42 LYS
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.089654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.066785 restraints weight = 9060.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.69
r_work: 0.2697 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5817  Z= 0.279
  Angle     :  0.541   9.627   7903  Z= 0.276
  Chirality :  0.044   0.138    878
  Planarity :  0.004   0.034   1025
  Dihedral  :  4.920  56.585    840
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 21.61 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.50 (0.31), residues: 726
  helix: -0.90 (1.02), residues: 26
  sheet: -0.32 (0.39), residues: 178
  loop :  0.81 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C  35 
 PHE   0.030   0.001   PHE C  27 
 TYR   0.014   0.001   TYR C  33 
 ARG   0.008   0.000   ARG A 517 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7811 (tmm)
REVERT: A  183 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8205 (tt)
REVERT: A  286 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8472 (mm-30)
REVERT: A  368 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8508 (mtpm)
REVERT: C    6 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6892 (mt-10)
REVERT: B   42 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8266 (mtpp)
REVERT: B   45 LYS cc_start: 0.8995 (ptmt) cc_final: 0.8144 (pttm)
  outliers start: 15
  outliers final: 6
  residues processed: 70
  average time/residue: 1.3809
  time to fit residues: 100.9755
Evaluate side-chains
  71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain B residue   42 LYS
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 67 optimal weight:    2.9990
   chunk 7 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.090256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.067396 restraints weight = 9115.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.72
r_work: 0.2715 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5817  Z= 0.209
  Angle     :  0.528   9.858   7903  Z= 0.267
  Chirality :  0.043   0.140    878
  Planarity :  0.004   0.034   1025
  Dihedral  :  4.835  55.889    840
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 21.45 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.50 (0.31), residues: 726
  helix: -0.83 (1.04), residues: 26
  sheet: -0.34 (0.39), residues: 178
  loop :  0.80 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  29 
 HIS   0.002   0.000   HIS C  35 
 PHE   0.007   0.001   PHE A 381 
 TYR   0.013   0.001   TYR C  33 
 ARG   0.007   0.000   ARG A 517 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7892 (tmm)
REVERT: A  183 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8198 (tt)
REVERT: A  286 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8472 (mm-30)
REVERT: A  368 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8526 (mtpm)
REVERT: C    6 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6848 (mt-10)
REVERT: B   42 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8317 (mtpp)
REVERT: B   45 LYS cc_start: 0.8986 (ptmt) cc_final: 0.8138 (pttm)
  outliers start: 16
  outliers final: 8
  residues processed: 70
  average time/residue: 1.2928
  time to fit residues: 94.6286
Evaluate side-chains
  72 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain A residue  373 SER
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain B residue   42 LYS
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0050
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.089540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.066939 restraints weight = 9485.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.81
r_work: 0.2688 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2549 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5817  Z= 0.234
  Angle     :  0.538  10.095   7903  Z= 0.271
  Chirality :  0.043   0.141    878
  Planarity :  0.004   0.034   1025
  Dihedral  :  4.816  54.093    840
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 21.77 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.47 (0.31), residues: 726
  helix: -0.78 (1.04), residues: 26
  sheet: -0.38 (0.39), residues: 178
  loop :  0.79 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  47 
 HIS   0.002   0.001   HIS C  35 
 PHE   0.034   0.001   PHE C  27 
 TYR   0.013   0.001   TYR C  33 
 ARG   0.007   0.000   ARG A 517 

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7834 (tmm)
REVERT: A  183 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8130 (tt)
REVERT: A  286 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8429 (mm-30)
REVERT: A  368 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8431 (mtpm)
REVERT: C    6 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6837 (mt-10)
REVERT: B   42 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8224 (mtpp)
REVERT: B   45 LYS cc_start: 0.8901 (ptmt) cc_final: 0.8025 (pttm)
  outliers start: 16
  outliers final: 8
  residues processed: 68
  average time/residue: 1.2828
  time to fit residues: 91.6496
Evaluate side-chains
  71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain A residue  373 SER
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain B residue   42 LYS
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 13 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
C  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.089548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.066939 restraints weight = 9391.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.80
r_work: 0.2687 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2549 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5817  Z= 0.242
  Angle     :  0.540  10.133   7903  Z= 0.272
  Chirality :  0.043   0.142    878
  Planarity :  0.004   0.034   1025
  Dihedral  :  4.820  53.182    840
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.45 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.46 (0.31), residues: 726
  helix: -0.81 (1.03), residues: 26
  sheet: -0.38 (0.39), residues: 178
  loop :  0.78 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  29 
 HIS   0.003   0.001   HIS C  35 
 PHE   0.008   0.001   PHE A 381 
 TYR   0.013   0.001   TYR C  33 
 ARG   0.007   0.000   ARG A 517 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4819.68 seconds
wall clock time: 85 minutes 33.60 seconds (5133.60 seconds total)