Starting phenix.real_space_refine
on Wed Jun 11 15:13:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c1i_45120/06_2025/9c1i_45120.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c1i_45120/06_2025/9c1i_45120.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c1i_45120/06_2025/9c1i_45120.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c1i_45120/06_2025/9c1i_45120.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c1i_45120/06_2025/9c1i_45120.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c1i_45120/06_2025/9c1i_45120.cif"
  }
  resolution = 3.52
  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
-------------------------------------------------------------------------------
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=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4228      2.51       5
     N    1092      2.21       5
     O    1306      1.98       5
     H    6348      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12996
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "2"
      Number of atoms: 6498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 6498
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 396}
          Chain breaks: 1
    Chain: "3"
      Number of atoms: 6498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 6498
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 396}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   GLY 2 156 " occ=0.50
      ... (5 atoms not shown)
      pdb=" HA3 GLY 2 156 " occ=0.50
    residue:
      pdb=" N   GLY 3 156 " occ=0.50
      ... (5 atoms not shown)
      pdb=" HA3 GLY 3 156 " occ=0.50
  Time building chain proxies: 6.63, per 1000 atoms: 0.51
  Number of scatterers: 12996
  At special positions: 0
  Unit cell: (92.4, 117.15, 94.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     O    1306      8.00
     N    1092      7.00
     C    4228      6.00
     H    6348      1.00
    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: 3.35
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1568

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 13 sheets defined
      5.2% alpha, 41.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain '2' and resid 193 through 197
    Processing helix  chain '2' and resid 212 through 222
    Processing helix  chain '2' and resid 359 through 364
      removed outlier: 3.859A  pdb=" N   ARG 2 363 " --> pdb=" O   SER 2 359 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN 2 364 " --> pdb=" O   GLN 2 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain '2' and resid 359 through 364'
    Processing helix  chain '3' and resid 193 through 197
    Processing helix  chain '3' and resid 212 through 222
    Processing helix  chain '3' and resid 359 through 364
      removed outlier: 3.566A  pdb=" N   ARG 3 363 " --> pdb=" O   SER 3 359 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain '2' and resid 48 through 50
  WARNING: can't find start of bonding for strands!
    previous: chain '2' and resid 48 through 50
    current: chain '2' and resid 310 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain '2' and resid 350 through 357
    current: chain '2' and resid 396 through 415
      removed outlier: 9.146A  pdb=" N   MET 2 397 " --> pdb=" O   PHE 2 437 " (cutoff:3.500A)
      removed outlier: 9.080A  pdb=" N   PHE 2 437 " --> pdb=" O   MET 2 397 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLY 2 399 " --> pdb=" O   PRO 2 435 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA 2 401 " --> pdb=" O   GLU 2 433 " (cutoff:3.500A)
      removed outlier: 5.488A  pdb=" N   ARG 2 427 " --> pdb=" O   ALA 2 407 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   VAL 2 409 " --> pdb=" O   ARG 2 425 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ARG 2 425 " --> pdb=" O   VAL 2 409 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LEU 2 411 " --> pdb=" O   SER 2 423 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   SER 2 423 " --> pdb=" O   LEU 2 411 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   THR 2 413 " --> pdb=" O   LEU 2 421 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   LEU 2 421 " --> pdb=" O   THR 2 413 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain '2' and resid 420 through 439
    current: chain '3' and resid 310 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain '3' and resid 350 through 357
    current: chain '3' and resid 401 through 416
      removed outlier: 5.580A  pdb=" N   LEU 3 404 " --> pdb=" O   THR 3 431 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   THR 3 431 " --> pdb=" O   LEU 3 404 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   SER 3 406 " --> pdb=" O   ARG 3 429 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ARG 3 429 " --> pdb=" O   SER 3 406 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   GLY 3 408 " --> pdb=" O   ARG 3 427 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG 3 427 " --> pdb=" O   GLY 3 408 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain '2' and resid 58 through 60
  WARNING: can't find start of bonding for strands!
    previous: chain '2' and resid 58 through 60
    current: chain '3' and resid 290 through 297
  WARNING: can't find start of bonding for strands!
    previous: chain '3' and resid 290 through 297
    current: chain '3' and resid 338 through 345
      removed outlier: 3.696A  pdb=" N   ILE 3 345 " --> pdb=" O   LEU 3 450 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU 3 450 " --> pdb=" O   ILE 3 345 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain '2' and resid 185 through 190
      removed outlier: 5.125A  pdb=" N   ALA 2 166 " --> pdb=" O   TYR 2 177 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   LYS 2 169 " --> pdb=" O   TYR 2  80 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   TYR 2  80 " --> pdb=" O   LYS 2 169 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain '2' and resid 153 through 160
      removed outlier: 6.382A  pdb=" N   PHE 2 140 " --> pdb=" O   PRO 2 157 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   GLN 2 159 " --> pdb=" O   TRP 2 138 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   TRP 2 138 " --> pdb=" O   GLN 2 159 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU 2 103 " --> pdb=" O   GLU 2  94 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   GLU 2  94 " --> pdb=" O   LEU 2 103 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   THR 2 105 " --> pdb=" O   VAL 2  92 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain '2' and resid 115 through 121
    Processing sheet with id=AA6, first strand: chain '2' and resid 252 through 257
      removed outlier: 7.182A  pdb=" N   GLU 3 264 " --> pdb=" O   VAL 2 256 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU 3 473 " --> pdb=" O   VAL 3 368 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   VAL 3 368 " --> pdb=" O   LEU 3 473 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain '2' and resid 368 through 375
      removed outlier: 5.913A  pdb=" N   VAL 2 368 " --> pdb=" O   LEU 2 473 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU 2 473 " --> pdb=" O   VAL 2 368 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   GLU 2 264 " --> pdb=" O   VAL 3 256 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU 3 252 " --> pdb=" O   ASN 2 268 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain '2' and resid 278 through 283
      removed outlier: 4.138A  pdb=" N   ALA 2 278 " --> pdb=" O   LYS 2 297 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain '2' and resid 450 through 451
    Processing sheet with id=AB1, first strand: chain '3' and resid 185 through 190
      removed outlier: 5.753A  pdb=" N   ALA 3 166 " --> pdb=" O   TYR 3 177 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LYS 3 169 " --> pdb=" O   TYR 3  80 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   TYR 3  80 " --> pdb=" O   LYS 3 169 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain '3' and resid 154 through 160
      removed outlier: 6.266A  pdb=" N   GLN 3 154 " --> pdb=" O   VAL 3 144 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   VAL 3 144 " --> pdb=" O   GLN 3 154 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   GLY 3 156 " --> pdb=" O   ASP 3 142 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ASP 3 142 " --> pdb=" O   GLY 3 156 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU 3 103 " --> pdb=" O   GLU 3  94 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU 3  94 " --> pdb=" O   LEU 3 103 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR 3 105 " --> pdb=" O   VAL 3  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain '3' and resid 112 through 121
      removed outlier: 3.682A  pdb=" N   SER 3 114 " --> pdb=" O   ILE 3 130 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ILE 3 130 " --> pdb=" O   SER 3 114 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   THR 3 116 " --> pdb=" O   ILE 3 128 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   ILE 3 128 " --> pdb=" O   THR 3 116 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   SER 3 118 " --> pdb=" O   GLU 3 126 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   GLU 3 126 " --> pdb=" O   SER 3 118 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   THR 3 120 " --> pdb=" O   THR 3 124 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   THR 3 124 " --> pdb=" O   THR 3 120 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain '3' and resid 385 through 386

    195 hydrogen bonds defined for protein.
    486 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: 4.35

  Time building geometry restraints manager: 4.05 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6340
        1.03 -     1.23: 11
        1.23 -     1.42: 2994
        1.42 -     1.61: 3791
        1.61 -     1.81: 36
  Bond restraints: 13172
  Sorted by residual:
  bond pdb=" C   GLU 3 180 "
       pdb=" N   THR 3 181 "
    ideal  model  delta    sigma   weight residual
    1.331  1.377 -0.046 2.83e-02 1.25e+03 2.59e+00
  bond pdb=" C   GLY 3 330 "
       pdb=" N   GLY 3 331 "
    ideal  model  delta    sigma   weight residual
    1.321  1.331 -0.009 1.24e-02 6.50e+03 5.77e-01
  bond pdb=" CB  THR 3 316 "
       pdb=" CG2 THR 3 316 "
    ideal  model  delta    sigma   weight residual
    1.521  1.496  0.025 3.30e-02 9.18e+02 5.64e-01
  bond pdb=" CB  VAL 3 353 "
       pdb=" CG1 VAL 3 353 "
    ideal  model  delta    sigma   weight residual
    1.521  1.497  0.024 3.30e-02 9.18e+02 5.46e-01
  bond pdb=" CG  PRO 2 162 "
       pdb=" CD  PRO 2 162 "
    ideal  model  delta    sigma   weight residual
    1.503  1.479  0.024 3.40e-02 8.65e+02 4.95e-01
  ... (remaining 13167 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 22715
        1.21 -     2.43: 822
        2.43 -     3.64: 71
        3.64 -     4.85: 19
        4.85 -     6.07: 3
  Bond angle restraints: 23630
  Sorted by residual:
  angle pdb=" C   GLY 2 156 "
        pdb=" N   PRO 2 157 "
        pdb=" CA  PRO 2 157 "
      ideal   model   delta    sigma   weight residual
     127.00  131.94   -4.94 2.40e+00 1.74e-01 4.24e+00
  angle pdb=" N   ARG 3 363 "
        pdb=" CA  ARG 3 363 "
        pdb=" C   ARG 3 363 "
      ideal   model   delta    sigma   weight residual
     111.71  109.59    2.12 1.15e+00 7.56e-01 3.39e+00
  angle pdb=" CA  PRO 3 162 "
        pdb=" N   PRO 3 162 "
        pdb=" CD  PRO 3 162 "
      ideal   model   delta    sigma   weight residual
     112.00  109.47    2.53 1.40e+00 5.10e-01 3.26e+00
  angle pdb=" N   VAL 3  92 "
        pdb=" CA  VAL 3  92 "
        pdb=" C   VAL 3  92 "
      ideal   model   delta    sigma   weight residual
     111.62  110.20    1.42 7.90e-01 1.60e+00 3.25e+00
  angle pdb=" CA  THR 3 161 "
        pdb=" C   THR 3 161 "
        pdb=" N   PRO 3 162 "
      ideal   model   delta    sigma   weight residual
     118.44  121.04   -2.60 1.59e+00 3.96e-01 2.67e+00
  ... (remaining 23625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.88: 5663
       16.88 -    33.75: 521
       33.75 -    50.63: 126
       50.63 -    67.51: 37
       67.51 -    84.38: 7
  Dihedral angle restraints: 6354
    sinusoidal: 3356
      harmonic: 2998
  Sorted by residual:
  dihedral pdb=" CA  ASN 2 229 "
           pdb=" C   ASN 2 229 "
           pdb=" N   THR 2 230 "
           pdb=" CA  THR 2 230 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.15  -16.85     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  ARG 3 429 "
           pdb=" C   ARG 3 429 "
           pdb=" N   LEU 3 430 "
           pdb=" CA  LEU 3 430 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.03  -15.97     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  LEU 3 450 "
           pdb=" CB  LEU 3 450 "
           pdb=" CG  LEU 3 450 "
           pdb=" CD1 LEU 3 450 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.62   58.38     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 6351 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 570
       0.031 -    0.062: 318
       0.062 -    0.092: 70
       0.092 -    0.123: 61
       0.123 -    0.154: 11
  Chirality restraints: 1030
  Sorted by residual:
  chirality pdb=" CA  ILE 3 294 "
            pdb=" N   ILE 3 294 "
            pdb=" C   ILE 3 294 "
            pdb=" CB  ILE 3 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" CA  ILE 2 294 "
            pdb=" N   ILE 2 294 "
            pdb=" C   ILE 2 294 "
            pdb=" CB  ILE 2 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  VAL 3 143 "
            pdb=" N   VAL 3 143 "
            pdb=" C   VAL 3 143 "
            pdb=" CB  VAL 3 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.12e-01
  ... (remaining 1027 not shown)

  Planarity restraints: 1996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE 3 208 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.54e+00
        pdb=" N   PRO 3 209 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO 3 209 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO 3 209 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR 2 161 "    0.018 5.00e-02 4.00e+02   2.72e-02 1.19e+00
        pdb=" N   PRO 2 162 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO 2 162 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO 2 162 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR 3 161 "    0.018 5.00e-02 4.00e+02   2.70e-02 1.17e+00
        pdb=" N   PRO 3 162 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO 3 162 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO 3 162 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1993 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 1238
        2.22 -     2.81: 27443
        2.81 -     3.41: 33001
        3.41 -     4.00: 46412
        4.00 -     4.60: 69181
  Nonbonded interactions: 177275
  Sorted by model distance:
  nonbonded pdb=" O   GLU 3 212 "
            pdb=" HG1 THR 3 215 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" H   SER 2 260 "
            pdb=" O   TRP 3 262 "
     model   vdw
     1.630 2.450
  nonbonded pdb=" H   THR 2  96 "
            pdb=" OD1 ASN 2 198 "
     model   vdw
     1.656 2.450
  nonbonded pdb=" OE1 GLN 2 228 "
            pdb=" HG  SER 3 438 "
     model   vdw
     1.660 2.450
  nonbonded pdb="HD21 ASN 3  97 "
            pdb=" OD1 ASP 3 100 "
     model   vdw
     1.660 2.450
  ... (remaining 177270 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain '2'
  selection = chain '3'
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.090
  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:             0.240
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     30.340
  Find NCS groups from input model:        0.260
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
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      :  0.004   0.046   6824  Z= 0.157
  Angle     :  0.552   6.069   9324  Z= 0.297
  Chirality :  0.045   0.154   1030
  Planarity :  0.004   0.031   1206
  Dihedral  : 13.697  84.383   2420
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 15.08 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -1.88 (0.28), residues: 832
  helix: -2.82 (0.78), residues: 36
  sheet: -0.92 (0.25), residues: 374
  loop : -1.32 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP 3  81 
 HIS   0.002   0.001   HIS 2 315 
 PHE   0.016   0.001   PHE 2 468 
 TYR   0.012   0.001   TYR 3 342 
 ARG   0.002   0.000   ARG 3 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12483 (  195)
  hydrogen bonds       : angle       6.90504 (  486)
  covalent geometry    : bond        0.00358 ( 6824)
  covalent geometry    : angle       0.55200 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6036 (pm20)
REVERT: 2  138 TRP cc_start: 0.5325 (m100) cc_final: 0.4975 (m100)
REVERT: 2  175 TYR cc_start: 0.4496 (m-80) cc_final: 0.4142 (m-80)
REVERT: 2  199 MET cc_start: 0.4971 (mmt) cc_final: 0.4698 (mtt)
REVERT: 2  323 MET cc_start: 0.8201 (ptp) cc_final: 0.7915 (ptp)
REVERT: 2  337 PHE cc_start: 0.8609 (t80) cc_final: 0.8315 (t80)
REVERT: 2  374 ASN cc_start: 0.7634 (m-40) cc_final: 0.7223 (p0)
REVERT: 3  154 GLN cc_start: 0.4470 (mt0) cc_final: 0.2824 (pm20)
REVERT: 3  213 GLU cc_start: 0.7344 (pt0) cc_final: 0.6880 (tm-30)
REVERT: 3  253 ASP cc_start: 0.7448 (p0) cc_final: 0.7074 (p0)
REVERT: 3  292 SER cc_start: 0.8901 (t) cc_final: 0.8386 (p)
REVERT: 3  297 LYS cc_start: 0.8839 (tttt) cc_final: 0.8468 (ttmt)
REVERT: 3  339 ILE cc_start: 0.8371 (mm) cc_final: 0.8152 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 229
  average time/residue: 0.3362
  time to fit residues: 106.1762
Evaluate side-chains
  166 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   81 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
3 393 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.204757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.177633 restraints weight = 30135.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.182247 restraints weight = 9536.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.184557 restraints weight = 4600.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4094 r_free = 0.4094    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4064 r_free = 0.4064    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
r_final: 0.4064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6824  Z= 0.223
  Angle     :  0.575   4.991   9324  Z= 0.310
  Chirality :  0.045   0.173   1030
  Planarity :  0.005   0.060   1206
  Dihedral  :  5.153  50.590    928
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.80 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.03 (0.28), residues: 832
  helix: -2.59 (0.74), residues: 36
  sheet: -1.08 (0.25), residues: 386
  loop : -1.40 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP 2 356 
 HIS   0.003   0.001   HIS 2 170 
 PHE   0.015   0.002   PHE 2 468 
 TYR   0.013   0.001   TYR 2 355 
 ARG   0.008   0.001   ARG 3 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04034 (  195)
  hydrogen bonds       : angle       5.99107 (  486)
  covalent geometry    : bond        0.00504 ( 6824)
  covalent geometry    : angle       0.57491 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 166
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6153 (pm20)
REVERT: 2  168 MET cc_start: 0.6465 (ttp) cc_final: 0.6052 (ttp)
REVERT: 2  175 TYR cc_start: 0.4518 (m-80) cc_final: 0.4165 (m-80)
REVERT: 2  199 MET cc_start: 0.4931 (mmt) cc_final: 0.4598 (mtt)
REVERT: 2  200 THR cc_start: 0.8309 (t) cc_final: 0.7996 (m)
REVERT: 2  337 PHE cc_start: 0.8633 (t80) cc_final: 0.8332 (t80)
REVERT: 2  374 ASN cc_start: 0.7673 (m-40) cc_final: 0.7202 (p0)
REVERT: 2  396 VAL cc_start: 0.6528 (OUTLIER) cc_final: 0.6237 (m)
REVERT: 3  177 TYR cc_start: 0.7480 (m-80) cc_final: 0.7187 (m-80)
REVERT: 3  213 GLU cc_start: 0.7290 (pt0) cc_final: 0.6823 (tm-30)
REVERT: 3  292 SER cc_start: 0.8838 (t) cc_final: 0.8455 (p)
REVERT: 3  297 LYS cc_start: 0.8882 (tttt) cc_final: 0.8485 (ttmt)
  outliers start: 19
  outliers final: 13
  residues processed: 177
  average time/residue: 0.3189
  time to fit residues: 79.5605
Evaluate side-chains
  162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  105 THR
Chi-restraints excluded: chain 2 residue  106 ILE
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  318 CYS
Chi-restraints excluded: chain 3 residue  338 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 7 optimal weight:    0.4980
   chunk 67 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    4.0988

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

Flipped N/Q/H residues before XYZ refinement:
2 178 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.200197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.172598 restraints weight = 30286.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.177203 restraints weight = 9435.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.179512 restraints weight = 4508.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4054 r_free = 0.4054    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
r_final: 0.4049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6824  Z= 0.172
  Angle     :  0.537   4.923   9324  Z= 0.289
  Chirality :  0.044   0.186   1030
  Planarity :  0.005   0.060   1206
  Dihedral  :  5.050  50.548    928
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.16 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.07 (0.27), residues: 832
  helix: -2.35 (0.79), residues: 34
  sheet: -1.06 (0.25), residues: 378
  loop : -1.52 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 3 170 
 PHE   0.016   0.001   PHE 2 468 
 TYR   0.011   0.001   TYR 2 355 
 ARG   0.003   0.000   ARG 3 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  195)
  hydrogen bonds       : angle       5.79061 (  486)
  covalent geometry    : bond        0.00394 ( 6824)
  covalent geometry    : angle       0.53659 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6020 (pm20)
REVERT: 2  119 TYR cc_start: 0.3881 (m-10) cc_final: 0.3667 (m-10)
REVERT: 2  168 MET cc_start: 0.6920 (ttp) cc_final: 0.6393 (ttp)
REVERT: 2  175 TYR cc_start: 0.4458 (m-80) cc_final: 0.4113 (m-80)
REVERT: 2  199 MET cc_start: 0.5080 (mmt) cc_final: 0.4756 (mtt)
REVERT: 2  200 THR cc_start: 0.8281 (t) cc_final: 0.7958 (m)
REVERT: 2  374 ASN cc_start: 0.7650 (m-40) cc_final: 0.7146 (p0)
REVERT: 2  396 VAL cc_start: 0.6565 (OUTLIER) cc_final: 0.6290 (m)
REVERT: 3  177 TYR cc_start: 0.7475 (m-80) cc_final: 0.7170 (m-80)
REVERT: 3  213 GLU cc_start: 0.7302 (pt0) cc_final: 0.6744 (tm-30)
REVERT: 3  292 SER cc_start: 0.8860 (t) cc_final: 0.8430 (p)
REVERT: 3  297 LYS cc_start: 0.8870 (tttt) cc_final: 0.8495 (ttmt)
  outliers start: 26
  outliers final: 19
  residues processed: 169
  average time/residue: 0.3289
  time to fit residues: 78.6186
Evaluate side-chains
  162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   59 THR
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  100 ASP
Chi-restraints excluded: chain 2 residue  106 ILE
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  391 VAL
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  257 SER
Chi-restraints excluded: chain 3 residue  287 LEU
Chi-restraints excluded: chain 3 residue  300 ASN
Chi-restraints excluded: chain 3 residue  318 CYS
Chi-restraints excluded: chain 3 residue  338 VAL
Chi-restraints excluded: chain 3 residue  391 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 56 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0970
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.9984

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.202786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.175388 restraints weight = 30238.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.179962 restraints weight = 9399.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.182323 restraints weight = 4492.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4066 r_free = 0.4066    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4065 r_free = 0.4065    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.4065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6824  Z= 0.141
  Angle     :  0.524   5.357   9324  Z= 0.277
  Chirality :  0.044   0.170   1030
  Planarity :  0.004   0.061   1206
  Dihedral  :  4.969  50.916    928
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.43 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.04 (0.27), residues: 832
  helix: -2.15 (0.81), residues: 34
  sheet: -1.05 (0.25), residues: 378
  loop : -1.49 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 3 170 
 PHE   0.022   0.002   PHE 2 140 
 TYR   0.009   0.001   TYR 3  45 
 ARG   0.002   0.000   ARG 3 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  195)
  hydrogen bonds       : angle       5.65364 (  486)
  covalent geometry    : bond        0.00325 ( 6824)
  covalent geometry    : angle       0.52371 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6058 (pm20)
REVERT: 2  168 MET cc_start: 0.7053 (ttp) cc_final: 0.6476 (ttp)
REVERT: 2  199 MET cc_start: 0.5071 (mmt) cc_final: 0.4792 (mtt)
REVERT: 2  200 THR cc_start: 0.8264 (t) cc_final: 0.7948 (m)
REVERT: 2  337 PHE cc_start: 0.8563 (t80) cc_final: 0.8301 (t80)
REVERT: 2  374 ASN cc_start: 0.7641 (m-40) cc_final: 0.7143 (p0)
REVERT: 2  396 VAL cc_start: 0.6545 (OUTLIER) cc_final: 0.6240 (m)
REVERT: 3  177 TYR cc_start: 0.7413 (m-80) cc_final: 0.7101 (m-80)
REVERT: 3  187 LYS cc_start: 0.6540 (mttt) cc_final: 0.6245 (tptt)
REVERT: 3  213 GLU cc_start: 0.7207 (pt0) cc_final: 0.6740 (tm-30)
REVERT: 3  292 SER cc_start: 0.8895 (t) cc_final: 0.8474 (p)
REVERT: 3  297 LYS cc_start: 0.8838 (tttt) cc_final: 0.8440 (ttmt)
  outliers start: 25
  outliers final: 18
  residues processed: 165
  average time/residue: 0.3272
  time to fit residues: 76.5706
Evaluate side-chains
  158 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   59 THR
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  100 ASP
Chi-restraints excluded: chain 2 residue  105 THR
Chi-restraints excluded: chain 2 residue  106 ILE
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  280 SER
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  391 VAL
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  300 ASN
Chi-restraints excluded: chain 3 residue  338 VAL
Chi-restraints excluded: chain 3 residue  391 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 63 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 15 optimal weight:   20.0000
   chunk 75 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** 3 266 GLN ** 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 = 0.4251 r_free = 0.4251 target = 0.197527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.169921 restraints weight = 30922.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.174388 restraints weight = 9692.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.176727 restraints weight = 4670.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3998 r_free = 0.3998    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3998 r_free = 0.3998    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   6824  Z= 0.267
  Angle     :  0.589   4.823   9324  Z= 0.318
  Chirality :  0.045   0.153   1030
  Planarity :  0.005   0.061   1206
  Dihedral  :  5.236  51.186    928
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.29 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.38 (0.27), residues: 832
  helix: -1.26 (0.94), residues: 22
  sheet: -1.45 (0.24), residues: 390
  loop : -1.64 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP 2 356 
 HIS   0.003   0.001   HIS 2 170 
 PHE   0.019   0.002   PHE 2 468 
 TYR   0.016   0.002   TYR 2 355 
 ARG   0.004   0.000   ARG 2 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  195)
  hydrogen bonds       : angle       5.81565 (  486)
  covalent geometry    : bond        0.00607 ( 6824)
  covalent geometry    : angle       0.58881 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6098 (pm20)
REVERT: 2  199 MET cc_start: 0.5275 (mmt) cc_final: 0.5006 (mtt)
REVERT: 2  200 THR cc_start: 0.8275 (t) cc_final: 0.7915 (m)
REVERT: 2  374 ASN cc_start: 0.7675 (m-40) cc_final: 0.7120 (p0)
REVERT: 2  396 VAL cc_start: 0.6532 (OUTLIER) cc_final: 0.6254 (m)
REVERT: 3  177 TYR cc_start: 0.7601 (m-80) cc_final: 0.7366 (m-80)
REVERT: 3  213 GLU cc_start: 0.7440 (pt0) cc_final: 0.6884 (tm-30)
REVERT: 3  292 SER cc_start: 0.8939 (t) cc_final: 0.8496 (p)
REVERT: 3  297 LYS cc_start: 0.8840 (tttt) cc_final: 0.8450 (ttmt)
  outliers start: 30
  outliers final: 26
  residues processed: 163
  average time/residue: 0.3141
  time to fit residues: 72.9338
Evaluate side-chains
  163 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  100 ASP
Chi-restraints excluded: chain 2 residue  105 THR
Chi-restraints excluded: chain 2 residue  106 ILE
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  147 THR
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  391 VAL
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 2 residue  423 SER
Chi-restraints excluded: chain 3 residue   59 THR
Chi-restraints excluded: chain 3 residue   62 GLU
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  257 SER
Chi-restraints excluded: chain 3 residue  287 LEU
Chi-restraints excluded: chain 3 residue  300 ASN
Chi-restraints excluded: chain 3 residue  318 CYS
Chi-restraints excluded: chain 3 residue  338 VAL
Chi-restraints excluded: chain 3 residue  347 GLU
Chi-restraints excluded: chain 3 residue  391 VAL
Chi-restraints excluded: chain 3 residue  416 THR
Chi-restraints excluded: chain 3 residue  444 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 52 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 49 optimal weight:   20.0000
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
3 456 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.200146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.172772 restraints weight = 30755.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.177313 restraints weight = 9526.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.179567 restraints weight = 4506.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4065 r_free = 0.4065    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4065 r_free = 0.4065    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.4065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6824  Z= 0.152
  Angle     :  0.532   4.520   9324  Z= 0.284
  Chirality :  0.044   0.160   1030
  Planarity :  0.005   0.058   1206
  Dihedral  :  5.075  51.788    928
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.65 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.38 (0.27), residues: 832
  helix: -2.17 (0.76), residues: 34
  sheet: -1.51 (0.24), residues: 398
  loop : -1.45 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 3 315 
 PHE   0.016   0.002   PHE 2 468 
 TYR   0.012   0.001   TYR 2 119 
 ARG   0.002   0.000   ARG 3 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03327 (  195)
  hydrogen bonds       : angle       5.65843 (  486)
  covalent geometry    : bond        0.00353 ( 6824)
  covalent geometry    : angle       0.53230 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6061 (pm20)
REVERT: 2  199 MET cc_start: 0.5270 (mmt) cc_final: 0.5001 (mtt)
REVERT: 2  200 THR cc_start: 0.8219 (t) cc_final: 0.7872 (m)
REVERT: 2  374 ASN cc_start: 0.7583 (m-40) cc_final: 0.7118 (p0)
REVERT: 2  396 VAL cc_start: 0.6541 (OUTLIER) cc_final: 0.6238 (m)
REVERT: 3  154 GLN cc_start: 0.5266 (mt0) cc_final: 0.3377 (pm20)
REVERT: 3  177 TYR cc_start: 0.7528 (m-80) cc_final: 0.7297 (m-80)
REVERT: 3  213 GLU cc_start: 0.7471 (pt0) cc_final: 0.6953 (tm-30)
REVERT: 3  289 TYR cc_start: 0.8100 (m-80) cc_final: 0.7872 (m-80)
REVERT: 3  292 SER cc_start: 0.8924 (t) cc_final: 0.8488 (p)
REVERT: 3  297 LYS cc_start: 0.8823 (tttt) cc_final: 0.8436 (ttmt)
  outliers start: 26
  outliers final: 20
  residues processed: 159
  average time/residue: 0.3016
  time to fit residues: 68.1146
Evaluate side-chains
  157 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  100 ASP
Chi-restraints excluded: chain 2 residue  105 THR
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  143 VAL
Chi-restraints excluded: chain 2 residue  221 ASN
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  327 ASN
Chi-restraints excluded: chain 2 residue  391 VAL
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  300 ASN
Chi-restraints excluded: chain 3 residue  318 CYS
Chi-restraints excluded: chain 3 residue  338 VAL
Chi-restraints excluded: chain 3 residue  347 GLU
Chi-restraints excluded: chain 3 residue  391 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 70 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 75 optimal weight:    7.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** 3 266 GLN ** 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 = 0.4265 r_free = 0.4265 target = 0.198546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.171246 restraints weight = 30734.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.175662 restraints weight = 9597.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.177935 restraints weight = 4614.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4048 r_free = 0.4048    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.4048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6824  Z= 0.202
  Angle     :  0.552   4.540   9324  Z= 0.296
  Chirality :  0.044   0.152   1030
  Planarity :  0.005   0.054   1206
  Dihedral  :  5.164  51.776    928
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.06 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.36 (0.27), residues: 832
  helix: -0.91 (0.95), residues: 22
  sheet: -1.36 (0.25), residues: 384
  loop : -1.74 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 2 170 
 PHE   0.018   0.002   PHE 2 468 
 TYR   0.017   0.001   TYR 2 119 
 ARG   0.003   0.000   ARG 3 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03472 (  195)
  hydrogen bonds       : angle       5.72140 (  486)
  covalent geometry    : bond        0.00464 ( 6824)
  covalent geometry    : angle       0.55205 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6087 (pm20)
REVERT: 2  152 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.3455 (m-80)
REVERT: 2  200 THR cc_start: 0.8246 (t) cc_final: 0.7831 (m)
REVERT: 2  374 ASN cc_start: 0.7631 (m-40) cc_final: 0.7121 (p0)
REVERT: 2  396 VAL cc_start: 0.6502 (OUTLIER) cc_final: 0.6219 (m)
REVERT: 3  154 GLN cc_start: 0.5296 (mt0) cc_final: 0.3326 (pm20)
REVERT: 3  213 GLU cc_start: 0.7531 (pt0) cc_final: 0.7012 (tm-30)
REVERT: 3  292 SER cc_start: 0.8951 (t) cc_final: 0.8512 (p)
REVERT: 3  297 LYS cc_start: 0.8804 (tttt) cc_final: 0.8431 (ttmt)
  outliers start: 30
  outliers final: 25
  residues processed: 165
  average time/residue: 0.3103
  time to fit residues: 73.0675
Evaluate side-chains
  167 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  100 ASP
Chi-restraints excluded: chain 2 residue  105 THR
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  143 VAL
Chi-restraints excluded: chain 2 residue  147 THR
Chi-restraints excluded: chain 2 residue  152 TYR
Chi-restraints excluded: chain 2 residue  176 THR
Chi-restraints excluded: chain 2 residue  191 THR
Chi-restraints excluded: chain 2 residue  221 ASN
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  327 ASN
Chi-restraints excluded: chain 2 residue  391 VAL
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 2 residue  423 SER
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  300 ASN
Chi-restraints excluded: chain 3 residue  318 CYS
Chi-restraints excluded: chain 3 residue  338 VAL
Chi-restraints excluded: chain 3 residue  347 GLU
Chi-restraints excluded: chain 3 residue  391 VAL
Chi-restraints excluded: chain 3 residue  416 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.3980
   chunk 57 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 70 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.199713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.172582 restraints weight = 30554.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.177036 restraints weight = 9408.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.179300 restraints weight = 4473.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4045 r_free = 0.4045    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4045 r_free = 0.4045    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       52 |
|-----------------------------------------------------------------------------|
r_final: 0.4045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6824  Z= 0.130
  Angle     :  0.522   4.461   9324  Z= 0.277
  Chirality :  0.044   0.161   1030
  Planarity :  0.004   0.052   1206
  Dihedral  :  4.991  51.397    928
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 22.01 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.27 (0.28), residues: 832
  helix: -0.43 (1.05), residues: 22
  sheet: -1.42 (0.24), residues: 398
  loop : -1.54 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP 2  81 
 HIS   0.002   0.001   HIS 2 315 
 PHE   0.021   0.001   PHE 2 205 
 TYR   0.015   0.001   TYR 3 289 
 ARG   0.006   0.000   ARG 3 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03170 (  195)
  hydrogen bonds       : angle       5.57397 (  486)
  covalent geometry    : bond        0.00305 ( 6824)
  covalent geometry    : angle       0.52161 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6061 (pm20)
REVERT: 2  200 THR cc_start: 0.8255 (t) cc_final: 0.7841 (m)
REVERT: 2  374 ASN cc_start: 0.7595 (m-40) cc_final: 0.7014 (p0)
REVERT: 2  396 VAL cc_start: 0.6521 (OUTLIER) cc_final: 0.6242 (m)
REVERT: 3  154 GLN cc_start: 0.5270 (mt0) cc_final: 0.3280 (pm20)
REVERT: 3  177 TYR cc_start: 0.7441 (m-80) cc_final: 0.7158 (m-80)
REVERT: 3  187 LYS cc_start: 0.6561 (mttt) cc_final: 0.6200 (tptt)
REVERT: 3  213 GLU cc_start: 0.7418 (pt0) cc_final: 0.6954 (tm-30)
REVERT: 3  292 SER cc_start: 0.8913 (t) cc_final: 0.8457 (p)
REVERT: 3  297 LYS cc_start: 0.8779 (tttt) cc_final: 0.8393 (ttmt)
  outliers start: 24
  outliers final: 20
  residues processed: 157
  average time/residue: 0.3405
  time to fit residues: 76.2636
Evaluate side-chains
  156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  100 ASP
Chi-restraints excluded: chain 2 residue  105 THR
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  143 VAL
Chi-restraints excluded: chain 2 residue  147 THR
Chi-restraints excluded: chain 2 residue  221 ASN
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  327 ASN
Chi-restraints excluded: chain 2 residue  391 VAL
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  318 CYS
Chi-restraints excluded: chain 3 residue  338 VAL
Chi-restraints excluded: chain 3 residue  347 GLU
Chi-restraints excluded: chain 3 residue  391 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
3 198 ASN
** 3 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.198470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.171549 restraints weight = 30618.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.175946 restraints weight = 9536.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.178170 restraints weight = 4577.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4027 r_free = 0.4027    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       52 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4027 r_free = 0.4027    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       60 |
|-----------------------------------------------------------------------------|
r_final: 0.4027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6824  Z= 0.194
  Angle     :  0.542   4.521   9324  Z= 0.291
  Chirality :  0.044   0.154   1030
  Planarity :  0.005   0.051   1206
  Dihedral  :  5.082  50.872    928
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.74 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.33 (0.27), residues: 832
  helix: -0.41 (1.03), residues: 22
  sheet: -1.33 (0.25), residues: 388
  loop : -1.76 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 3 170 
 PHE   0.018   0.002   PHE 2 468 
 TYR   0.020   0.001   TYR 3 289 
 ARG   0.006   0.000   ARG 3 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03359 (  195)
  hydrogen bonds       : angle       5.63235 (  486)
  covalent geometry    : bond        0.00443 ( 6824)
  covalent geometry    : angle       0.54194 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6057 (pm20)
REVERT: 2  152 TYR cc_start: 0.4945 (OUTLIER) cc_final: 0.3416 (m-80)
REVERT: 2  200 THR cc_start: 0.8195 (t) cc_final: 0.7739 (m)
REVERT: 2  374 ASN cc_start: 0.7630 (m-40) cc_final: 0.7118 (p0)
REVERT: 2  396 VAL cc_start: 0.6559 (OUTLIER) cc_final: 0.6268 (m)
REVERT: 3  154 GLN cc_start: 0.5344 (mt0) cc_final: 0.3302 (pm20)
REVERT: 3  187 LYS cc_start: 0.6609 (mttt) cc_final: 0.6242 (tptt)
REVERT: 3  213 GLU cc_start: 0.7436 (pt0) cc_final: 0.6967 (tm-30)
REVERT: 3  267 TYR cc_start: 0.8472 (m-80) cc_final: 0.8167 (m-80)
REVERT: 3  292 SER cc_start: 0.8948 (t) cc_final: 0.8520 (p)
REVERT: 3  297 LYS cc_start: 0.8776 (tttt) cc_final: 0.8408 (ttmt)
  outliers start: 30
  outliers final: 24
  residues processed: 162
  average time/residue: 0.3256
  time to fit residues: 74.2372
Evaluate side-chains
  165 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  100 ASP
Chi-restraints excluded: chain 2 residue  105 THR
Chi-restraints excluded: chain 2 residue  106 ILE
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  143 VAL
Chi-restraints excluded: chain 2 residue  147 THR
Chi-restraints excluded: chain 2 residue  152 TYR
Chi-restraints excluded: chain 2 residue  191 THR
Chi-restraints excluded: chain 2 residue  221 ASN
Chi-restraints excluded: chain 2 residue  280 SER
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  327 ASN
Chi-restraints excluded: chain 2 residue  391 VAL
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 2 residue  471 ILE
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  287 LEU
Chi-restraints excluded: chain 3 residue  318 CYS
Chi-restraints excluded: chain 3 residue  338 VAL
Chi-restraints excluded: chain 3 residue  391 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 18 optimal weight:    0.4980
   chunk 6 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    4.0988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.198253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.171468 restraints weight = 30381.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.175871 restraints weight = 9329.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.178059 restraints weight = 4388.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4024 r_free = 0.4024    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       60 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4023 r_free = 0.4023    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       64 |
|-----------------------------------------------------------------------------|
r_final: 0.4023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6824  Z= 0.169
  Angle     :  0.534   4.487   9324  Z= 0.286
  Chirality :  0.044   0.158   1030
  Planarity :  0.004   0.051   1206
  Dihedral  :  5.063  51.127    928
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 22.01 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.29 (0.27), residues: 832
  helix: -0.31 (1.05), residues: 22
  sheet: -1.34 (0.25), residues: 394
  loop : -1.68 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 3 170 
 PHE   0.018   0.002   PHE 2 468 
 TYR   0.018   0.001   TYR 3 289 
 ARG   0.006   0.000   ARG 3 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03291 (  195)
  hydrogen bonds       : angle       5.62324 (  486)
  covalent geometry    : bond        0.00392 ( 6824)
  covalent geometry    : angle       0.53449 ( 9324)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2  109 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6065 (pm20)
REVERT: 2  152 TYR cc_start: 0.4936 (OUTLIER) cc_final: 0.3391 (m-80)
REVERT: 2  200 THR cc_start: 0.8160 (t) cc_final: 0.7706 (m)
REVERT: 2  374 ASN cc_start: 0.7637 (m-40) cc_final: 0.7094 (p0)
REVERT: 2  396 VAL cc_start: 0.6546 (OUTLIER) cc_final: 0.6261 (m)
REVERT: 3  154 GLN cc_start: 0.5211 (mt0) cc_final: 0.3321 (pm20)
REVERT: 3  187 LYS cc_start: 0.6590 (mttt) cc_final: 0.6214 (tptt)
REVERT: 3  213 GLU cc_start: 0.7427 (pt0) cc_final: 0.6951 (tm-30)
REVERT: 3  267 TYR cc_start: 0.8459 (m-80) cc_final: 0.8101 (m-80)
REVERT: 3  292 SER cc_start: 0.8948 (t) cc_final: 0.8503 (p)
REVERT: 3  297 LYS cc_start: 0.8781 (tttt) cc_final: 0.8397 (ttmt)
  outliers start: 24
  outliers final: 21
  residues processed: 158
  average time/residue: 0.3247
  time to fit residues: 71.9035
Evaluate side-chains
  162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   81 TRP
Chi-restraints excluded: chain 2 residue  100 ASP
Chi-restraints excluded: chain 2 residue  105 THR
Chi-restraints excluded: chain 2 residue  134 SER
Chi-restraints excluded: chain 2 residue  143 VAL
Chi-restraints excluded: chain 2 residue  147 THR
Chi-restraints excluded: chain 2 residue  152 TYR
Chi-restraints excluded: chain 2 residue  191 THR
Chi-restraints excluded: chain 2 residue  221 ASN
Chi-restraints excluded: chain 2 residue  292 SER
Chi-restraints excluded: chain 2 residue  304 THR
Chi-restraints excluded: chain 2 residue  306 THR
Chi-restraints excluded: chain 2 residue  327 ASN
Chi-restraints excluded: chain 2 residue  391 VAL
Chi-restraints excluded: chain 2 residue  396 VAL
Chi-restraints excluded: chain 2 residue  471 ILE
Chi-restraints excluded: chain 3 residue  141 ILE
Chi-restraints excluded: chain 3 residue  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  186 THR
Chi-restraints excluded: chain 3 residue  318 CYS
Chi-restraints excluded: chain 3 residue  338 VAL
Chi-restraints excluded: chain 3 residue  391 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 7 optimal weight:   20.0000
   chunk 78 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 76 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   overall best weight:    4.5786

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

Flipped N/Q/H residues before XYZ refinement:
3  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.198093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.171345 restraints weight = 30584.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.175715 restraints weight = 9545.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.177911 restraints weight = 4572.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4012 r_free = 0.4012    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       64 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4012 r_free = 0.4012    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       65 |
|-----------------------------------------------------------------------------|
r_final: 0.4012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6824  Z= 0.184
  Angle     :  0.542   4.487   9324  Z= 0.291
  Chirality :  0.044   0.156   1030
  Planarity :  0.005   0.050   1206
  Dihedral  :  5.110  51.771    928
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 21.74 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    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: -2.30 (0.28), residues: 832
  helix: -0.39 (1.05), residues: 22
  sheet: -1.34 (0.25), residues: 394
  loop : -1.70 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 3 170 
 PHE   0.019   0.002   PHE 2 468 
 TYR   0.018   0.001   TYR 3 289 
 ARG   0.005   0.001   ARG 3 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03342 (  195)
  hydrogen bonds       : angle       5.64553 (  486)
  covalent geometry    : bond        0.00423 ( 6824)
  covalent geometry    : angle       0.54183 ( 9324)

===============================================================================
Job complete
usr+sys time: 5096.82 seconds
wall clock time: 87 minutes 52.44 seconds (5272.44 seconds total)