Starting phenix.real_space_refine
on Thu May 15 08:52:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c1i_45120/05_2025/9c1i_45120.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c1i_45120/05_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_45120/05_2025/9c1i_45120.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c1i_45120/05_2025/9c1i_45120.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c1i_45120/05_2025/9c1i_45120.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c1i_45120/05_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-5687/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: 6.10, per 1000 atoms: 0.47
  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: 2.99
  Conformation dependent library (CDL) restraints added in 992.0 milliseconds
  

  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: 1.07
  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: 4.23

  Time building geometry restraints manager: 3.68 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:             0.130
  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:             0.210
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     28.300
  Find NCS groups from input model:        0.240
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.260
-------------------------------------------------------------------------------
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  : 1.061 
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: 0.3207
  time to fit residues: 101.6773
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  : 0.974 
-------------------------------------------------------------------------------
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 = 0.204760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.177613 restraints weight = 30133.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.182190 restraints weight = 9584.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.184528 restraints weight = 4635.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
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= 0.222
  Angle     :  0.575   4.991   9324  Z= 0.310
  Chirality :  0.045   0.173   1030
  Planarity :  0.005   0.060   1206
  Dihedral  :  5.153  50.585    928
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 8.18
  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       5.99144 (  486)
  covalent geometry    : bond        0.00504 ( 6824)
  covalent geometry    : angle       0.57483 ( 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  : 1.002 
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: 0.7144 (mt-10) cc_final: 0.6149 (pm20)
REVERT: 2  168 MET cc_start: 0.6452 (ttp) cc_final: 0.6040 (ttp)
REVERT: 2  175 TYR cc_start: 0.4520 (m-80) cc_final: 0.4166 (m-80)
REVERT: 2  199 MET cc_start: 0.4932 (mmt) cc_final: 0.4598 (mtt)
REVERT: 2  200 THR cc_start: 0.8309 (t) cc_final: 0.7995 (m)
REVERT: 2  337 PHE cc_start: 0.8633 (t80) cc_final: 0.8333 (t80)
REVERT: 2  374 ASN cc_start: 0.7672 (m-40) cc_final: 0.7201 (p0)
REVERT: 2  396 VAL cc_start: 0.6529 (OUTLIER) cc_final: 0.6237 (m)
REVERT: 3  177 TYR cc_start: 0.7482 (m-80) cc_final: 0.7188 (m-80)
REVERT: 3  213 GLU cc_start: 0.7294 (pt0) cc_final: 0.6823 (tm-30)
REVERT: 3  292 SER cc_start: 0.8839 (t) cc_final: 0.8455 (p)
REVERT: 3  297 LYS cc_start: 0.8882 (tttt) cc_final: 0.8486 (ttmt)
  outliers start: 19
  outliers final: 13
  residues processed: 177
  average time/residue: 0.3063
  time to fit residues: 76.3818
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  : 0.976 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0030
   chunk 67 optimal weight:    0.0470
   chunk 54 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.5892

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

Flipped N/Q/H residues before XYZ refinement:
2 178 ASN
2 329 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.205459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.177993 restraints weight = 30150.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.182688 restraints weight = 9337.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.185048 restraints weight = 4435.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4122 r_free = 0.4122    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4117 r_free = 0.4117    target_work(ls_wunit_k1) = 0.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.4117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6824  Z= 0.111
  Angle     :  0.510   4.886   9324  Z= 0.272
  Chirality :  0.044   0.193   1030
  Planarity :  0.004   0.062   1206
  Dihedral  :  4.897  50.861    928
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.11 %
    Favored  : 77.45 %
  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: -1.90 (0.28), residues: 832
  helix: -2.21 (0.82), residues: 34
  sheet: -0.98 (0.25), residues: 378
  loop : -1.36 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP 3 356 
 HIS   0.002   0.001   HIS 3 170 
 PHE   0.013   0.001   PHE 3 468 
 TYR   0.008   0.001   TYR 3  45 
 ARG   0.003   0.000   ARG 3 443 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  195)
  hydrogen bonds       : angle       5.67498 (  486)
  covalent geometry    : bond        0.00261 ( 6824)
  covalent geometry    : angle       0.50961 ( 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
  170 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 1.059 
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: 0.7164 (mt-10) cc_final: 0.6000 (pm20)
REVERT: 2  119 TYR cc_start: 0.3875 (m-10) cc_final: 0.3665 (m-10)
REVERT: 2  168 MET cc_start: 0.6725 (ttp) cc_final: 0.6145 (ttp)
REVERT: 2  175 TYR cc_start: 0.4467 (m-80) cc_final: 0.4110 (m-80)
REVERT: 2  200 THR cc_start: 0.8271 (t) cc_final: 0.7970 (m)
REVERT: 2  374 ASN cc_start: 0.7589 (m-40) cc_final: 0.7137 (p0)
REVERT: 2  396 VAL cc_start: 0.6519 (OUTLIER) cc_final: 0.6239 (m)
REVERT: 3  187 LYS cc_start: 0.6545 (mttt) cc_final: 0.6277 (tptt)
REVERT: 3  213 GLU cc_start: 0.7239 (pt0) cc_final: 0.6708 (tm-30)
REVERT: 3  292 SER cc_start: 0.8846 (t) cc_final: 0.8419 (p)
REVERT: 3  297 LYS cc_start: 0.8843 (tttt) cc_final: 0.8460 (ttmt)
  outliers start: 18
  outliers final: 12
  residues processed: 164
  average time/residue: 0.3242
  time to fit residues: 75.1475
Evaluate side-chains
  160 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
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  106 ILE
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  143 VAL
Chi-restraints excluded: chain 3 residue  176 THR
Chi-restraints excluded: chain 3 residue  287 LEU
Chi-restraints excluded: chain 3 residue  300 ASN
Chi-restraints excluded: chain 3 residue  338 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0980
   chunk 52 optimal weight:   10.0000
   overall best weight:    4.8188

-------------------------------------------------------------------------------
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 = 0.4292 r_free = 0.4292 target = 0.201430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.173651 restraints weight = 30235.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.178211 restraints weight = 9452.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.180523 restraints weight = 4539.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4070 r_free = 0.4070    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4070 r_free = 0.4070    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
r_final: 0.4070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6824  Z= 0.190
  Angle     :  0.547   5.170   9324  Z= 0.292
  Chirality :  0.044   0.163   1030
  Planarity :  0.005   0.061   1206
  Dihedral  :  5.047  51.035    928
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.89 %
    Favored  : 77.45 %
  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: -2.11 (0.27), residues: 832
  helix: -2.25 (0.78), residues: 34
  sheet: -1.11 (0.25), residues: 382
  loop : -1.51 (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   0.015   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        0.03487 (  195)
  hydrogen bonds       : angle       5.65840 (  486)
  covalent geometry    : bond        0.00434 ( 6824)
  covalent geometry    : angle       0.54720 ( 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
  176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 1.150 
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: 0.7237 (mt-10) cc_final: 0.6067 (pm20)
REVERT: 2  119 TYR cc_start: 0.3906 (m-10) cc_final: 0.3666 (m-10)
REVERT: 2  168 MET cc_start: 0.7170 (ttp) cc_final: 0.6538 (ttp)
REVERT: 2  175 TYR cc_start: 0.4609 (m-80) cc_final: 0.4261 (m-80)
REVERT: 2  200 THR cc_start: 0.8382 (t) cc_final: 0.8008 (m)
REVERT: 2  337 PHE cc_start: 0.8610 (t80) cc_final: 0.8334 (t80)
REVERT: 2  374 ASN cc_start: 0.7658 (m-40) cc_final: 0.7151 (p0)
REVERT: 2  396 VAL cc_start: 0.6561 (OUTLIER) cc_final: 0.6270 (m)
REVERT: 2  456 ASN cc_start: 0.8289 (m-40) cc_final: 0.8082 (t0)
REVERT: 3  177 TYR cc_start: 0.7456 (m-80) cc_final: 0.7153 (m-80)
REVERT: 3  187 LYS cc_start: 0.6530 (mttt) cc_final: 0.6239 (tptt)
REVERT: 3  213 GLU cc_start: 0.7241 (pt0) cc_final: 0.6755 (tm-30)
REVERT: 3  292 SER cc_start: 0.8910 (t) cc_final: 0.8479 (p)
REVERT: 3  297 LYS cc_start: 0.8870 (tttt) cc_final: 0.8482 (ttmt)
  outliers start: 27
  outliers final: 19
  residues processed: 167
  average time/residue: 0.3011
  time to fit residues: 72.1074
Evaluate side-chains
  164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
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  199 MET
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   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  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:    8.9990
   chunk 72 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 75 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   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 = 0.4257 r_free = 0.4257 target = 0.198008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.170555 restraints weight = 30749.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.175010 restraints weight = 9634.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.177283 restraints weight = 4607.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4003 r_free = 0.4003    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4003 r_free = 0.4003    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.4003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   6824  Z= 0.267
  Angle     :  0.595   4.796   9324  Z= 0.322
  Chirality :  0.045   0.152   1030
  Planarity :  0.005   0.059   1206
  Dihedral  :  5.303  51.013    928
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 19.43 %
    Favored  : 76.22 %
  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: -2.48 (0.27), residues: 832
  helix: -2.53 (0.68), residues: 34
  sheet: -1.49 (0.25), residues: 394
  loop : -1.61 (0.29), residues: 404

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   0.029   0.002   PHE 2 140 
 TYR   0.016   0.002   TYR 2 355 
 ARG   0.004   0.001   ARG 3 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03744 (  195)
  hydrogen bonds       : angle       5.84820 (  486)
  covalent geometry    : bond        0.00606 ( 6824)
  covalent geometry    : angle       0.59515 ( 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
  178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.912 
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: 0.7190 (mt-10) cc_final: 0.6076 (pm20)
REVERT: 2  119 TYR cc_start: 0.4123 (m-10) cc_final: 0.3868 (m-10)
REVERT: 2  175 TYR cc_start: 0.4616 (m-80) cc_final: 0.4249 (m-80)
REVERT: 2  200 THR cc_start: 0.8320 (t) cc_final: 0.7920 (m)
REVERT: 2  337 PHE cc_start: 0.8675 (t80) cc_final: 0.8361 (t80)
REVERT: 2  374 ASN cc_start: 0.7667 (m-40) cc_final: 0.7141 (p0)
REVERT: 2  396 VAL cc_start: 0.6538 (OUTLIER) cc_final: 0.6273 (m)
REVERT: 2  456 ASN cc_start: 0.8273 (m-40) cc_final: 0.8062 (t0)
REVERT: 3  154 GLN cc_start: 0.5284 (mt0) cc_final: 0.3356 (pm20)
REVERT: 3  177 TYR cc_start: 0.7610 (m-80) cc_final: 0.7407 (m-80)
REVERT: 3  199 MET cc_start: 0.7602 (mmt) cc_final: 0.6721 (mmt)
REVERT: 3  213 GLU cc_start: 0.7454 (pt0) cc_final: 0.6891 (tm-30)
REVERT: 3  292 SER cc_start: 0.8947 (t) cc_final: 0.8503 (p)
REVERT: 3  297 LYS cc_start: 0.8833 (tttt) cc_final: 0.8445 (ttmt)
  outliers start: 32
  outliers final: 28
  residues processed: 165
  average time/residue: 0.2955
  time to fit residues: 69.7947
Evaluate side-chains
  167 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
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  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 2 residue  423 SER
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  431 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:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 62 optimal weight:    0.1980
   chunk 6 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0030
   overall best weight:    2.8396

-------------------------------------------------------------------------------
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 = 0.4279 r_free = 0.4279 target = 0.200363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.172791 restraints weight = 30694.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.177341 restraints weight = 9456.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.179575 restraints weight = 4462.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4064
|-occupancy refinement: start-------------------------------------------------|
| 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:       38 |
|-----------------------------------------------------------------------------|
|-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:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.4064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6824  Z= 0.134
  Angle     :  0.522   4.513   9324  Z= 0.277
  Chirality :  0.044   0.161   1030
  Planarity :  0.004   0.057   1206
  Dihedral  :  5.047  51.959    928
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 21.60 %
    Favored  : 75.27 %
  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: -2.22 (0.27), residues: 832
  helix: -0.81 (1.02), residues: 22
  sheet: -1.23 (0.25), residues: 372
  loop : -1.69 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 3 170 
 PHE   0.015   0.002   PHE 2 468 
 TYR   0.010   0.001   TYR 3  45 
 ARG   0.002   0.000   ARG 3 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03227 (  195)
  hydrogen bonds       : angle       5.61481 (  486)
  covalent geometry    : bond        0.00313 ( 6824)
  covalent geometry    : angle       0.52218 ( 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
  163 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 1.084 
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: 2  109 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6077 (pm20)
REVERT: 2  119 TYR cc_start: 0.4017 (m-10) cc_final: 0.3756 (m-10)
REVERT: 2  175 TYR cc_start: 0.4579 (m-80) cc_final: 0.4196 (m-80)
REVERT: 2  200 THR cc_start: 0.8258 (t) cc_final: 0.7867 (m)
REVERT: 2  337 PHE cc_start: 0.8617 (t80) cc_final: 0.8323 (t80)
REVERT: 2  374 ASN cc_start: 0.7587 (m-40) cc_final: 0.7126 (p0)
REVERT: 2  396 VAL cc_start: 0.6548 (OUTLIER) cc_final: 0.6248 (m)
REVERT: 2  456 ASN cc_start: 0.8269 (m-40) cc_final: 0.8030 (t0)
REVERT: 3  154 GLN cc_start: 0.5161 (mt0) cc_final: 0.3249 (pm20)
REVERT: 3  177 TYR cc_start: 0.7469 (m-80) cc_final: 0.7248 (m-80)
REVERT: 3  199 MET cc_start: 0.7552 (mmt) cc_final: 0.6683 (mmt)
REVERT: 3  213 GLU cc_start: 0.7474 (pt0) cc_final: 0.6923 (tm-30)
REVERT: 3  289 TYR cc_start: 0.8111 (m-80) cc_final: 0.7884 (m-80)
REVERT: 3  292 SER cc_start: 0.8928 (t) cc_final: 0.8449 (p)
REVERT: 3  297 LYS cc_start: 0.8812 (tttt) cc_final: 0.8414 (ttmt)
REVERT: 3  443 ARG cc_start: 0.8472 (ptp-170) cc_final: 0.8246 (ptp-170)
  outliers start: 23
  outliers final: 17
  residues processed: 156
  average time/residue: 0.3047
  time to fit residues: 67.6864
Evaluate side-chains
  155 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 75 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.4264 r_free = 0.4264 target = 0.199029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.171478 restraints weight = 30772.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.175919 restraints weight = 9566.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.178186 restraints weight = 4591.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4043 r_free = 0.4043    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4043 r_free = 0.4043    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.4043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6824  Z= 0.182
  Angle     :  0.534   4.505   9324  Z= 0.285
  Chirality :  0.044   0.153   1030
  Planarity :  0.004   0.054   1206
  Dihedral  :  5.096  52.072    928
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.20 %
    Favored  : 75.14 %
  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 (0.27), residues: 832
  helix: -0.72 (0.99), residues: 22
  sheet: -1.25 (0.25), residues: 378
  loop : -1.74 (0.28), residues: 432

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        0.03330 (  195)
  hydrogen bonds       : angle       5.65158 (  486)
  covalent geometry    : bond        0.00417 ( 6824)
  covalent geometry    : angle       0.53426 ( 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
  171 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.083 
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: 2  109 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6156 (pm20)
REVERT: 2  152 TYR cc_start: 0.4874 (OUTLIER) cc_final: 0.3347 (m-80)
REVERT: 2  175 TYR cc_start: 0.4580 (m-80) cc_final: 0.4182 (m-80)
REVERT: 2  200 THR cc_start: 0.8279 (t) cc_final: 0.7885 (m)
REVERT: 2  337 PHE cc_start: 0.8655 (t80) cc_final: 0.8361 (t80)
REVERT: 2  374 ASN cc_start: 0.7605 (m-40) cc_final: 0.7116 (p0)
REVERT: 2  396 VAL cc_start: 0.6500 (OUTLIER) cc_final: 0.6220 (m)
REVERT: 2  456 ASN cc_start: 0.8261 (m-40) cc_final: 0.8031 (t0)
REVERT: 3  154 GLN cc_start: 0.5244 (mt0) cc_final: 0.3288 (pm20)
REVERT: 3  177 TYR cc_start: 0.7538 (m-80) cc_final: 0.7299 (m-80)
REVERT: 3  213 GLU cc_start: 0.7490 (pt0) cc_final: 0.6997 (tm-30)
REVERT: 3  292 SER cc_start: 0.8933 (t) cc_final: 0.8484 (p)
REVERT: 3  297 LYS cc_start: 0.8786 (tttt) cc_final: 0.8406 (ttmt)
  outliers start: 27
  outliers final: 22
  residues processed: 164
  average time/residue: 0.2995
  time to fit residues: 70.1561
Evaluate side-chains
  160 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 47 optimal weight:   20.0000
   chunk 14 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 61 optimal weight:    0.4980
   chunk 56 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9980
   overall best weight:    4.6986

-------------------------------------------------------------------------------
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 = 0.4264 r_free = 0.4264 target = 0.198645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.171357 restraints weight = 30557.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.175820 restraints weight = 9478.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.178061 restraints weight = 4506.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
r_final: 0.4051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.3510

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     :  0.541   4.397   9324  Z= 0.289
  Chirality :  0.044   0.154   1030
  Planarity :  0.005   0.051   1206
  Dihedral  :  5.098  52.207    928
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.33 %
    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: -2.34 (0.27), residues: 832
  helix: -0.56 (0.99), residues: 22
  sheet: -1.33 (0.25), residues: 384
  loop : -1.76 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 2 170 
 PHE   0.018   0.002   PHE 2 468 
 TYR   0.020   0.001   TYR 2 119 
 ARG   0.005   0.000   ARG 3 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03335 (  195)
  hydrogen bonds       : angle       5.65241 (  486)
  covalent geometry    : bond        0.00424 ( 6824)
  covalent geometry    : angle       0.54063 ( 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
  170 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 1.203 
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: 0.7305 (mt-10) cc_final: 0.6160 (pm20)
REVERT: 2  152 TYR cc_start: 0.4953 (OUTLIER) cc_final: 0.3493 (m-80)
REVERT: 2  175 TYR cc_start: 0.4591 (m-80) cc_final: 0.4156 (m-80)
REVERT: 2  200 THR cc_start: 0.8259 (t) cc_final: 0.7866 (m)
REVERT: 2  337 PHE cc_start: 0.8660 (t80) cc_final: 0.8357 (t80)
REVERT: 2  374 ASN cc_start: 0.7605 (m-40) cc_final: 0.7141 (p0)
REVERT: 2  396 VAL cc_start: 0.6524 (OUTLIER) cc_final: 0.6247 (m)
REVERT: 2  456 ASN cc_start: 0.8249 (m-40) cc_final: 0.8023 (t0)
REVERT: 3  154 GLN cc_start: 0.5307 (mt0) cc_final: 0.3277 (pm20)
REVERT: 3  177 TYR cc_start: 0.7539 (m-80) cc_final: 0.7337 (m-80)
REVERT: 3  187 LYS cc_start: 0.6612 (mttt) cc_final: 0.6255 (tptt)
REVERT: 3  213 GLU cc_start: 0.7437 (pt0) cc_final: 0.6988 (tm-30)
REVERT: 3  292 SER cc_start: 0.8934 (t) cc_final: 0.8513 (p)
REVERT: 3  297 LYS cc_start: 0.8770 (tttt) cc_final: 0.8400 (ttmt)
  outliers start: 29
  outliers final: 24
  residues processed: 163
  average time/residue: 0.3018
  time to fit residues: 70.6065
Evaluate side-chains
  164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
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  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  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:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
3 198 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 = 0.198512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.171254 restraints weight = 30654.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.175668 restraints weight = 9506.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.177949 restraints weight = 4530.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4020 r_free = 0.4020    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4020 r_free = 0.4020    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|
r_final: 0.4020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3619

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= 0.177
  Angle     :  0.538   4.411   9324  Z= 0.287
  Chirality :  0.044   0.156   1030
  Planarity :  0.004   0.051   1206
  Dihedral  :  5.098  52.182    928
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.60 %
    Favored  : 74.46 %
  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: -2.34 (0.27), residues: 832
  helix: -0.42 (1.02), residues: 22
  sheet: -1.37 (0.25), residues: 390
  loop : -1.73 (0.28), 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   0.018   0.002   PHE 2 468 
 TYR   0.019   0.001   TYR 3 289 
 ARG   0.004   0.000   ARG 3 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03302 (  195)
  hydrogen bonds       : angle       5.65591 (  486)
  covalent geometry    : bond        0.00409 ( 6824)
  covalent geometry    : angle       0.53761 ( 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
  168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 0.931 
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: 0.7336 (mt-10) cc_final: 0.6178 (pm20)
REVERT: 2  152 TYR cc_start: 0.4909 (OUTLIER) cc_final: 0.3404 (m-80)
REVERT: 2  175 TYR cc_start: 0.4577 (m-80) cc_final: 0.4137 (m-80)
REVERT: 2  374 ASN cc_start: 0.7611 (m-40) cc_final: 0.7115 (p0)
REVERT: 2  396 VAL cc_start: 0.6528 (OUTLIER) cc_final: 0.6248 (m)
REVERT: 2  456 ASN cc_start: 0.8280 (m-40) cc_final: 0.8054 (t0)
REVERT: 3  154 GLN cc_start: 0.5204 (mt0) cc_final: 0.3299 (pm20)
REVERT: 3  177 TYR cc_start: 0.7507 (m-80) cc_final: 0.7296 (m-80)
REVERT: 3  213 GLU cc_start: 0.7419 (pt0) cc_final: 0.6941 (tm-30)
REVERT: 3  292 SER cc_start: 0.8941 (t) cc_final: 0.8492 (p)
REVERT: 3  297 LYS cc_start: 0.8779 (tttt) cc_final: 0.8405 (ttmt)
  outliers start: 29
  outliers final: 26
  residues processed: 161
  average time/residue: 0.3124
  time to fit residues: 70.8087
Evaluate side-chains
  164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
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  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  308 ASP
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  413 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   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  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.199427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.172273 restraints weight = 30571.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.176715 restraints weight = 9505.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.178958 restraints weight = 4532.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4020 r_free = 0.4020    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4020 r_free = 0.4020    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|
r_final: 0.4020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6824  Z= 0.152
  Angle     :  0.526   4.369   9324  Z= 0.281
  Chirality :  0.044   0.160   1030
  Planarity :  0.004   0.051   1206
  Dihedral  :  5.044  51.854    928
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.55 %
    Favored  : 74.05 %
  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: -0.25 (1.06), residues: 22
  sheet: -1.34 (0.25), residues: 390
  loop : -1.70 (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   0.016   0.001   PHE 2 468 
 TYR   0.018   0.001   TYR 3 289 
 ARG   0.007   0.000   ARG 2 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03171 (  195)
  hydrogen bonds       : angle       5.61670 (  486)
  covalent geometry    : bond        0.00352 ( 6824)
  covalent geometry    : angle       0.52578 ( 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
  161 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.916 
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: 0.7316 (mt-10) cc_final: 0.6160 (pm20)
REVERT: 2  152 TYR cc_start: 0.4957 (OUTLIER) cc_final: 0.3444 (m-80)
REVERT: 2  175 TYR cc_start: 0.4510 (m-80) cc_final: 0.4072 (m-80)
REVERT: 2  337 PHE cc_start: 0.8647 (t80) cc_final: 0.8391 (t80)
REVERT: 2  374 ASN cc_start: 0.7575 (m-40) cc_final: 0.7113 (p0)
REVERT: 2  396 VAL cc_start: 0.6518 (OUTLIER) cc_final: 0.6238 (m)
REVERT: 2  456 ASN cc_start: 0.8265 (m-40) cc_final: 0.8040 (t0)
REVERT: 3  154 GLN cc_start: 0.5219 (mt0) cc_final: 0.3322 (pm20)
REVERT: 3  177 TYR cc_start: 0.7473 (m-80) cc_final: 0.7265 (m-80)
REVERT: 3  187 LYS cc_start: 0.6558 (mttt) cc_final: 0.6189 (tptt)
REVERT: 3  213 GLU cc_start: 0.7382 (pt0) cc_final: 0.6941 (tm-30)
REVERT: 3  292 SER cc_start: 0.8949 (t) cc_final: 0.8507 (p)
REVERT: 3  297 LYS cc_start: 0.8768 (tttt) cc_final: 0.8397 (ttmt)
  outliers start: 25
  outliers final: 22
  residues processed: 154
  average time/residue: 0.3207
  time to fit residues: 69.0573
Evaluate side-chains
  158 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 78 optimal weight:    7.9990
   chunk 67 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 11 optimal weight:    8.9990
   overall best weight:    4.9388

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.195661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.168499 restraints weight = 30501.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.172887 restraints weight = 9433.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.175160 restraints weight = 4485.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4013
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4013 r_free = 0.4013    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       54 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4013 r_free = 0.4013    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       61 |
|-----------------------------------------------------------------------------|
r_final: 0.4013
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3785

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= 0.193
  Angle     :  0.548   4.414   9324  Z= 0.294
  Chirality :  0.044   0.154   1030
  Planarity :  0.005   0.050   1206
  Dihedral  :  5.136  51.619    928
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.15 %
    Favored  : 73.78 %
  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: -2.38 (0.27), residues: 832
  helix: -0.48 (1.02), residues: 22
  sheet: -1.38 (0.25), residues: 384
  loop : -1.76 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP 2 356 
 HIS   0.002   0.001   HIS 3 170 
 PHE   0.020   0.002   PHE 2 468 
 TYR   0.016   0.002   TYR 3 289 
 ARG   0.005   0.000   ARG 3 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (  195)
  hydrogen bonds       : angle       5.70010 (  486)
  covalent geometry    : bond        0.00444 ( 6824)
  covalent geometry    : angle       0.54846 ( 9324)

===============================================================================
Job complete
usr+sys time: 4745.50 seconds
wall clock time: 82 minutes 21.75 seconds (4941.75 seconds total)