Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 03:28:03 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/04_2023/7sl9_25195_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/04_2023/7sl9_25195.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/04_2023/7sl9_25195.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/04_2023/7sl9_25195.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/04_2023/7sl9_25195_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/04_2023/7sl9_25195_neut_updated.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3091      2.51       5
     N     749      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   80": "NH1" <-> "NH2"
    Residue "A ARG  122": "NH1" <-> "NH2"
    Residue "A ARG  128": "NH1" <-> "NH2"
    Residue "A GLU  366": "OE1" <-> "OE2"
    Residue "B ARG   33": "NH1" <-> "NH2"
    Residue "B GLU   90": "OE1" <-> "OE2"
    Residue "B ARG  107": "NH1" <-> "NH2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 4712
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3763
          Classifications: {'peptide': 497}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 19, 'TRANS': 477}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 943
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'BUA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.96, per 1000 atoms: 0.63
  Number of scatterers: 4712
  At special positions: 0
  Unit cell: (91.16, 77.38, 90.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     844      8.00
     N     749      7.00
     C    3091      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 480 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.91
  Conformation dependent library (CDL) restraints added in 714.6 milliseconds
  

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1120

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 2 sheets defined
      55.9% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 33
      removed outlier: 3.795A  pdb=" N   SER A  25 " --> pdb=" O   MET A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 65
      removed outlier: 3.549A  pdb=" N   LEU A  59 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A  64 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 72
      No H-bonds generated for 'chain 'A' and resid 69 through 72'
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.815A  pdb=" N   ARG A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   ALA A  83 " --> pdb=" O   TYR A  79 " (cutoff:3.500A)
      removed outlier: 8.850A  pdb=" N   ILE A  84 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   PHE A  85 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   SER A  86 " --> pdb=" O   GLY A  82 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ILE A  87 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   PHE A  88 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   ALA A  89 " --> pdb=" O   PHE A  85 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   PHE A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR A  91 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 119 through 122
      No H-bonds generated for 'chain 'A' and resid 119 through 122'
    Processing helix  chain 'A' and resid 126 through 129
      No H-bonds generated for 'chain 'A' and resid 126 through 129'
    Processing helix  chain 'A' and resid 132 through 158
      removed outlier: 3.689A  pdb=" N   GLY A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ILE A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      Proline residue:  A 150  - end of helix
      removed outlier: 4.035A  pdb=" N   GLN A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 174
      removed outlier: 3.756A  pdb=" N   VAL A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   CYS A 173 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 211
      removed outlier: 3.991A  pdb=" N   PHE A 191 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLN A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 193 " --> pdb=" O   ASP A 189 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA A 198 " --> pdb=" O   GLY A 194 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN A 206 " --> pdb=" O   SER A 202 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 223
      removed outlier: 4.029A  pdb=" N   ASN A 219 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   TYR A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 257
      removed outlier: 3.511A  pdb=" N   PHE A 251 " --> pdb=" O   ILE A 247 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   SER A 255 " --> pdb=" O   PHE A 251 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 268
      removed outlier: 4.691A  pdb=" N   ARG A 266 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   TYR A 267 " --> pdb=" O   GLN A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 304
      removed outlier: 3.652A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN A 283 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   VAL A 285 " --> pdb=" O   TYR A 281 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   CYS A 297 " --> pdb=" O   CYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 321
      No H-bonds generated for 'chain 'A' and resid 319 through 321'
    Processing helix  chain 'A' and resid 323 through 330
      removed outlier: 3.622A  pdb=" N   LEU A 328 " --> pdb=" O   PRO A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 368
      removed outlier: 3.668A  pdb=" N   VAL A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLY A 348 " --> pdb=" O   CYS A 344 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU A 350 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER A 354 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A 363 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 404
      removed outlier: 3.730A  pdb=" N   GLN A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   SER A 389 " --> pdb=" O   SER A 385 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER A 404 " --> pdb=" O   ALA A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
      removed outlier: 3.531A  pdb=" N   VAL A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 432
      removed outlier: 3.503A  pdb=" N   LEU A 427 " --> pdb=" O   PRO A 423 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   PHE A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 462
      removed outlier: 3.787A  pdb=" N   VAL A 444 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLN A 461 " --> pdb=" O   GLY A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 470
      No H-bonds generated for 'chain 'A' and resid 467 through 470'
    Processing helix  chain 'A' and resid 511 through 515
    Processing helix  chain 'A' and resid 526 through 532
      removed outlier: 4.139A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 542
      removed outlier: 3.690A  pdb=" N   SER A 540 " --> pdb=" O   GLY A 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 65
      No H-bonds generated for 'chain 'B' and resid 63 through 65'
    Processing sheet with id=  A, first strand: chain 'B' and resid 19 through 24
      removed outlier: 3.775A  pdb=" N   THR B  79 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 39 through 41
      removed outlier: 3.741A  pdb=" N   ALA B  93 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)

    192 hydrogen bonds defined for protein.
    567 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1428
        1.34 -     1.46: 1175
        1.46 -     1.58: 2183
        1.58 -     1.70: 0
        1.70 -     1.81: 43
  Bond restraints: 4829
  Sorted by residual:
  bond pdb=" C   THR A 510 "
       pdb=" N   PRO A 511 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.08e-02 8.57e+03 4.38e+00
  bond pdb=" C   SER A 317 "
       pdb=" N   ALA A 318 "
    ideal  model  delta    sigma   weight residual
    1.329  1.276  0.052 3.03e-02 1.09e+03 2.99e+00
  bond pdb=" C3  BUA A 701 "
       pdb=" C4  BUA A 701 "
    ideal  model  delta    sigma   weight residual
    1.539  1.506  0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" N   LYS A 314 "
       pdb=" CA  LYS A 314 "
    ideal  model  delta    sigma   weight residual
    1.460  1.485 -0.024 1.51e-02 4.39e+03 2.58e+00
  bond pdb=" N   VAL A 316 "
       pdb=" CA  VAL A 316 "
    ideal  model  delta    sigma   weight residual
    1.458  1.440  0.018 1.19e-02 7.06e+03 2.39e+00
  ... (remaining 4824 not shown)

  Histogram of bond angle deviations from ideal:
       98.81 -   105.85: 101
      105.85 -   112.88: 2461
      112.88 -   119.92: 1790
      119.92 -   126.95: 2175
      126.95 -   133.98: 65
  Bond angle restraints: 6592
  Sorted by residual:
  angle pdb=" N   LYS A 315 "
        pdb=" CA  LYS A 315 "
        pdb=" C   LYS A 315 "
      ideal   model   delta    sigma   weight residual
     110.35  122.13  -11.78 1.36e+00 5.41e-01 7.50e+01
  angle pdb=" N   VAL A 316 "
        pdb=" CA  VAL A 316 "
        pdb=" C   VAL A 316 "
      ideal   model   delta    sigma   weight residual
     108.12   98.81    9.31 1.44e+00 4.82e-01 4.18e+01
  angle pdb=" N   GLN A 508 "
        pdb=" CA  GLN A 508 "
        pdb=" C   GLN A 508 "
      ideal   model   delta    sigma   weight residual
     112.68  107.28    5.40 1.33e+00 5.65e-01 1.65e+01
  angle pdb=" C   PHE A 160 "
        pdb=" N   ASP A 161 "
        pdb=" CA  ASP A 161 "
      ideal   model   delta    sigma   weight residual
     121.54  129.16   -7.62 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" C   THR A 178 "
        pdb=" N   LEU A 179 "
        pdb=" CA  LEU A 179 "
      ideal   model   delta    sigma   weight residual
     124.31  130.91   -6.60 1.67e+00 3.59e-01 1.56e+01
  ... (remaining 6587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 2473
       17.66 -    35.32: 236
       35.32 -    52.98: 36
       52.98 -    70.64: 7
       70.64 -    88.30: 2
  Dihedral angle restraints: 2754
    sinusoidal: 983
      harmonic: 1771
  Sorted by residual:
  dihedral pdb=" CA  TYR B 111 "
           pdb=" C   TYR B 111 "
           pdb=" N   TYR B 112 "
           pdb=" CA  TYR B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.42  -29.58     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  LEU A 409 "
           pdb=" C   LEU A 409 "
           pdb=" N   LEU A 410 "
           pdb=" CA  LEU A 410 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.76   22.24     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  ILE A 477 "
           pdb=" C   ILE A 477 "
           pdb=" N   GLN A 478 "
           pdb=" CA  GLN A 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.94  -22.06     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 2751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 695
       0.092 -    0.184: 67
       0.184 -    0.276: 6
       0.276 -    0.368: 0
       0.368 -    0.460: 1
  Chirality restraints: 769
  Sorted by residual:
  chirality pdb=" CA  LYS A 315 "
            pdb=" N   LYS A 315 "
            pdb=" C   LYS A 315 "
            pdb=" CB  LYS A 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.29e+00
  chirality pdb=" CA  VAL A 316 "
            pdb=" N   VAL A 316 "
            pdb=" C   VAL A 316 "
            pdb=" CB  VAL A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CB  VAL A 203 "
            pdb=" CA  VAL A 203 "
            pdb=" CG1 VAL A 203 "
            pdb=" CG2 VAL A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 766 not shown)

  Planarity restraints: 813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  BUA A 701 "   -0.019 2.00e-02 2.50e+03   3.90e-02 1.52e+01
        pdb=" C4  BUA A 701 "    0.067 2.00e-02 2.50e+03
        pdb=" O1  BUA A 701 "   -0.024 2.00e-02 2.50e+03
        pdb=" O2  BUA A 701 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 309 "   -0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO A 310 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 310 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 310 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 422 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO A 423 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 423 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 423 "    0.032 5.00e-02 4.00e+02
  ... (remaining 810 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1300
        2.79 -     3.32: 4374
        3.32 -     3.84: 7733
        3.84 -     4.37: 9210
        4.37 -     4.90: 15380
  Nonbonded interactions: 37997
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 472 "
            pdb=" OH  TYR B 111 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" OG1 THR B  92 "
            pdb=" O   VAL B 120 "
     model   vdw
     2.290 2.440
  nonbonded pdb=" O   GLY A 224 "
            pdb=" OG  SER B  31 "
     model   vdw
     2.304 2.440
  nonbonded pdb=" O   ILE A 246 "
            pdb=" OG1 THR A 250 "
     model   vdw
     2.304 2.440
  nonbonded pdb=" O   THR A 250 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.312 2.440
  ... (remaining 37992 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:                  0.010
  Normalize map: mean=0, sd=1:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          2.010
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     16.240
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.060   4829  Z= 0.311
  Angle     :  0.951  11.781   6592  Z= 0.523
  Chirality :  0.058   0.460    769
  Planarity :  0.007   0.061    813
  Dihedral  : 13.950  88.296   1628
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer Outliers :  0.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.01 (0.22), residues: 611
  helix: -4.33 (0.11), residues: 357
  sheet: -2.43 (0.71), residues: 45
  loop : -3.26 (0.35), residues: 209

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 163
  average time/residue: 0.1501
  time to fit residues: 31.6217
Evaluate side-chains
  126 residues out of total 504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.542 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0475
  time to fit residues: 0.8345
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0000
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 156 GLN
A 358 ASN
A 386 GLN
B   3 GLN
B   5 GLN
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4829  Z= 0.216
  Angle     :  0.695  11.942   6592  Z= 0.352
  Chirality :  0.043   0.191    769
  Planarity :  0.005   0.042    813
  Dihedral  :  5.611  26.577    671
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer Outliers :  4.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.95 (0.28), residues: 611
  helix: -2.35 (0.21), residues: 355
  sheet: -3.23 (0.67), residues: 47
  loop : -2.62 (0.39), residues: 209

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 15
  residues processed: 153
  average time/residue: 0.1522
  time to fit residues: 30.0702
Evaluate side-chains
  136 residues out of total 504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.493 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0510
  time to fit residues: 2.0645
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0040
   chunk 37 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4829  Z= 0.193
  Angle     :  0.676  11.521   6592  Z= 0.335
  Chirality :  0.041   0.165    769
  Planarity :  0.004   0.040    813
  Dihedral  :  5.215  24.680    671
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer Outliers :  3.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.31), residues: 611
  helix: -1.36 (0.25), residues: 360
  sheet: -3.19 (0.65), residues: 47
  loop : -2.42 (0.40), residues: 204

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1512
  time to fit residues: 30.4727
Evaluate side-chains
  141 residues out of total 504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.532 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0537
  time to fit residues: 1.8141
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0970
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 GLN
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3040
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: