Starting phenix.real_space_refine (version: dev)
on Sat Feb 18 20:18:46 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_26104/02_2023/6pb1_26104_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_26104/02_2023/6pb1_26104.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_26104/02_2023/6pb1_26104.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_26104/02_2023/6pb1_26104.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_26104/02_2023/6pb1_26104_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_26104/02_2023/6pb1_26104_updated.pdb"
  }
  resolution = 2.8
  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=   0.006
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
Process input model

  Symmetric amino acids flipped
    Residue "P ARG  114": "NH1" <-> "NH2"
    Residue "P ARG  142": "NH1" <-> "NH2"
    Residue "P ARG  145": "NH1" <-> "NH2"
    Residue "P ARG  295": "NH1" <-> "NH2"
    Residue "A ARG   13": "NH1" <-> "NH2"
    Residue "A ARG   38": "NH1" <-> "NH2"
    Residue "A ARG  317": "NH1" <-> "NH2"
    Residue "B ARG   46": "NH1" <-> "NH2"
    Residue "B ARG  129": "NH1" <-> "NH2"
    Residue "B ARG  137": "NH1" <-> "NH2"
    Residue "B ARG  314": "NH1" <-> "NH2"
    Residue "N PHE   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 8785
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "P"
      Number of atoms: 2363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2363
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
    Chain: "U"
      Number of atoms: 330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 330
          Classifications: {'peptide': 40}
          Link IDs: {'PTRANS': 1, 'TRANS': 38}
    Chain: "A"
      Number of atoms: 1892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1892
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "P"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 202
          Unusual residues: {'CLR': 4, 'PLM': 5}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 5.67, per 1000 atoms: 0.65
  Number of scatterers: 8785
  At special positions: 0
  Unit cell: (106.47, 96.33, 137.904, 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      52     16.00
     O    1584      8.00
     N    1507      7.00
     C    5642      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS P 184 " - pdb=" SG  CYS P 254 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02

  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: 3.09
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      38.4% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'P' and resid 111 through 140
      removed outlier: 4.083A  pdb=" N   ALA P 133 " --> pdb=" O   ALA P 129 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 147 through 169
    Processing helix  chain 'P' and resid 174 through 178
    Processing helix  chain 'P' and resid 182 through 213
    Processing helix  chain 'P' and resid 224 through 231
    Processing helix  chain 'P' and resid 234 through 247
      Proline residue:  P 237  - end of helix
      removed outlier: 4.233A  pdb=" N   ALA P 241 " --> pdb=" O   ILE P 238 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   ILE P 244 " --> pdb=" O   ALA P 241 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU P 247 " --> pdb=" O   ILE P 244 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 253 through 255
      No H-bonds generated for 'chain 'P' and resid 253 through 255'
    Processing helix  chain 'P' and resid 264 through 297
      removed outlier: 3.867A  pdb=" N   TYR P 268 " --> pdb=" O   ASP P 265 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   GLN P 269 " --> pdb=" O   TYR P 266 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLY P 270 " --> pdb=" O   ILE P 267 " (cutoff:3.500A)
      Proline residue:  P 271  - end of helix
      removed outlier: 3.631A  pdb=" N   ARG P 295 " --> pdb=" O   THR P 292 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA P 296 " --> pdb=" O   LYS P 293 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER P 297 " --> pdb=" O   LEU P 294 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 301 through 319
      Proline residue:  P 317  - end of helix
    Processing helix  chain 'P' and resid 321 through 324
    Processing helix  chain 'P' and resid 334 through 349
      removed outlier: 3.678A  pdb=" N   ILE P 338 " --> pdb=" O   ASP P 334 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   MET P 339 " --> pdb=" O   LEU P 335 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 351 through 360
    Processing helix  chain 'P' and resid 364 through 381
    Processing helix  chain 'U' and resid 9 through 39
      removed outlier: 3.587A  pdb=" N   THR U  16 " --> pdb=" O   HIS U  12 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU U  17 " --> pdb=" O   LEU U  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.191A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 59
    Processing helix  chain 'A' and resid 265 through 277
    Processing helix  chain 'A' and resid 294 through 300
    Processing helix  chain 'A' and resid 308 through 311
      No H-bonds generated for 'chain 'A' and resid 308 through 311'
    Processing helix  chain 'A' and resid 313 through 315
      No H-bonds generated for 'chain 'A' and resid 313 through 315'
    Processing helix  chain 'A' and resid 332 through 349
      removed outlier: 4.045A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 390
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 35
      removed outlier: 3.664A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 30 through 35'
    Processing helix  chain 'G' and resid 8 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'N' and resid 29 through 31
      No H-bonds generated for 'chain 'N' and resid 29 through 31'
    Processing helix  chain 'N' and resid 88 through 90
      No H-bonds generated for 'chain 'N' and resid 88 through 90'
    Processing sheet with id=  A, first strand: chain 'A' and resid 359 through 363
      removed outlier: 7.031A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP A 223 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.061A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.870A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.833A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.779A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.880A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.602A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.812A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'N' and resid 122 through 124
      removed outlier: 5.996A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1074 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: 2.15

  Time building geometry restraints manager: 3.39 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: 2774
        1.34 -     1.46: 1744
        1.46 -     1.58: 4386
        1.58 -     1.70: 0
        1.70 -     1.81: 72
  Bond restraints: 8976
  Sorted by residual:
  bond pdb=" CA  LEU P 171 "
       pdb=" C   LEU P 171 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.024 1.30e-02 5.92e+03 3.51e+00
  bond pdb=" C   ILE P 234 "
       pdb=" N   PRO P 235 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.040 2.34e-02 1.83e+03 2.86e+00
  bond pdb=" CA  VAL P 172 "
       pdb=" C   VAL P 172 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.021 1.35e-02 5.49e+03 2.47e+00
  bond pdb=" C5  CLR P 401 "
       pdb=" C6  CLR P 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.301  0.031 2.00e-02 2.50e+03 2.37e+00
  bond pdb=" C5  CLR P 403 "
       pdb=" C6  CLR P 403 "
    ideal  model  delta    sigma   weight residual
    1.332  1.301  0.031 2.00e-02 2.50e+03 2.35e+00
  ... (remaining 8971 not shown)

  Histogram of bond angle deviations from ideal:
       99.81 -   106.66: 209
      106.66 -   113.50: 4926
      113.50 -   120.34: 3453
      120.34 -   127.19: 3469
      127.19 -   134.03: 90
  Bond angle restraints: 12147
  Sorted by residual:
  angle pdb=" N   VAL P 172 "
        pdb=" CA  VAL P 172 "
        pdb=" C   VAL P 172 "
      ideal   model   delta    sigma   weight residual
     109.63  121.67  -12.04 1.44e+00 4.82e-01 6.99e+01
  angle pdb=" N   LEU P 171 "
        pdb=" CA  LEU P 171 "
        pdb=" C   LEU P 171 "
      ideal   model   delta    sigma   weight residual
     111.28  119.28   -8.00 1.09e+00 8.42e-01 5.39e+01
  angle pdb=" CA  ILE P 234 "
        pdb=" C   ILE P 234 "
        pdb=" N   PRO P 235 "
      ideal   model   delta    sigma   weight residual
     118.88  123.00   -4.12 1.54e+00 4.22e-01 7.16e+00
  angle pdb=" CA  PHE P 236 "
        pdb=" C   PHE P 236 "
        pdb=" N   PRO P 237 "
      ideal   model   delta    sigma   weight residual
     118.44  122.67   -4.23 1.59e+00 3.96e-01 7.09e+00
  angle pdb=" C   ASP B 163 "
        pdb=" N   THR B 164 "
        pdb=" CA  THR B 164 "
      ideal   model   delta    sigma   weight residual
     122.40  126.21   -3.81 1.45e+00 4.76e-01 6.92e+00
  ... (remaining 12142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.06: 5092
       15.06 -    30.12: 165
       30.12 -    45.18: 41
       45.18 -    60.23: 6
       60.23 -    75.29: 7
  Dihedral angle restraints: 5311
    sinusoidal: 2194
      harmonic: 3117
  Sorted by residual:
  dihedral pdb=" CA  PRO P 235 "
           pdb=" C   PRO P 235 "
           pdb=" N   PHE P 236 "
           pdb=" CA  PHE P 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.51   16.49     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ASN N  35 "
           pdb=" C   ASN N  35 "
           pdb=" N   TRP N  36 "
           pdb=" CA  TRP N  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.66   16.34     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  TYR N  60 "
           pdb=" C   TYR N  60 "
           pdb=" N   THR N  61 "
           pdb=" CA  THR N  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.25   15.75     0      5.00e+00 4.00e-02 9.92e+00
  ... (remaining 5308 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1216
       0.084 -    0.168: 113
       0.168 -    0.252: 15
       0.252 -    0.336: 3
       0.336 -    0.420: 5
  Chirality restraints: 1352
  Sorted by residual:
  chirality pdb=" C14 CLR P 403 "
            pdb=" C13 CLR P 403 "
            pdb=" C15 CLR P 403 "
            pdb=" C8  CLR P 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.40e+00
  chirality pdb=" C14 CLR P 401 "
            pdb=" C13 CLR P 401 "
            pdb=" C15 CLR P 401 "
            pdb=" C8  CLR P 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.73    0.42 2.00e-01 2.50e+01 4.34e+00
  chirality pdb=" C14 CLR P 402 "
            pdb=" C13 CLR P 402 "
            pdb=" C15 CLR P 402 "
            pdb=" C8  CLR P 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.72    0.41 2.00e-01 2.50e+01 4.12e+00
  ... (remaining 1349 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN P 170 "   -0.015 2.00e-02 2.50e+03   2.98e-02 8.89e+00
        pdb=" C   GLN P 170 "    0.052 2.00e-02 2.50e+03
        pdb=" O   GLN P 170 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU P 171 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL P 314 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.64e+00
        pdb=" C   VAL P 314 "    0.045 2.00e-02 2.50e+03
        pdb=" O   VAL P 314 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU P 315 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 301 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.53e+00
        pdb=" C   VAL A 301 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL A 301 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 302 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2343
        2.81 -     3.33: 7350
        3.33 -     3.86: 13889
        3.86 -     4.38: 16284
        4.38 -     4.90: 28560
  Nonbonded interactions: 68426
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.288 2.440
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.313 2.440
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.335 2.440
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.346 2.520
  nonbonded pdb=" OG  SER P 297 "
            pdb=" NH1 ARG A 385 "
     model   vdw
     2.371 2.520
  ... (remaining 68421 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
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5642      2.51       5
     N    1507      2.21       5
     O    1584      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.430
  Check model and map are aligned:         0.140
  Process input model:                     24.810
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.090
  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:14.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0155
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      :  0.003   0.040   8976  Z= 0.223
  Angle     :  0.788  12.041  12147  Z= 0.421
  Chirality :  0.059   0.420   1352
  Planarity :  0.006   0.063   1523
  Dihedral  :  8.983  75.292   3282
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer Outliers :  0.00 %
  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 (0.20), residues: 1051
  helix: -1.45 (0.19), residues: 420
  sheet: -1.51 (0.30), residues: 226
  loop : -2.58 (0.23), residues: 405

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.9943
  time to fit residues: 94.3863
Evaluate side-chains
  45 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.858 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4012
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 94 optimal weight:    7.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
P 152 HIS
P 170 GLN
P 177 HIS
P 285 ASN
P 344 ASN
** P 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 380 HIS
P 381 HIS
A  23 ASN
A  59 GLN
A 267 GLN
B 142 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0905
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8976  Z= 0.253
  Angle     :  0.715   9.527  12147  Z= 0.363
  Chirality :  0.046   0.230   1352
  Planarity :  0.006   0.056   1523
  Dihedral  :  8.262  57.355   1280
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer Outliers :  1.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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: -1.74 (0.23), residues: 1051
  helix: -0.12 (0.23), residues: 418
  sheet: -0.95 (0.33), residues: 196
  loop : -2.26 (0.24), residues: 437

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 5
  residues processed: 70
  average time/residue: 0.7154
  time to fit residues: 56.7154
Evaluate side-chains
  50 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.853 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 3
  residues processed: 2
  average time/residue: 0.1093
  time to fit residues: 1.8022
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 64 optimal weight:   30.0000
   chunk 26 optimal weight:    1.9990
   chunk 94 optimal weight:    7.9990
   chunk 102 optimal weight:    0.0980
   chunk 84 optimal weight:    8.9990
   chunk 93 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
P 154 ASN
P 351 GLN
A  23 ASN
A 220 HIS
B  88 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1064
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8976  Z= 0.201
  Angle     :  0.590   6.551  12147  Z= 0.307
  Chirality :  0.042   0.138   1352
  Planarity :  0.005   0.054   1523
  Dihedral  :  8.918  98.462   1280
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer Outliers :  2.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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: -1.33 (0.24), residues: 1051
  helix:  0.46 (0.24), residues: 425
  sheet: -0.98 (0.32), residues: 202
  loop : -2.23 (0.26), residues: 424

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 16
  residues processed: 66
  average time/residue: 0.7817
  time to fit residues: 58.2017
Evaluate side-chains
  61 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.862 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 8
  residues processed: 8
  average time/residue: 0.6179
  time to fit residues: 6.9315
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.4980
   chunk 71 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 63 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 89 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    2.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1211
moved from start:          0.5020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8976  Z= 0.205
  Angle     :  0.604   7.683  12147  Z= 0.312
  Chirality :  0.042   0.159   1352
  Planarity :  0.005   0.041   1523
  Dihedral  :  8.519  95.618   1280
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer Outliers :  3.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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: -1.03 (0.24), residues: 1051
  helix:  0.69 (0.25), residues: 419
  sheet: -0.72 (0.33), residues: 206
  loop : -2.07 (0.26), residues: 426

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 45
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
  outliers start: 30
  outliers final: 21
  residues processed: 63
  average time/residue: 0.7875
  time to fit residues: 56.0449
Evaluate side-chains
  63 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 42
  time to evaluate  : 0.912 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 13
  residues processed: 8
  average time/residue: 0.8622
  time to fit residues: 8.8460
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 85 optimal weight:   40.0000
   chunk 69 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 51 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1269
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8976  Z= 0.182
  Angle     :  0.562   6.815  12147  Z= 0.292
  Chirality :  0.041   0.149   1352
  Planarity :  0.005   0.094   1523
  Dihedral  :  8.605  99.803   1280
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer Outliers :  3.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.25), residues: 1051
  helix:  0.80 (0.25), residues: 417
  sheet: -0.59 (0.33), residues: 207
  loop : -1.98 (0.27), residues: 427

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 43
  time to evaluate  : 0.974 
Fit side-chains
  outliers start: 32
  outliers final: 22
  residues processed: 64
  average time/residue: 0.7413
  time to fit residues: 53.6466
Evaluate side-chains
  63 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 41
  time to evaluate  : 0.953 
Switching outliers to nearest non-outliers
  outliers start: 22
  outliers final: 12
  residues processed: 10
  average time/residue: 0.8455
  time to fit residues: 10.5748
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 59 optimal weight:   30.0000
   chunk 24 optimal weight:    1.9990
   chunk 100 optimal weight:   30.0000
   chunk 83 optimal weight:    2.9990
   chunk 46 optimal weight:   40.0000
   chunk 8 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:    0.1980
   chunk 97 optimal weight:    1.9990
   overall best weight:    2.0388

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

Flipped N/Q/H residues before XYZ refinement:
P 170 GLN
P 344 ASN
A 220 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1309
moved from start:          0.6018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8976  Z= 0.175
  Angle     :  0.562   7.506  12147  Z= 0.289
  Chirality :  0.041   0.159   1352
  Planarity :  0.004   0.052   1523
  Dihedral  :  8.438  98.974   1280
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer Outliers :  3.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.25), residues: 1051
  helix:  0.73 (0.25), residues: 421
  sheet: -0.48 (0.34), residues: 196
  loop : -1.86 (0.27), residues: 434

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 42
  time to evaluate  : 1.052 
Fit side-chains
  outliers start: 32
  outliers final: 19
  residues processed: 64
  average time/residue: 0.7333
  time to fit residues: 53.2630
Evaluate side-chains
  59 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.902 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 14
  residues processed: 5
  average time/residue: 0.5702
  time to fit residues: 4.8495
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    0.0270
   chunk 57 optimal weight:    0.5980
   chunk 73 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 84 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 62 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 46 optimal weight:   40.0000
   chunk 40 optimal weight:   50.0000
   chunk 59 optimal weight:   10.0000
   overall best weight:    5.1244

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

Flipped N/Q/H residues before XYZ refinement:
** P 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
A  41 HIS
A 220 HIS
B  88 ASN
B 142 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1597
moved from start:          0.7449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.087   8976  Z= 0.343
  Angle     :  0.860  11.434  12147  Z= 0.436
  Chirality :  0.050   0.271   1352
  Planarity :  0.007   0.097   1523
  Dihedral  : 10.055  96.562   1280
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 19.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.04 %
    Favored  : 94.86 %
  Rotamer Outliers :  3.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.19 %

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: -1.45 (0.24), residues: 1051
  helix:  0.10 (0.25), residues: 395
  sheet: -0.64 (0.34), residues: 211
  loop : -2.09 (0.27), residues: 445

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 51
  time to evaluate  : 0.926 
Fit side-chains
  outliers start: 36
  outliers final: 20
  residues processed: 78
  average time/residue: 0.7277
  time to fit residues: 64.1524
Evaluate side-chains
  64 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.897 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 16
  residues processed: 4
  average time/residue: 0.8326
  time to fit residues: 4.9248
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 91 optimal weight:    0.8980
   chunk 96 optimal weight:    9.9990
   chunk 87 optimal weight:   20.0000
   chunk 93 optimal weight:    0.8980
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** P 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1510
moved from start:          0.7575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8976  Z= 0.195
  Angle     :  0.631   7.207  12147  Z= 0.325
  Chirality :  0.043   0.171   1352
  Planarity :  0.005   0.071   1523
  Dihedral  :  8.928  97.512   1280
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer Outliers :  2.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.10 %

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: -1.13 (0.25), residues: 1051
  helix:  0.33 (0.25), residues: 406
  sheet: -0.33 (0.36), residues: 197
  loop : -1.97 (0.27), residues: 448

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 44
  time to evaluate  : 0.949 
Fit side-chains
  outliers start: 26
  outliers final: 16
  residues processed: 66
  average time/residue: 0.7138
  time to fit residues: 54.1791
Evaluate side-chains
  57 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 1.009 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 15
  residues processed: 1
  average time/residue: 0.3134
  time to fit residues: 1.8966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 56 optimal weight:   50.0000
   chunk 40 optimal weight:   40.0000
   chunk 73 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0070
   chunk 84 optimal weight:    5.9990
   chunk 88 optimal weight:   20.0000
   chunk 93 optimal weight:    0.0070
   chunk 61 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    3.4022

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

Flipped N/Q/H residues before XYZ refinement:
** P 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1606
moved from start:          0.8084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8976  Z= 0.244
  Angle     :  0.702   8.312  12147  Z= 0.362
  Chirality :  0.045   0.197   1352
  Planarity :  0.006   0.088   1523
  Dihedral  :  9.511  99.600   1280
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer Outliers :  2.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.10 %

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: -1.24 (0.25), residues: 1051
  helix:  0.15 (0.25), residues: 405
  sheet: -0.51 (0.36), residues: 197
  loop : -1.85 (0.28), residues: 449

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.983 
Fit side-chains
  outliers start: 25
  outliers final: 17
  residues processed: 64
  average time/residue: 0.7107
  time to fit residues: 51.7496
Evaluate side-chains
  58 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.949 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 15
  residues processed: 2
  average time/residue: 0.7196
  time to fit residues: 2.9691
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 103 optimal weight:   50.0000
   chunk 95 optimal weight:   40.0000
   chunk 82 optimal weight:    0.6980
   chunk 8 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 87 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   overall best weight:    3.5386

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

Flipped N/Q/H residues before XYZ refinement:
** P 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1630
moved from start:          0.8514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8976  Z= 0.251
  Angle     :  0.700  10.851  12147  Z= 0.362
  Chirality :  0.045   0.180   1352
  Planarity :  0.006   0.089   1523
  Dihedral  :  9.504  99.886   1280
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer Outliers :  2.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.10 %

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: -1.27 (0.25), residues: 1051
  helix:  0.20 (0.26), residues: 395
  sheet: -0.41 (0.36), residues: 198
  loop : -1.98 (0.27), residues: 458

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.790 
Fit side-chains
  outliers start: 19
  outliers final: 19
  residues processed: 57
  average time/residue: 0.7345
  time to fit residues: 47.6945
Evaluate side-chains
  60 residues out of total 931 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.849 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 17
  residues processed: 4
  average time/residue: 0.7003
  time to fit residues: 4.3689
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:   50.0000
   chunk 12 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 72 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 59 optimal weight:   30.0000
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
P 351 GLN
B 142 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5493 r_free = 0.5493 target = 0.369785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.5426 r_free = 0.5426 target = 0.359590 restraints weight = 14453.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.5423 rms_B_bonded: 1.71
r_work: 0.5357 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.5357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1972
moved from start:          0.8383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8976  Z= 0.141
  Angle     :  0.544   9.683  12147  Z= 0.283
  Chirality :  0.041   0.151   1352
  Planarity :  0.004   0.056   1523
  Dihedral  :  8.287  92.219   1280
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer Outliers :  2.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.25), residues: 1051
  helix:  0.50 (0.26), residues: 408
  sheet: -0.35 (0.36), residues: 192
  loop : -1.71 (0.28), residues: 451

===============================================================================
Job complete
usr+sys time: 2113.18 seconds
wall clock time: 39 minutes 18.92 seconds (2358.92 seconds total)