Starting phenix.real_space_refine
on Fri Oct 10 13:07:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r8q_19006/10_2025/8r8q_19006.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r8q_19006/10_2025/8r8q_19006.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r8q_19006/10_2025/8r8q_19006.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r8q_19006/10_2025/8r8q_19006.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r8q_19006/10_2025/8r8q_19006.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r8q_19006/10_2025/8r8q_19006.cif"
  }
  resolution = 4.08
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.054
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      43      5.16       5
     C    3743      2.51       5
     N     917      2.21       5
     O     999      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5702
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3041
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 3041
          Classifications: {'peptide': 391}
          Link IDs: {'PTRANS': 9, 'TRANS': 381}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2591
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 28, 'TRANS': 312}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.51, per 1000 atoms: 0.26
  Number of scatterers: 5702
  At special positions: 0
  Unit cell: (70.4, 91.3, 125.4, 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      43     16.00
     O     999      8.00
     N     917      7.00
     C    3743      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B 501 " - " ASN B  85 "
      " NAG B 502 " - " ASN B 157 "
      " NAG B 503 " - " ASN B 228 "
      " NAG B 504 " - " ASN B 331 "
      " NAG B 505 " - " ASN B  94 "
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 216.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1342

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 4 sheets defined
      53.4% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 51
      removed outlier: 3.653A  pdb=" N   CYS A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
      removed outlier: 3.501A  pdb=" N   PHE A  57 " --> pdb=" O   PHE A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 65
    Processing helix  chain 'A' and resid 76 through 81
      removed outlier: 3.603A  pdb=" N   MET A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 86
      removed outlier: 3.636A  pdb=" N   TRP A  86 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 105
    Processing helix  chain 'A' and resid 106 through 132
      removed outlier: 4.437A  pdb=" N   TRP A 110 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   THR A 112 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   VAL A 113 " --> pdb=" O   ARG A 109 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE A 114 " --> pdb=" O   TRP A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 141
      removed outlier: 3.677A  pdb=" N   MET A 138 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 164
      removed outlier: 4.727A  pdb=" N   ILE A 147 " --> pdb=" O   PHE A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 203
      removed outlier: 4.208A  pdb=" N   PHE A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA A 180 " --> pdb=" O   GLN A 176 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   THR A 185 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   VAL A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY A 192 " --> pdb=" O   MET A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 240
      removed outlier: 3.552A  pdb=" N   ILE A 219 " --> pdb=" O   MET A 215 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   THR A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   CYS A 221 " --> pdb=" O   GLY A 217 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE A 222 " --> pdb=" O   CYS A 218 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   PHE A 223 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER A 224 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   LYS A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 286
      removed outlier: 4.270A  pdb=" N   ILE A 266 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   PHE A 280 " --> pdb=" O   TYR A 276 " (cutoff:3.500A)
      Proline residue:  A 281  - end of helix
    Processing helix  chain 'A' and resid 286 through 293
      removed outlier: 3.752A  pdb=" N   PHE A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 3.635A  pdb=" N   ASN A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 311
      removed outlier: 4.012A  pdb=" N   ILE A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 325
      removed outlier: 3.828A  pdb=" N   ASP A 324 " --> pdb=" O   GLY A 320 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   LYS A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 350
      removed outlier: 3.653A  pdb=" N   THR A 350 " --> pdb=" O   MET A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 367
      removed outlier: 3.658A  pdb=" N   ALA A 357 " --> pdb=" O   ASN A 353 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LEU A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY A 362 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE A 363 " --> pdb=" O   CYS A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 380
      removed outlier: 3.682A  pdb=" N   PHE A 378 " --> pdb=" O   PRO A 374 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 415
      removed outlier: 3.981A  pdb=" N   GLY A 390 " --> pdb=" O   GLY A 386 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A 406 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ASP A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER A 413 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 445
      removed outlier: 4.205A  pdb=" N   ALA A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLN A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 99
    Processing helix  chain 'B' and resid 111 through 115
    Processing helix  chain 'B' and resid 157 through 162
      removed outlier: 4.242A  pdb=" N   SER B 161 " --> pdb=" O   ASN B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 321
    Processing helix  chain 'B' and resid 365 through 391
      removed outlier: 3.750A  pdb=" N   ALA B 378 " --> pdb=" O   VAL B 374 " (cutoff:3.500A)
      Proline residue:  B 379  - end of helix
      removed outlier: 3.720A  pdb=" N   MET B 382 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE B 383 " --> pdb=" O   PRO B 379 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 384 " --> pdb=" O   GLY B 380 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 45
      removed outlier: 3.589A  pdb=" N   THR B  84 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL B  82 " --> pdb=" O   HIS B  68 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B  72 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ALA B  83 " --> pdb=" O   PHE B 117 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   PHE B 117 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU B 126 " --> pdb=" O   TYR B 148 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   GLU B 128 " --> pdb=" O   PRO B 146 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 45
      removed outlier: 3.589A  pdb=" N   THR B  84 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL B  82 " --> pdb=" O   HIS B  68 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B  72 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ALA B  83 " --> pdb=" O   PHE B 117 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   PHE B 117 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   LEU B 121 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   LEU B 239 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   PHE B 123 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ALA B 237 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ARG B 125 " --> pdb=" O   GLU B 235 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE B 232 " --> pdb=" O   PHE B 334 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171
      removed outlier: 3.550A  pdb=" N   VAL B 192 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU B 217 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU B 354 " --> pdb=" O   CYS B 214 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN B 279 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY B 355 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU B 268 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B 251 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN B 267 " --> pdb=" O   ASN B 249 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASN B 249 " --> pdb=" O   GLN B 267 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU B 269 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER B 247 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171
      removed outlier: 3.550A  pdb=" N   VAL B 192 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU B 217 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B 220 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU B 348 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    876 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: 0.85

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1345
        1.33 -     1.45: 1294
        1.45 -     1.58: 3149
        1.58 -     1.70: 0
        1.70 -     1.82: 67
  Bond restraints: 5855
  Sorted by residual:
  bond pdb=" CA  TYR B 347 "
       pdb=" C   TYR B 347 "
    ideal  model  delta    sigma   weight residual
    1.521  1.554 -0.032 1.28e-02 6.10e+03 6.38e+00
  bond pdb=" CZ  TYR B 347 "
       pdb=" OH  TYR B 347 "
    ideal  model  delta    sigma   weight residual
    1.376  1.325  0.051 2.10e-02 2.27e+03 5.92e+00
  bond pdb=" CB  TYR B 347 "
       pdb=" CG  TYR B 347 "
    ideal  model  delta    sigma   weight residual
    1.512  1.461  0.051 2.20e-02 2.07e+03 5.44e+00
  bond pdb=" N   TYR B 347 "
       pdb=" CA  TYR B 347 "
    ideal  model  delta    sigma   weight residual
    1.455  1.435  0.021 1.18e-02 7.18e+03 3.06e+00
  bond pdb=" C   TYR B 347 "
       pdb=" O   TYR B 347 "
    ideal  model  delta    sigma   weight residual
    1.234  1.213  0.021 1.30e-02 5.92e+03 2.60e+00
  ... (remaining 5850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 7787
        2.04 -     4.09: 154
        4.09 -     6.13: 22
        6.13 -     8.18: 6
        8.18 -    10.22: 2
  Bond angle restraints: 7971
  Sorted by residual:
  angle pdb=" N   TYR B 347 "
        pdb=" CA  TYR B 347 "
        pdb=" CB  TYR B 347 "
      ideal   model   delta    sigma   weight residual
     110.99  101.80    9.19 1.77e+00 3.19e-01 2.70e+01
  angle pdb=" C   VAL B 361 "
        pdb=" N   ASP B 362 "
        pdb=" CA  ASP B 362 "
      ideal   model   delta    sigma   weight residual
     122.19  132.41  -10.22 2.30e+00 1.89e-01 1.98e+01
  angle pdb=" C   TYR B 347 "
        pdb=" CA  TYR B 347 "
        pdb=" CB  TYR B 347 "
      ideal   model   delta    sigma   weight residual
     109.86  116.56   -6.70 1.80e+00 3.09e-01 1.39e+01
  angle pdb=" N   TYR B 347 "
        pdb=" CA  TYR B 347 "
        pdb=" C   TYR B 347 "
      ideal   model   delta    sigma   weight residual
     108.55  114.37   -5.82 1.62e+00 3.81e-01 1.29e+01
  angle pdb=" CB  MET A 208 "
        pdb=" CG  MET A 208 "
        pdb=" SD  MET A 208 "
      ideal   model   delta    sigma   weight residual
     112.70  120.48   -7.78 3.00e+00 1.11e-01 6.72e+00
  ... (remaining 7966 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 3063
       17.29 -    34.58: 309
       34.58 -    51.87: 60
       51.87 -    69.16: 4
       69.16 -    86.45: 5
  Dihedral angle restraints: 3441
    sinusoidal: 1351
      harmonic: 2090
  Sorted by residual:
  dihedral pdb=" CA  GLY A 286 "
           pdb=" C   GLY A 286 "
           pdb=" N   LYS A 287 "
           pdb=" CA  LYS A 287 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.59  -17.41     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  PRO B  76 "
           pdb=" C   PRO B  76 "
           pdb=" N   PRO B  77 "
           pdb=" CA  PRO B  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.36   16.64     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  LYS A 287 "
           pdb=" C   LYS A 287 "
           pdb=" N   VAL A 288 "
           pdb=" CA  VAL A 288 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.12  -15.88     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 3438 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 616
       0.036 -    0.071: 214
       0.071 -    0.107: 79
       0.107 -    0.142: 12
       0.142 -    0.177: 1
  Chirality restraints: 922
  Sorted by residual:
  chirality pdb=" CG  LEU A 171 "
            pdb=" CB  LEU A 171 "
            pdb=" CD1 LEU A 171 "
            pdb=" CD2 LEU A 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.87e-01
  chirality pdb=" C1  NAG B 505 "
            pdb=" ND2 ASN B  94 "
            pdb=" C2  NAG B 505 "
            pdb=" O5  NAG B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CA  VAL B  79 "
            pdb=" N   VAL B  79 "
            pdb=" C   VAL B  79 "
            pdb=" CB  VAL B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.66e-01
  ... (remaining 919 not shown)

  Planarity restraints: 993
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 347 "    0.010 2.00e-02 2.50e+03   1.47e-02 4.31e+00
        pdb=" CG  TYR B 347 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 347 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 347 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 347 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 347 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 347 "   -0.015 2.00e-02 2.50e+03
        pdb=" OH  TYR B 347 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 313 "    0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO A 314 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 314 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 314 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  75 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO B  76 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B  76 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  76 "    0.022 5.00e-02 4.00e+02
  ... (remaining 990 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 590
        2.75 -     3.29: 5762
        3.29 -     3.82: 8889
        3.82 -     4.36: 9552
        4.36 -     4.90: 16711
  Nonbonded interactions: 41504
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 340 "
            pdb=" OG  SER A 364 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG1 THR B  66 "
            pdb=" OG1 THR B  84 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   PHE A  57 "
            pdb=" ND2 ASN A 187 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" OG  SER B 131 "
            pdb=" O   ALA B 134 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG  SER A 343 "
            pdb=" O   ALA A 357 "
     model   vdw
     2.305 3.040
  ... (remaining 41499 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.770
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
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   0.051   5860  Z= 0.162
  Angle     :  0.688  10.222   7986  Z= 0.340
  Chirality :  0.041   0.177    922
  Planarity :  0.004   0.045    988
  Dihedral  : 13.963  86.451   2099
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.33 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.26 (0.32), residues: 720
  helix:  1.02 (0.29), residues: 329
  sheet: -1.33 (0.52), residues: 114
  loop : -3.00 (0.33), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  71 
 TYR   0.027   0.001   TYR B 347 
 PHE   0.014   0.001   PHE B 117 
 TRP   0.012   0.001   TRP A 163 
 HIS   0.007   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5855)
  covalent geometry    : angle       0.68698 ( 7971)
  hydrogen bonds       : bond        0.20626 (  275)
  hydrogen bonds       : angle       7.20078 (  876)
  link_NAG-ASN         : bond        0.00290 (    5)
  link_NAG-ASN         : angle       1.00339 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6345 (tm-30)
REVERT: B  304 HIS cc_start: 0.7324 (m-70) cc_final: 0.7055 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0551
  time to fit residues: 9.9602
Evaluate side-chains
  112 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.170082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.133638 restraints weight = 8949.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.133601 restraints weight = 8335.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.133988 restraints weight = 7930.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.134292 restraints weight = 7198.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.134529 restraints weight = 6769.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5860  Z= 0.143
  Angle     :  0.606   6.240   7986  Z= 0.310
  Chirality :  0.041   0.150    922
  Planarity :  0.004   0.041    988
  Dihedral  :  5.036  51.441    876
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.32), residues: 720
  helix:  1.03 (0.29), residues: 344
  sheet: -1.29 (0.50), residues: 117
  loop : -2.99 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.008   0.001   TYR A 159 
 PHE   0.014   0.001   PHE A 422 
 TRP   0.010   0.001   TRP A 136 
 HIS   0.003   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 5855)
  covalent geometry    : angle       0.60465 ( 7971)
  hydrogen bonds       : bond        0.04592 (  275)
  hydrogen bonds       : angle       4.79819 (  876)
  link_NAG-ASN         : bond        0.00486 (    5)
  link_NAG-ASN         : angle       1.00624 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.9272 (mp) cc_final: 0.9049 (mp)
REVERT: A  176 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7861 (tm-30)
REVERT: A  193 TRP cc_start: 0.7543 (t60) cc_final: 0.7312 (t60)
REVERT: A  212 VAL cc_start: 0.8830 (t) cc_final: 0.8557 (p)
REVERT: A  282 PHE cc_start: 0.8301 (t80) cc_final: 0.8017 (t80)
REVERT: A  346 MET cc_start: 0.8247 (ttm) cc_final: 0.8029 (ttm)
REVERT: B  269 LEU cc_start: 0.9185 (mm) cc_final: 0.8645 (pt)
REVERT: B  304 HIS cc_start: 0.7414 (m-70) cc_final: 0.7115 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.0647
  time to fit residues: 11.8824
Evaluate side-chains
  106 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    1.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.164604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.130321 restraints weight = 9028.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.129649 restraints weight = 9707.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.131454 restraints weight = 10003.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.131535 restraints weight = 8052.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.132569 restraints weight = 7084.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5860  Z= 0.224
  Angle     :  0.705   7.531   7986  Z= 0.363
  Chirality :  0.044   0.160    922
  Planarity :  0.005   0.055    988
  Dihedral  :  5.428  49.701    876
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.32), residues: 720
  helix:  0.93 (0.29), residues: 338
  sheet: -1.16 (0.50), residues: 119
  loop : -3.09 (0.34), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  59 
 TYR   0.012   0.001   TYR A 275 
 PHE   0.020   0.002   PHE A 280 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.003   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 5855)
  covalent geometry    : angle       0.70399 ( 7971)
  hydrogen bonds       : bond        0.05529 (  275)
  hydrogen bonds       : angle       4.72270 (  876)
  link_NAG-ASN         : bond        0.00274 (    5)
  link_NAG-ASN         : angle       1.08255 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6611 (mm-30)
REVERT: A  175 LEU cc_start: 0.9391 (mp) cc_final: 0.9169 (mp)
REVERT: A  191 MET cc_start: 0.8079 (tpp) cc_final: 0.7842 (tpp)
REVERT: A  197 LYS cc_start: 0.8968 (tptp) cc_final: 0.8753 (tptt)
REVERT: A  315 MET cc_start: 0.8263 (tpp) cc_final: 0.7777 (tpp)
REVERT: B  304 HIS cc_start: 0.7538 (m-70) cc_final: 0.7206 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0587
  time to fit residues: 10.8852
Evaluate side-chains
  107 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.168226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.132810 restraints weight = 8906.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.133148 restraints weight = 8967.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.135067 restraints weight = 8318.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.134992 restraints weight = 6488.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.135127 restraints weight = 6121.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5860  Z= 0.157
  Angle     :  0.642   7.564   7986  Z= 0.323
  Chirality :  0.041   0.143    922
  Planarity :  0.004   0.049    988
  Dihedral  :  5.240  51.664    876
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.33), residues: 720
  helix:  1.07 (0.29), residues: 339
  sheet: -1.15 (0.51), residues: 119
  loop : -3.06 (0.35), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.011   0.001   TYR B 347 
 PHE   0.015   0.001   PHE B 117 
 TRP   0.011   0.001   TRP A 136 
 HIS   0.006   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5855)
  covalent geometry    : angle       0.64129 ( 7971)
  hydrogen bonds       : bond        0.04393 (  275)
  hydrogen bonds       : angle       4.47277 (  876)
  link_NAG-ASN         : bond        0.00329 (    5)
  link_NAG-ASN         : angle       0.96475 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6515 (mm-30)
REVERT: A  175 LEU cc_start: 0.9396 (mp) cc_final: 0.9182 (mp)
REVERT: A  197 LYS cc_start: 0.9036 (tptp) cc_final: 0.8806 (tptt)
REVERT: A  282 PHE cc_start: 0.8329 (t80) cc_final: 0.8123 (t80)
REVERT: A  315 MET cc_start: 0.8126 (tpp) cc_final: 0.7514 (tpp)
REVERT: B  304 HIS cc_start: 0.7557 (m-70) cc_final: 0.7209 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0561
  time to fit residues: 11.6402
Evaluate side-chains
  102 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.167515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.130892 restraints weight = 9042.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.130295 restraints weight = 8282.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.130943 restraints weight = 7832.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.131521 restraints weight = 6954.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.131754 restraints weight = 6494.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5860  Z= 0.164
  Angle     :  0.650   7.834   7986  Z= 0.331
  Chirality :  0.042   0.152    922
  Planarity :  0.005   0.051    988
  Dihedral  :  5.224  51.215    876
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.33), residues: 720
  helix:  1.16 (0.29), residues: 341
  sheet: -1.09 (0.50), residues: 121
  loop : -3.12 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 200 
 TYR   0.011   0.001   TYR B 347 
 PHE   0.015   0.001   PHE A 280 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.005   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5855)
  covalent geometry    : angle       0.64945 ( 7971)
  hydrogen bonds       : bond        0.04416 (  275)
  hydrogen bonds       : angle       4.40415 (  876)
  link_NAG-ASN         : bond        0.00290 (    5)
  link_NAG-ASN         : angle       0.98727 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6452 (mm-30)
REVERT: A  193 TRP cc_start: 0.7355 (t60) cc_final: 0.7147 (t60)
REVERT: A  197 LYS cc_start: 0.9236 (tptp) cc_final: 0.8948 (tptt)
REVERT: A  220 THR cc_start: 0.8243 (p) cc_final: 0.7767 (t)
REVERT: A  282 PHE cc_start: 0.8416 (t80) cc_final: 0.8174 (t80)
REVERT: B  269 LEU cc_start: 0.9219 (mm) cc_final: 0.8625 (pt)
REVERT: B  304 HIS cc_start: 0.7474 (m-70) cc_final: 0.7113 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0573
  time to fit residues: 11.2799
Evaluate side-chains
  109 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0170
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.170760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.135194 restraints weight = 8939.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.135796 restraints weight = 9185.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.136213 restraints weight = 8323.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.137294 restraints weight = 7265.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.137470 restraints weight = 6245.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5860  Z= 0.120
  Angle     :  0.616   8.439   7986  Z= 0.305
  Chirality :  0.040   0.147    922
  Planarity :  0.004   0.049    988
  Dihedral  :  4.989  52.796    876
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.33), residues: 720
  helix:  1.25 (0.29), residues: 341
  sheet: -1.09 (0.51), residues: 121
  loop : -3.07 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  71 
 TYR   0.010   0.001   TYR B 347 
 PHE   0.013   0.001   PHE B 117 
 TRP   0.010   0.001   TRP A 136 
 HIS   0.004   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5855)
  covalent geometry    : angle       0.61546 ( 7971)
  hydrogen bonds       : bond        0.03661 (  275)
  hydrogen bonds       : angle       4.22785 (  876)
  link_NAG-ASN         : bond        0.00324 (    5)
  link_NAG-ASN         : angle       0.90948 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.9129 (tptp) cc_final: 0.8861 (tptt)
REVERT: A  202 LEU cc_start: 0.8657 (tp) cc_final: 0.8428 (tt)
REVERT: A  282 PHE cc_start: 0.8448 (t80) cc_final: 0.8047 (t80)
REVERT: A  315 MET cc_start: 0.8056 (tpp) cc_final: 0.7514 (tpp)
REVERT: B  269 LEU cc_start: 0.9187 (mm) cc_final: 0.8625 (pt)
REVERT: B  304 HIS cc_start: 0.7435 (m-70) cc_final: 0.7078 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0585
  time to fit residues: 11.6890
Evaluate side-chains
  120 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 72 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 65 optimal weight:    0.1980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.170002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.135803 restraints weight = 8961.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.135451 restraints weight = 9150.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.136766 restraints weight = 8752.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.136886 restraints weight = 7371.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.137195 restraints weight = 6826.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5860  Z= 0.131
  Angle     :  0.638   8.359   7986  Z= 0.313
  Chirality :  0.041   0.148    922
  Planarity :  0.004   0.051    988
  Dihedral  :  4.970  51.934    876
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.33), residues: 720
  helix:  1.17 (0.29), residues: 346
  sheet: -1.11 (0.51), residues: 121
  loop : -3.01 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  39 
 TYR   0.010   0.001   TYR B 347 
 PHE   0.014   0.001   PHE A 118 
 TRP   0.009   0.001   TRP A 136 
 HIS   0.006   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5855)
  covalent geometry    : angle       0.63721 ( 7971)
  hydrogen bonds       : bond        0.03830 (  275)
  hydrogen bonds       : angle       4.22284 (  876)
  link_NAG-ASN         : bond        0.00298 (    5)
  link_NAG-ASN         : angle       0.92260 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6705 (mm-30)
REVERT: A  197 LYS cc_start: 0.9001 (tptp) cc_final: 0.8781 (tptt)
REVERT: A  282 PHE cc_start: 0.8382 (t80) cc_final: 0.7957 (t80)
REVERT: A  315 MET cc_start: 0.7919 (tpp) cc_final: 0.7364 (tpp)
REVERT: B  269 LEU cc_start: 0.9213 (mm) cc_final: 0.8623 (pt)
REVERT: B  304 HIS cc_start: 0.7441 (m-70) cc_final: 0.7096 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0554
  time to fit residues: 11.0144
Evaluate side-chains
  115 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 54 optimal weight:    0.1980
   chunk 9 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 7 optimal weight:    0.3980
   chunk 23 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0030
   chunk 64 optimal weight:    0.0570
   overall best weight:    0.2308

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.174734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.141190 restraints weight = 8815.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.139993 restraints weight = 7070.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140141 restraints weight = 6646.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.140258 restraints weight = 6550.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.140648 restraints weight = 6115.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5860  Z= 0.115
  Angle     :  0.653  10.426   7986  Z= 0.312
  Chirality :  0.041   0.155    922
  Planarity :  0.004   0.051    988
  Dihedral  :  4.852  53.079    876
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.33), residues: 720
  helix:  1.30 (0.29), residues: 343
  sheet: -0.98 (0.51), residues: 121
  loop : -3.02 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  71 
 TYR   0.010   0.001   TYR B 347 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 136 
 HIS   0.006   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5855)
  covalent geometry    : angle       0.65274 ( 7971)
  hydrogen bonds       : bond        0.03378 (  275)
  hydrogen bonds       : angle       4.15235 (  876)
  link_NAG-ASN         : bond        0.00324 (    5)
  link_NAG-ASN         : angle       0.92008 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 LEU cc_start: 0.8487 (tp) cc_final: 0.8224 (tt)
REVERT: A  197 LYS cc_start: 0.9187 (tptp) cc_final: 0.8858 (tptt)
REVERT: A  282 PHE cc_start: 0.8502 (t80) cc_final: 0.8047 (t80)
REVERT: A  315 MET cc_start: 0.7792 (tpp) cc_final: 0.7257 (tpp)
REVERT: B  206 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.7856 (mtp85)
REVERT: B  269 LEU cc_start: 0.9181 (mm) cc_final: 0.8641 (pt)
REVERT: B  304 HIS cc_start: 0.7493 (m-70) cc_final: 0.7031 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0590
  time to fit residues: 11.7141
Evaluate side-chains
  121 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0770
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0370
   chunk 3 optimal weight:    0.0040
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.4228

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.171926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.137580 restraints weight = 8844.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.136680 restraints weight = 8618.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.137749 restraints weight = 8335.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.138118 restraints weight = 7209.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.138397 restraints weight = 6427.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5860  Z= 0.124
  Angle     :  0.644  10.626   7986  Z= 0.313
  Chirality :  0.040   0.153    922
  Planarity :  0.004   0.052    988
  Dihedral  :  4.821  52.280    876
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.33), residues: 720
  helix:  1.32 (0.29), residues: 345
  sheet: -0.91 (0.52), residues: 121
  loop : -3.02 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  41 
 TYR   0.009   0.001   TYR B 347 
 PHE   0.016   0.001   PHE A 118 
 TRP   0.009   0.001   TRP A 136 
 HIS   0.006   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5855)
  covalent geometry    : angle       0.64314 ( 7971)
  hydrogen bonds       : bond        0.03465 (  275)
  hydrogen bonds       : angle       4.11847 (  876)
  link_NAG-ASN         : bond        0.00305 (    5)
  link_NAG-ASN         : angle       0.90893 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 LEU cc_start: 0.8550 (tp) cc_final: 0.8300 (tt)
REVERT: A  197 LYS cc_start: 0.9100 (tptp) cc_final: 0.8817 (tptt)
REVERT: A  282 PHE cc_start: 0.8448 (t80) cc_final: 0.7996 (t80)
REVERT: A  315 MET cc_start: 0.7852 (tpp) cc_final: 0.7273 (tpp)
REVERT: B  269 LEU cc_start: 0.9241 (mm) cc_final: 0.8654 (pt)
REVERT: B  304 HIS cc_start: 0.7522 (m-70) cc_final: 0.7011 (m-70)
REVERT: B  382 MET cc_start: 0.8158 (tpp) cc_final: 0.7413 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0533
  time to fit residues: 10.6557
Evaluate side-chains
  117 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.170097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.135005 restraints weight = 8945.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.133986 restraints weight = 8770.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.134602 restraints weight = 8450.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.135203 restraints weight = 7521.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.135581 restraints weight = 6668.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5860  Z= 0.141
  Angle     :  0.662  11.723   7986  Z= 0.324
  Chirality :  0.041   0.142    922
  Planarity :  0.004   0.054    988
  Dihedral  :  4.947  51.680    876
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.36 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.33), residues: 720
  helix:  1.24 (0.29), residues: 347
  sheet: -0.89 (0.52), residues: 121
  loop : -2.98 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  41 
 TYR   0.010   0.001   TYR A 159 
 PHE   0.014   0.001   PHE B 117 
 TRP   0.010   0.001   TRP A 136 
 HIS   0.004   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5855)
  covalent geometry    : angle       0.66177 ( 7971)
  hydrogen bonds       : bond        0.03803 (  275)
  hydrogen bonds       : angle       4.14833 (  876)
  link_NAG-ASN         : bond        0.00283 (    5)
  link_NAG-ASN         : angle       0.92740 (   15)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 LEU cc_start: 0.8597 (tp) cc_final: 0.8331 (tt)
REVERT: A  282 PHE cc_start: 0.8367 (t80) cc_final: 0.7985 (t80)
REVERT: A  315 MET cc_start: 0.7912 (tpp) cc_final: 0.7330 (tpp)
REVERT: B  269 LEU cc_start: 0.9248 (mm) cc_final: 0.8685 (pt)
REVERT: B  304 HIS cc_start: 0.7543 (m-70) cc_final: 0.7027 (m-70)
REVERT: B  382 MET cc_start: 0.8161 (tpp) cc_final: 0.7435 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0547
  time to fit residues: 10.6588
Evaluate side-chains
  111 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0670
   chunk 23 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.5318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.170336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.134646 restraints weight = 8780.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.135433 restraints weight = 8354.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.136918 restraints weight = 7318.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.137259 restraints weight = 6092.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.137498 restraints weight = 5812.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5860  Z= 0.136
  Angle     :  0.682  12.132   7986  Z= 0.332
  Chirality :  0.041   0.153    922
  Planarity :  0.004   0.054    988
  Dihedral  :  4.937  52.147    876
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.78 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.33), residues: 720
  helix:  1.21 (0.29), residues: 347
  sheet: -0.85 (0.52), residues: 121
  loop : -2.97 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  41 
 TYR   0.009   0.001   TYR B 347 
 PHE   0.020   0.001   PHE A 118 
 TRP   0.017   0.001   TRP A 163 
 HIS   0.007   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5855)
  covalent geometry    : angle       0.68174 ( 7971)
  hydrogen bonds       : bond        0.03658 (  275)
  hydrogen bonds       : angle       4.15024 (  876)
  link_NAG-ASN         : bond        0.00310 (    5)
  link_NAG-ASN         : angle       0.92122 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1043.33 seconds
wall clock time: 18 minutes 46.35 seconds (1126.35 seconds total)