Starting phenix.real_space_refine
on Fri Jul 19 02:04:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8q_19006/07_2024/8r8q_19006.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8q_19006/07_2024/8r8q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8q_19006/07_2024/8r8q_19006.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8q_19006/07_2024/8r8q_19006.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8q_19006/07_2024/8r8q_19006.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8q_19006/07_2024/8r8q_19006.cif"
  }
  resolution = 4.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
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
    Residue "A GLU  139": "OE1" <-> "OE2"
    Residue "A GLU  292": "OE1" <-> "OE2"
    Residue "A GLU  382": "OE1" <-> "OE2"
    Residue "A PHE  422": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  128": "OE1" <-> "OE2"
    Residue "B GLU  217": "OE1" <-> "OE2"
    Residue "B GLU  235": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: 3.88, per 1000 atoms: 0.68
  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  - 3.50
        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
  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: 2.09
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.63
  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: 1.62

  Time building geometry restraints manager: 2.33 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:
      100.05 -   106.84: 202
      106.84 -   113.63: 3186
      113.63 -   120.42: 2162
      120.42 -   127.21: 2340
      127.21 -   134.00: 81
  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 2.440
  nonbonded pdb=" OG1 THR B  66 "
            pdb=" OG1 THR B  84 "
     model   vdw
     2.229 2.440
  nonbonded pdb=" O   PHE A  57 "
            pdb=" ND2 ASN A 187 "
     model   vdw
     2.230 2.520
  nonbonded pdb=" OG  SER B 131 "
            pdb=" O   ALA B 134 "
     model   vdw
     2.299 2.440
  nonbonded pdb=" OG  SER A 343 "
            pdb=" O   ALA A 357 "
     model   vdw
     2.305 2.440
  ... (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
========== 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:             1.140
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.220
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.470
-------------------------------------------------------------------------------
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   5855  Z= 0.221
  Angle     :  0.687  10.222   7971  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 (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: -1.26 (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
 TRP   0.012   0.001   TRP A 163 
 HIS   0.007   0.001   HIS B 229 
 PHE   0.014   0.001   PHE B 117 
 TYR   0.027   0.001   TYR B 347 
 ARG   0.004   0.001   ARG A  71 

*********************** 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 fitting.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.617 
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: 0.1327
  time to fit residues: 23.3855
Evaluate side-chains
  112 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.0670
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.6518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5855  Z= 0.214
  Angle     :  0.590   6.013   7971  Z= 0.300
  Chirality :  0.041   0.156    922
  Planarity :  0.004   0.041    988
  Dihedral  :  5.054  51.068    876
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  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: -1.08 (0.33), residues: 720
  helix:  1.11 (0.29), residues: 343
  sheet: -1.39 (0.50), residues: 117
  loop : -2.97 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 136 
 HIS   0.004   0.001   HIS B 229 
 PHE   0.014   0.001   PHE A 422 
 TYR   0.008   0.001   TYR A 159 
 ARG   0.003   0.000   ARG A  71 

*********************** 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
  138 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7785 (tm-30)
REVERT: A  191 MET cc_start: 0.8157 (tpp) cc_final: 0.7936 (tpp)
REVERT: A  282 PHE cc_start: 0.8316 (t80) cc_final: 0.8070 (t80)
REVERT: B  269 LEU cc_start: 0.9177 (mm) cc_final: 0.8683 (pt)
REVERT: B  304 HIS cc_start: 0.7395 (m-70) cc_final: 0.7135 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1364
  time to fit residues: 26.0018
Evaluate side-chains
  110 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0070
   chunk 18 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.5998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5855  Z= 0.212
  Angle     :  0.599   7.141   7971  Z= 0.302
  Chirality :  0.041   0.154    922
  Planarity :  0.004   0.046    988
  Dihedral  :  4.964  51.682    876
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  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: -1.03 (0.33), residues: 720
  helix:  1.17 (0.29), residues: 344
  sheet: -1.16 (0.49), residues: 123
  loop : -3.15 (0.35), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 136 
 HIS   0.004   0.001   HIS B 229 
 PHE   0.015   0.001   PHE B 129 
 TYR   0.009   0.001   TYR B 347 
 ARG   0.002   0.000   ARG A  71 

*********************** 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
  145 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: A  191 MET cc_start: 0.8150 (tpp) cc_final: 0.7808 (tpp)
REVERT: A  197 LYS cc_start: 0.9209 (tptp) cc_final: 0.8979 (tptt)
REVERT: A  220 THR cc_start: 0.8242 (p) cc_final: 0.7763 (t)
REVERT: A  282 PHE cc_start: 0.8318 (t80) cc_final: 0.8049 (t80)
REVERT: A  315 MET cc_start: 0.8179 (tpp) cc_final: 0.7785 (tpp)
REVERT: B  269 LEU cc_start: 0.9203 (mm) cc_final: 0.8663 (pt)
REVERT: B  304 HIS cc_start: 0.7442 (m-70) cc_final: 0.7186 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1405
  time to fit residues: 27.6633
Evaluate side-chains
  112 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 44 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0170
   chunk 70 optimal weight:    0.0970
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.5016

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5855  Z= 0.190
  Angle     :  0.610   9.137   7971  Z= 0.302
  Chirality :  0.040   0.153    922
  Planarity :  0.004   0.044    988
  Dihedral  :  4.900  52.129    876
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  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: -0.91 (0.33), residues: 720
  helix:  1.35 (0.30), residues: 335
  sheet: -1.15 (0.50), residues: 121
  loop : -3.02 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 136 
 HIS   0.005   0.001   HIS A 344 
 PHE   0.013   0.001   PHE B 117 
 TYR   0.007   0.001   TYR A 159 
 ARG   0.006   0.000   ARG A 295 

*********************** 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
  142 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8645 (mm) cc_final: 0.8384 (mm)
REVERT: A  197 LYS cc_start: 0.9227 (tptp) cc_final: 0.8946 (tptt)
REVERT: A  220 THR cc_start: 0.8250 (p) cc_final: 0.7618 (t)
REVERT: A  315 MET cc_start: 0.8156 (tpp) cc_final: 0.7671 (tpp)
REVERT: B  256 ASP cc_start: 0.7723 (t0) cc_final: 0.7484 (t0)
REVERT: B  304 HIS cc_start: 0.7464 (m-70) cc_final: 0.7119 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1256
  time to fit residues: 24.9367
Evaluate side-chains
  114 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5855  Z= 0.243
  Angle     :  0.629   6.897   7971  Z= 0.317
  Chirality :  0.041   0.145    922
  Planarity :  0.004   0.048    988
  Dihedral  :  5.029  51.285    876
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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: -1.01 (0.33), residues: 720
  helix:  1.20 (0.30), residues: 340
  sheet: -1.18 (0.50), residues: 119
  loop : -3.06 (0.35), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 136 
 HIS   0.004   0.001   HIS A 344 
 PHE   0.014   0.001   PHE B 117 
 TYR   0.009   0.001   TYR A 275 
 ARG   0.005   0.000   ARG A 295 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7812 (tm-30)
REVERT: A  220 THR cc_start: 0.8266 (p) cc_final: 0.7789 (t)
REVERT: A  233 TYR cc_start: 0.8426 (t80) cc_final: 0.8138 (t80)
REVERT: A  282 PHE cc_start: 0.8408 (t80) cc_final: 0.7821 (t80)
REVERT: A  315 MET cc_start: 0.8276 (tpp) cc_final: 0.7985 (tpp)
REVERT: B  177 ASP cc_start: 0.6494 (p0) cc_final: 0.6238 (p0)
REVERT: B  269 LEU cc_start: 0.9205 (mm) cc_final: 0.8683 (pt)
REVERT: B  304 HIS cc_start: 0.7510 (m-70) cc_final: 0.7165 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1214
  time to fit residues: 24.0156
Evaluate side-chains
  118 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0870
   chunk 70 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7160

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5855  Z= 0.226
  Angle     :  0.620   7.347   7971  Z= 0.310
  Chirality :  0.041   0.148    922
  Planarity :  0.004   0.051    988
  Dihedral  :  5.027  51.851    876
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  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: -0.99 (0.33), residues: 720
  helix:  1.25 (0.30), residues: 338
  sheet: -1.22 (0.50), residues: 119
  loop : -3.03 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 136 
 HIS   0.004   0.001   HIS B 229 
 PHE   0.014   0.001   PHE B 117 
 TYR   0.008   0.001   TYR B 347 
 ARG   0.005   0.000   ARG A 295 

*********************** 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
  141 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 LEU cc_start: 0.8845 (tp) cc_final: 0.8612 (tt)
REVERT: A  220 THR cc_start: 0.8297 (p) cc_final: 0.7782 (t)
REVERT: A  233 TYR cc_start: 0.8422 (t80) cc_final: 0.8107 (t80)
REVERT: A  282 PHE cc_start: 0.8460 (t80) cc_final: 0.8205 (t80)
REVERT: A  315 MET cc_start: 0.7967 (tpp) cc_final: 0.7455 (tpp)
REVERT: B  269 LEU cc_start: 0.9219 (mm) cc_final: 0.8657 (pt)
REVERT: B  304 HIS cc_start: 0.7515 (m-70) cc_final: 0.7128 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1252
  time to fit residues: 24.9129
Evaluate side-chains
  118 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 42 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5855  Z= 0.215
  Angle     :  0.642   7.573   7971  Z= 0.319
  Chirality :  0.041   0.150    922
  Planarity :  0.004   0.051    988
  Dihedral  :  4.993  51.965    876
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  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: -0.95 (0.33), residues: 720
  helix:  1.19 (0.29), residues: 345
  sheet: -1.17 (0.50), residues: 119
  loop : -3.01 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 136 
 HIS   0.007   0.001   HIS B 229 
 PHE   0.014   0.001   PHE B 117 
 TYR   0.008   0.001   TYR A 159 
 ARG   0.004   0.000   ARG A 295 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8556 (mm) cc_final: 0.8332 (mt)
REVERT: A  191 MET cc_start: 0.7916 (tpp) cc_final: 0.7691 (tpp)
REVERT: A  197 LYS cc_start: 0.9212 (tptt) cc_final: 0.8952 (tptp)
REVERT: A  202 LEU cc_start: 0.8839 (tp) cc_final: 0.8626 (tt)
REVERT: A  220 THR cc_start: 0.8297 (p) cc_final: 0.7723 (t)
REVERT: A  233 TYR cc_start: 0.8465 (t80) cc_final: 0.8250 (t80)
REVERT: A  282 PHE cc_start: 0.8434 (t80) cc_final: 0.7821 (t80)
REVERT: A  315 MET cc_start: 0.7974 (tpp) cc_final: 0.7416 (tpp)
REVERT: B  304 HIS cc_start: 0.7535 (m-70) cc_final: 0.7135 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1276
  time to fit residues: 24.6639
Evaluate side-chains
  118 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5855  Z= 0.210
  Angle     :  0.650   7.757   7971  Z= 0.318
  Chirality :  0.041   0.155    922
  Planarity :  0.004   0.054    988
  Dihedral  :  4.962  52.059    876
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  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: -0.92 (0.33), residues: 720
  helix:  1.22 (0.29), residues: 347
  sheet: -1.20 (0.50), residues: 121
  loop : -3.01 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 136 
 HIS   0.006   0.001   HIS A 344 
 PHE   0.014   0.001   PHE B 117 
 TYR   0.008   0.001   TYR B 347 
 ARG   0.004   0.000   ARG A 295 

*********************** 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
  134 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8557 (mm) cc_final: 0.8329 (mt)
REVERT: A  202 LEU cc_start: 0.8831 (tp) cc_final: 0.8621 (tt)
REVERT: A  220 THR cc_start: 0.8300 (p) cc_final: 0.7721 (t)
REVERT: A  225 LEU cc_start: 0.9372 (tp) cc_final: 0.9143 (tp)
REVERT: A  233 TYR cc_start: 0.8473 (t80) cc_final: 0.8265 (t80)
REVERT: A  282 PHE cc_start: 0.8442 (t80) cc_final: 0.7949 (t80)
REVERT: A  315 MET cc_start: 0.8047 (tpp) cc_final: 0.7480 (tpp)
REVERT: B  269 LEU cc_start: 0.9201 (mm) cc_final: 0.8687 (pt)
REVERT: B  304 HIS cc_start: 0.7585 (m-70) cc_final: 0.7178 (m-70)
REVERT: B  382 MET cc_start: 0.8155 (tpp) cc_final: 0.7410 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1153
  time to fit residues: 22.4131
Evaluate side-chains
  116 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    0.0970
   chunk 67 optimal weight:    3.9990
   chunk 39 optimal weight:    0.3980
   chunk 28 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0980
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.3578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5855  Z= 0.187
  Angle     :  0.639   8.145   7971  Z= 0.311
  Chirality :  0.040   0.156    922
  Planarity :  0.004   0.054    988
  Dihedral  :  4.878  52.803    876
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  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 (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 (0.33), residues: 720
  helix:  1.33 (0.29), residues: 345
  sheet: -1.16 (0.50), residues: 121
  loop : -3.13 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 136 
 HIS   0.005   0.001   HIS B 229 
 PHE   0.019   0.001   PHE A 351 
 TYR   0.008   0.001   TYR B 347 
 ARG   0.004   0.000   ARG A 295 

*********************** 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
  136 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8572 (mm) cc_final: 0.8354 (mt)
REVERT: A  202 LEU cc_start: 0.8836 (tp) cc_final: 0.8625 (tt)
REVERT: A  220 THR cc_start: 0.8251 (p) cc_final: 0.7638 (t)
REVERT: A  233 TYR cc_start: 0.8463 (t80) cc_final: 0.8249 (t80)
REVERT: A  282 PHE cc_start: 0.8544 (t80) cc_final: 0.8068 (t80)
REVERT: A  315 MET cc_start: 0.7995 (tpp) cc_final: 0.7505 (tpp)
REVERT: B  269 LEU cc_start: 0.9158 (mm) cc_final: 0.8664 (pt)
REVERT: B  304 HIS cc_start: 0.7574 (m-70) cc_final: 0.7053 (m-70)
REVERT: B  382 MET cc_start: 0.8208 (tpp) cc_final: 0.7426 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1165
  time to fit residues: 22.9333
Evaluate side-chains
  119 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 72 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0570
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0270
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5855  Z= 0.206
  Angle     :  0.653   8.265   7971  Z= 0.318
  Chirality :  0.041   0.141    922
  Planarity :  0.004   0.053    988
  Dihedral  :  4.879  52.013    876
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  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: -0.85 (0.33), residues: 720
  helix:  1.33 (0.29), residues: 344
  sheet: -1.14 (0.51), residues: 121
  loop : -3.03 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 136 
 HIS   0.006   0.001   HIS B 229 
 PHE   0.014   0.001   PHE A 351 
 TYR   0.008   0.001   TYR B 347 
 ARG   0.004   0.000   ARG A 295 

********************** 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
  133 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8576 (mm) cc_final: 0.8352 (mt)
REVERT: A  220 THR cc_start: 0.8308 (p) cc_final: 0.7733 (t)
REVERT: A  282 PHE cc_start: 0.8448 (t80) cc_final: 0.7935 (t80)
REVERT: A  315 MET cc_start: 0.8042 (tpp) cc_final: 0.7511 (tpp)
REVERT: B  269 LEU cc_start: 0.9199 (mm) cc_final: 0.8714 (pt)
REVERT: B  304 HIS cc_start: 0.7598 (m-70) cc_final: 0.7072 (m-70)
REVERT: B  382 MET cc_start: 0.8174 (tpp) cc_final: 0.7384 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1187
  time to fit residues: 23.0127
Evaluate side-chains
  112 residues out of total 605 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0570
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.173271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.139644 restraints weight = 8835.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.138738 restraints weight = 8444.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.139506 restraints weight = 7660.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5855  Z= 0.228
  Angle     :  0.662   9.258   7971  Z= 0.324
  Chirality :  0.042   0.153    922
  Planarity :  0.004   0.054    988
  Dihedral  :  4.917  51.972    876
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  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: -0.88 (0.33), residues: 720
  helix:  1.25 (0.29), residues: 345
  sheet: -1.11 (0.51), residues: 121
  loop : -2.99 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 136 
 HIS   0.007   0.001   HIS B 229 
 PHE   0.016   0.001   PHE A 118 
 TYR   0.009   0.001   TYR B 347 
 ARG   0.003   0.000   ARG A 295 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1484.39 seconds
wall clock time: 27 minutes 15.55 seconds (1635.55 seconds total)