Starting phenix.real_space_refine
on Wed Sep 17 18:37:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kah_22770/09_2025/7kah_22770.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kah_22770/09_2025/7kah_22770.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kah_22770/09_2025/7kah_22770.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kah_22770/09_2025/7kah_22770.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kah_22770/09_2025/7kah_22770.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kah_22770/09_2025/7kah_22770.map"
  }
  resolution = 3.1
  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=   0.003 sd=   0.034
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      42      5.16       5
     C    6849      2.51       5
     N    1762      2.21       5
     O    1842      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10495
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3362
          Classifications: {'peptide': 441}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 20, 'TRANS': 420}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 67
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 435
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "B"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 229
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 3869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3869
          Classifications: {'peptide': 493}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 28, 'TRANS': 464}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 86
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1129
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "F"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1471
          Classifications: {'peptide': 190}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 2.49, per 1000 atoms: 0.24
  Number of scatterers: 10495
  At special positions: 0
  Unit cell: (109.48, 127.33, 135.66, 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      42     16.00
     O    1842      8.00
     N    1762      7.00
     C    6849      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
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 420.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2544

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 6 sheets defined
      66.3% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 47
      removed outlier: 3.525A  pdb=" N   TRP A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY A  47 " --> pdb=" O   PHE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 70
    Processing helix  chain 'A' and resid 82 through 98
    Processing helix  chain 'A' and resid 108 through 137
      removed outlier: 3.671A  pdb=" N   LYS A 119 " --> pdb=" O   GLN A 115 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ILE A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 174
      removed outlier: 3.725A  pdb=" N   LEU A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
    Processing helix  chain 'A' and resid 213 through 225
      removed outlier: 3.562A  pdb=" N   ARG A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 4.126A  pdb=" N   VAL A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   TYR A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 260
      removed outlier: 3.852A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 314
      removed outlier: 4.542A  pdb=" N   ILE A 293 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 341 through 347
      removed outlier: 3.541A  pdb=" N   ILE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 358
      removed outlier: 3.501A  pdb=" N   ALA A 355 " --> pdb=" O   SER A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 384
      removed outlier: 3.594A  pdb=" N   THR A 362 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   CYS A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 409 through 415
    Processing helix  chain 'A' and resid 417 through 440
    Processing helix  chain 'A' and resid 444 through 466
      removed outlier: 3.588A  pdb=" N   TYR A 458 " --> pdb=" O   THR A 454 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 4.065A  pdb=" N   LYS C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE C  64 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   HIS C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ILE C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'B' and resid 53 through 82
      removed outlier: 3.766A  pdb=" N   GLY B  79 " --> pdb=" O   SER B  75 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 36
      removed outlier: 3.817A  pdb=" N   VAL D  25 " --> pdb=" O   GLY D  21 " (cutoff:3.500A)
      Proline residue:  D  28  - end of helix
    Processing helix  chain 'D' and resid 58 through 65
      removed outlier: 4.224A  pdb=" N   LEU D  62 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLU D  64 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU D  65 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 78
      removed outlier: 3.647A  pdb=" N   PHE D  74 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 113
    Processing helix  chain 'D' and resid 219 through 233
      removed outlier: 3.927A  pdb=" N   LEU D 223 " --> pdb=" O   ALA D 219 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL D 224 " --> pdb=" O   SER D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 247
    Processing helix  chain 'D' and resid 255 through 268
      removed outlier: 3.713A  pdb=" N   ASN D 268 " --> pdb=" O   SER D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 285
      removed outlier: 3.688A  pdb=" N   ILE D 280 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 294
      removed outlier: 3.612A  pdb=" N   GLN D 292 " --> pdb=" O   HIS D 288 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE D 293 " --> pdb=" O   GLU D 289 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE D 294 " --> pdb=" O   PHE D 290 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 288 through 294'
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 3.861A  pdb=" N   ARG D 324 " --> pdb=" O   ASN D 320 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   HIS D 330 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 362
      removed outlier: 3.779A  pdb=" N   ALA D 349 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 386
      removed outlier: 3.843A  pdb=" N   THR D 384 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 397
      removed outlier: 3.522A  pdb=" N   LEU D 395 " --> pdb=" O   THR D 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 408
      removed outlier: 3.939A  pdb=" N   GLY D 404 " --> pdb=" O   ASP D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 423
      removed outlier: 4.348A  pdb=" N   GLU D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   THR D 418 " --> pdb=" O   LYS D 414 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER D 423 " --> pdb=" O   LEU D 419 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 466 through 470
    Processing helix  chain 'D' and resid 480 through 485
    Processing helix  chain 'D' and resid 490 through 494
      removed outlier: 3.505A  pdb=" N   LYS D 493 " --> pdb=" O   MET D 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 537 through 541
    Processing helix  chain 'E' and resid 71 through 86
      removed outlier: 3.869A  pdb=" N   TYR E  75 " --> pdb=" O   ALA E  71 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU E  83 " --> pdb=" O   LYS E  79 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 124
      removed outlier: 3.756A  pdb=" N   LYS E  93 " --> pdb=" O   GLU E  89 " (cutoff:3.500A)
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 128 through 156
      removed outlier: 4.044A  pdb=" N   LYS E 132 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 182
      removed outlier: 4.022A  pdb=" N   VAL E 164 " --> pdb=" O   VAL E 160 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   MET E 165 " --> pdb=" O   GLN E 161 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   PHE E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
      removed outlier: 4.155A  pdb=" N   GLU E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   CYS E 190 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
      removed outlier: 3.548A  pdb=" N   GLY E 202 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG E 203 " --> pdb=" O   ASN E 200 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 199 through 203'
    Processing helix  chain 'F' and resid 21 through 41
      removed outlier: 3.764A  pdb=" N   GLY F  40 " --> pdb=" O   THR F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 52 through 71
      removed outlier: 4.070A  pdb=" N   ASN F  68 " --> pdb=" O   SER F  64 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU F  69 " --> pdb=" O   GLY F  65 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLN F  70 " --> pdb=" O   MET F  66 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN F  71 " --> pdb=" O   LYS F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 91
      removed outlier: 3.704A  pdb=" N   LYS F  79 " --> pdb=" O   ASN F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 120
      Proline residue:  F 103  - end of helix
      removed outlier: 3.932A  pdb=" N   SER F 111 " --> pdb=" O   PHE F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.728A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL F 144 " --> pdb=" O   PRO F 140 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ARG F 145 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 168
    Processing helix  chain 'F' and resid 174 through 192
      removed outlier: 4.080A  pdb=" N   ALA F 178 " --> pdb=" O   MET F 174 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204
    Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284
    Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 327
    Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436
      removed outlier: 3.777A  pdb=" N   LYS D 432 " --> pdb=" O   LYS D 454 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP D 434 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532
    Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6

    637 hydrogen bonds defined for protein.
    1872 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: 1.33

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3297
        1.34 -     1.46: 2048
        1.46 -     1.58: 5293
        1.58 -     1.69: 0
        1.69 -     1.81: 67
  Bond restraints: 10705
  Sorted by residual:
  bond pdb=" CA  VAL D 610 "
       pdb=" CB  VAL D 610 "
    ideal  model  delta    sigma   weight residual
    1.540  1.529  0.011 1.36e-02 5.41e+03 6.26e-01
  bond pdb=" CG  LEU F 129 "
       pdb=" CD2 LEU F 129 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.22e-01
  bond pdb=" CB  LYS E  86 "
       pdb=" CG  LYS E  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.76e-01
  bond pdb=" CB  VAL C  61 "
       pdb=" CG1 VAL C  61 "
    ideal  model  delta    sigma   weight residual
    1.521  1.497  0.024 3.30e-02 9.18e+02 5.17e-01
  bond pdb=" CA  GLN A 102 "
       pdb=" CB  GLN A 102 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.70e-02 3.46e+03 4.96e-01
  ... (remaining 10700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 14206
        1.46 -     2.92: 244
        2.92 -     4.38: 43
        4.38 -     5.83: 15
        5.83 -     7.29: 5
  Bond angle restraints: 14513
  Sorted by residual:
  angle pdb=" N   SER A 289 "
        pdb=" CA  SER A 289 "
        pdb=" C   SER A 289 "
      ideal   model   delta    sigma   weight residual
     111.37  115.17   -3.80 1.64e+00 3.72e-01 5.36e+00
  angle pdb=" CA  LYS E  86 "
        pdb=" CB  LYS E  86 "
        pdb=" CG  LYS E  86 "
      ideal   model   delta    sigma   weight residual
     114.10  118.13   -4.03 2.00e+00 2.50e-01 4.06e+00
  angle pdb=" N   TRP D  14 "
        pdb=" CA  TRP D  14 "
        pdb=" C   TRP D  14 "
      ideal   model   delta    sigma   weight residual
     109.81  114.09   -4.28 2.21e+00 2.05e-01 3.75e+00
  angle pdb=" CA  LEU F 129 "
        pdb=" CB  LEU F 129 "
        pdb=" CG  LEU F 129 "
      ideal   model   delta    sigma   weight residual
     116.30  123.00   -6.70 3.50e+00 8.16e-02 3.67e+00
  angle pdb=" CA  LEU F   4 "
        pdb=" CB  LEU F   4 "
        pdb=" CG  LEU F   4 "
      ideal   model   delta    sigma   weight residual
     116.30  122.74   -6.44 3.50e+00 8.16e-02 3.39e+00
  ... (remaining 14508 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.11: 5821
       16.11 -    32.22: 486
       32.22 -    48.33: 117
       48.33 -    64.43: 10
       64.43 -    80.54: 13
  Dihedral angle restraints: 6447
    sinusoidal: 2528
      harmonic: 3919
  Sorted by residual:
  dihedral pdb=" CA  ARG D 509 "
           pdb=" C   ARG D 509 "
           pdb=" N   ARG D 510 "
           pdb=" CA  ARG D 510 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.52   16.48     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  GLN F 155 "
           pdb=" C   GLN F 155 "
           pdb=" N   TRP F 156 "
           pdb=" CA  TRP F 156 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.72  -15.28     0      5.00e+00 4.00e-02 9.34e+00
  dihedral pdb=" CA  LEU F 153 "
           pdb=" C   LEU F 153 "
           pdb=" N   ARG F 154 "
           pdb=" CA  ARG F 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.91   15.09     0      5.00e+00 4.00e-02 9.11e+00
  ... (remaining 6444 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1171
       0.035 -    0.069: 398
       0.069 -    0.104: 121
       0.104 -    0.138: 29
       0.138 -    0.173: 2
  Chirality restraints: 1721
  Sorted by residual:
  chirality pdb=" CG  LEU F 129 "
            pdb=" CB  LEU F 129 "
            pdb=" CD1 LEU F 129 "
            pdb=" CD2 LEU F 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.44e-01
  chirality pdb=" CA  ILE D 470 "
            pdb=" N   ILE D 470 "
            pdb=" C   ILE D 470 "
            pdb=" CB  ILE D 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  THR A 291 "
            pdb=" N   THR A 291 "
            pdb=" C   THR A 291 "
            pdb=" CB  THR A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 1718 not shown)

  Planarity restraints: 1805
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.028 5.00e-02 4.00e+02   4.21e-02 2.83e+00
        pdb=" N   PRO F  48 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 366 "    0.023 5.00e-02 4.00e+02   3.46e-02 1.91e+00
        pdb=" N   PRO D 367 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO D 367 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D 367 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP D  14 "   -0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO D  15 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO D  15 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D  15 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1802 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2392
        2.79 -     3.31: 9871
        3.31 -     3.84: 16199
        3.84 -     4.37: 18004
        4.37 -     4.90: 32727
  Nonbonded interactions: 79193
  Sorted by model distance:
  nonbonded pdb=" O   LYS E  79 "
            pdb=" OG  SER E  82 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   TYR A 237 "
            pdb=" ND2 ASN A 243 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" OE2 GLU E 102 "
            pdb=" NH2 ARG E 105 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   THR D 444 "
            pdb=" OG  SER D 447 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OD1 ASN D 427 "
            pdb=" OG1 THR D 599 "
     model   vdw
     2.314 3.040
  ... (remaining 79188 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.050
  Find NCS groups from input model:        0.050
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
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   0.029  10705  Z= 0.137
  Angle     :  0.533   7.293  14513  Z= 0.281
  Chirality :  0.039   0.173   1721
  Planarity :  0.004   0.042   1805
  Dihedral  : 12.901  80.542   3903
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  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: -1.32 (0.22), residues: 1325
  helix:  0.10 (0.17), residues: 815
  sheet: -2.50 (0.46), residues: 90
  loop : -2.32 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 178 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.015   0.001   PHE D 547 
 TRP   0.009   0.001   TRP D  14 
 HIS   0.006   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10705)
  covalent geometry    : angle       0.53329 (14513)
  hydrogen bonds       : bond        0.12427 (  637)
  hydrogen bonds       : angle       4.57408 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 ASP cc_start: 0.8258 (t70) cc_final: 0.8025 (t0)
REVERT: C   52 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8265 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1216
  time to fit residues: 14.5512
Evaluate side-chains
  62 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN
D 330 HIS
E  88 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.065818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.047746 restraints weight = 37708.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 3.06
r_work: 0.2725 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10705  Z= 0.145
  Angle     :  0.532  10.472  14513  Z= 0.263
  Chirality :  0.039   0.148   1721
  Planarity :  0.004   0.045   1805
  Dihedral  :  3.533  18.149   1429
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 10.44 %
    Favored  : 88.67 %
  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:  0.31 (0.24), residues: 1325
  helix:  1.44 (0.19), residues: 815
  sheet: -2.02 (0.47), residues: 90
  loop : -1.76 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 145 
 TYR   0.010   0.001   TYR F 190 
 PHE   0.010   0.001   PHE A 424 
 TRP   0.007   0.001   TRP F 156 
 HIS   0.005   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10705)
  covalent geometry    : angle       0.53240 (14513)
  hydrogen bonds       : bond        0.04080 (  637)
  hydrogen bonds       : angle       3.53396 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8983 (tttp) cc_final: 0.8608 (ttpp)
REVERT: C   52 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8072 (ttmm)
  outliers start: 10
  outliers final: 5
  residues processed: 68
  average time/residue: 0.1062
  time to fit residues: 10.8327
Evaluate side-chains
  62 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain E residue   74 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 118 optimal weight:    1.9990
   chunk 7 optimal weight:   20.0000
   chunk 83 optimal weight:    0.6980
   chunk 98 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 108 optimal weight:    4.9990
   chunk 79 optimal weight:    0.2980
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
D 330 HIS
F  68 ASN
F 106 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.064444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.046308 restraints weight = 37907.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 3.06
r_work: 0.2690 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  10705  Z= 0.192
  Angle     :  0.549   9.720  14513  Z= 0.274
  Chirality :  0.040   0.147   1721
  Planarity :  0.004   0.046   1805
  Dihedral  :  3.594  17.681   1429
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.49 %
    Favored  : 85.91 %
  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:  0.89 (0.24), residues: 1325
  helix:  1.88 (0.19), residues: 815
  sheet: -1.80 (0.47), residues: 92
  loop : -1.48 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 145 
 TYR   0.013   0.001   TYR F 190 
 PHE   0.014   0.001   PHE B  66 
 TRP   0.007   0.001   TRP F 156 
 HIS   0.005   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (10705)
  covalent geometry    : angle       0.54926 (14513)
  hydrogen bonds       : bond        0.04521 (  637)
  hydrogen bonds       : angle       3.53650 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.9026 (tttp) cc_final: 0.8647 (ttpp)
REVERT: C   46 GLU cc_start: 0.8998 (pt0) cc_final: 0.8743 (pt0)
  outliers start: 18
  outliers final: 10
  residues processed: 72
  average time/residue: 0.0981
  time to fit residues: 10.7250
Evaluate side-chains
  68 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  532 ILE
Chi-restraints excluded: chain D residue  608 MET
Chi-restraints excluded: chain E residue   74 LEU
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue  153 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 124 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9990
   chunk 120 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
D 330 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.065136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.046975 restraints weight = 38047.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 3.11
r_work: 0.2708 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10705  Z= 0.138
  Angle     :  0.510   9.201  14513  Z= 0.252
  Chirality :  0.039   0.143   1721
  Planarity :  0.004   0.048   1805
  Dihedral  :  3.452  16.406   1429
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.18 %
    Favored  : 83.94 %
  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:  1.31 (0.24), residues: 1325
  helix:  2.16 (0.19), residues: 816
  sheet: -1.57 (0.48), residues: 92
  loop : -1.21 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 145 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.009   0.001   PHE D 481 
 TRP   0.009   0.001   TRP F 156 
 HIS   0.005   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10705)
  covalent geometry    : angle       0.50974 (14513)
  hydrogen bonds       : bond        0.03896 (  637)
  hydrogen bonds       : angle       3.38728 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 ASP cc_start: 0.9061 (t70) cc_final: 0.8835 (t0)
REVERT: C   40 LYS cc_start: 0.8976 (tttp) cc_final: 0.8589 (ttpp)
REVERT: C   44 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7841 (tt)
REVERT: C   46 GLU cc_start: 0.9030 (pt0) cc_final: 0.8796 (pt0)
REVERT: D   57 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7863 (mp0)
REVERT: D  553 MET cc_start: 0.8249 (mmm) cc_final: 0.7987 (mmm)
  outliers start: 21
  outliers final: 11
  residues processed: 77
  average time/residue: 0.0967
  time to fit residues: 11.3832
Evaluate side-chains
  69 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  608 MET
Chi-restraints excluded: chain E residue   74 LEU
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue  153 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0000
   chunk 48 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0670
   chunk 77 optimal weight:    0.3980
   chunk 45 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    0.4922

-------------------------------------------------------------------------------
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 = 0.3379 r_free = 0.3379 target = 0.066925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.048904 restraints weight = 38267.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 3.09
r_work: 0.2765 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10705  Z= 0.090
  Angle     :  0.472   8.189  14513  Z= 0.233
  Chirality :  0.037   0.160   1721
  Planarity :  0.004   0.061   1805
  Dihedral  :  3.215  15.473   1429
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.54 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.65 (0.24), residues: 1325
  helix:  2.38 (0.19), residues: 823
  sheet: -1.34 (0.49), residues: 92
  loop : -1.03 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  90 
 TYR   0.008   0.001   TYR A 287 
 PHE   0.017   0.001   PHE B  66 
 TRP   0.009   0.001   TRP D  14 
 HIS   0.005   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 (10705)
  covalent geometry    : angle       0.47210 (14513)
  hydrogen bonds       : bond        0.02983 (  637)
  hydrogen bonds       : angle       3.20768 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.8035 (mmp) cc_final: 0.7828 (mmp)
REVERT: A  390 ASP cc_start: 0.8954 (t70) cc_final: 0.8749 (t0)
REVERT: C   40 LYS cc_start: 0.8908 (tttp) cc_final: 0.8465 (ttpp)
REVERT: C   45 LYS cc_start: 0.8813 (tptp) cc_final: 0.8457 (tptp)
REVERT: C   46 GLU cc_start: 0.9031 (pt0) cc_final: 0.8808 (pt0)
REVERT: D   57 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7733 (mp0)
REVERT: F  139 GLN cc_start: 0.8949 (mt0) cc_final: 0.8496 (mm-40)
  outliers start: 18
  outliers final: 8
  residues processed: 81
  average time/residue: 0.1000
  time to fit residues: 12.2782
Evaluate side-chains
  64 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  526 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 103 optimal weight:    0.3980
   chunk 95 optimal weight:    0.3980
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.065934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.047790 restraints weight = 38241.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 3.12
r_work: 0.2733 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10705  Z= 0.113
  Angle     :  0.488   8.329  14513  Z= 0.241
  Chirality :  0.038   0.164   1721
  Planarity :  0.004   0.070   1805
  Dihedral  :  3.214  15.475   1429
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.27 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.83 (0.24), residues: 1325
  helix:  2.49 (0.19), residues: 823
  sheet: -1.13 (0.49), residues: 92
  loop : -0.92 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  90 
 TYR   0.009   0.001   TYR F 190 
 PHE   0.010   0.001   PHE B  66 
 TRP   0.007   0.001   TRP F 156 
 HIS   0.005   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10705)
  covalent geometry    : angle       0.48751 (14513)
  hydrogen bonds       : bond        0.03427 (  637)
  hydrogen bonds       : angle       3.24090 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.8118 (mmp) cc_final: 0.7912 (mmp)
REVERT: C   40 LYS cc_start: 0.8924 (tttp) cc_final: 0.8421 (ttpp)
REVERT: C   43 ASP cc_start: 0.8374 (p0) cc_final: 0.6692 (p0)
REVERT: C   45 LYS cc_start: 0.8852 (tptp) cc_final: 0.8596 (tptp)
REVERT: D   57 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7766 (mp0)
  outliers start: 23
  outliers final: 15
  residues processed: 81
  average time/residue: 0.0954
  time to fit residues: 11.7794
Evaluate side-chains
  74 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue   92 PHE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain C residue   50 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain E residue   74 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 117 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
D 330 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.064234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.045975 restraints weight = 38263.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 3.11
r_work: 0.2680 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  10705  Z= 0.188
  Angle     :  0.554   8.547  14513  Z= 0.278
  Chirality :  0.040   0.176   1721
  Planarity :  0.004   0.072   1805
  Dihedral  :  3.496  17.160   1429
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.08 %
    Favored  : 82.69 %
  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:  1.77 (0.24), residues: 1325
  helix:  2.44 (0.19), residues: 823
  sheet: -1.15 (0.49), residues: 92
  loop : -0.94 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  90 
 TYR   0.013   0.001   TYR F 190 
 PHE   0.018   0.001   PHE B  66 
 TRP   0.006   0.001   TRP A 380 
 HIS   0.005   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (10705)
  covalent geometry    : angle       0.55438 (14513)
  hydrogen bonds       : bond        0.04404 (  637)
  hydrogen bonds       : angle       3.45697 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8101 (mmp) cc_final: 0.7895 (mmp)
REVERT: C   40 LYS cc_start: 0.9015 (tttp) cc_final: 0.8541 (ttpp)
REVERT: C   43 ASP cc_start: 0.8784 (p0) cc_final: 0.8524 (p0)
REVERT: D   57 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7856 (mp0)
  outliers start: 25
  outliers final: 17
  residues processed: 80
  average time/residue: 0.0915
  time to fit residues: 11.2512
Evaluate side-chains
  77 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain C residue   50 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  532 ILE
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain E residue   74 LEU
Chi-restraints excluded: chain E residue  126 ILE
Chi-restraints excluded: chain F residue   13 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 12 optimal weight:    0.2980
   chunk 55 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    2.2588

-------------------------------------------------------------------------------
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 = 0.3323 r_free = 0.3323 target = 0.064413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.046247 restraints weight = 37955.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 3.09
r_work: 0.2688 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10705  Z= 0.169
  Angle     :  0.550   8.967  14513  Z= 0.273
  Chirality :  0.040   0.163   1721
  Planarity :  0.004   0.074   1805
  Dihedral  :  3.476  16.641   1429
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.41 %
    Favored  : 81.53 %
  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:  1.78 (0.24), residues: 1325
  helix:  2.43 (0.19), residues: 823
  sheet: -1.11 (0.50), residues: 92
  loop : -0.93 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  90 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.011   0.001   PHE D 481 
 TRP   0.008   0.001   TRP D  14 
 HIS   0.006   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (10705)
  covalent geometry    : angle       0.54961 (14513)
  hydrogen bonds       : bond        0.04150 (  637)
  hydrogen bonds       : angle       3.45665 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8916 (tttp) cc_final: 0.8492 (ttpp)
REVERT: D   57 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7830 (mp0)
  outliers start: 23
  outliers final: 20
  residues processed: 78
  average time/residue: 0.0966
  time to fit residues: 11.5803
Evaluate side-chains
  81 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain C residue   50 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  532 ILE
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain D residue  608 MET
Chi-restraints excluded: chain E residue   74 LEU
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue  153 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   chunk 96 optimal weight:    5.9990
   chunk 102 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    2.2788

-------------------------------------------------------------------------------
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 = 0.3319 r_free = 0.3319 target = 0.064214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.046037 restraints weight = 38106.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 3.10
r_work: 0.2683 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10705  Z= 0.171
  Angle     :  0.554   9.386  14513  Z= 0.276
  Chirality :  0.040   0.164   1721
  Planarity :  0.004   0.074   1805
  Dihedral  :  3.498  16.882   1429
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.86 %
    Favored  : 81.27 %
  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:  1.78 (0.24), residues: 1325
  helix:  2.43 (0.19), residues: 823
  sheet: -1.10 (0.50), residues: 92
  loop : -0.92 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  90 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.020   0.001   PHE B  66 
 TRP   0.007   0.001   TRP F 156 
 HIS   0.006   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10705)
  covalent geometry    : angle       0.55383 (14513)
  hydrogen bonds       : bond        0.04237 (  637)
  hydrogen bonds       : angle       3.47190 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8878 (tttp) cc_final: 0.8482 (ttpp)
REVERT: D   57 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7762 (mp0)
REVERT: F   70 GLN cc_start: 0.9106 (mp10) cc_final: 0.8757 (pm20)
  outliers start: 21
  outliers final: 20
  residues processed: 74
  average time/residue: 0.0938
  time to fit residues: 10.6587
Evaluate side-chains
  78 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain C residue   50 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  532 ILE
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain D residue  608 MET
Chi-restraints excluded: chain E residue   74 LEU
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue  153 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0010
   chunk 30 optimal weight:   20.0000
   chunk 119 optimal weight:    5.9990
   overall best weight:    2.3792

-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.064073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.045922 restraints weight = 37805.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 3.09
r_work: 0.2679 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10705  Z= 0.178
  Angle     :  0.561   9.835  14513  Z= 0.280
  Chirality :  0.040   0.164   1721
  Planarity :  0.004   0.074   1805
  Dihedral  :  3.520  17.035   1429
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.86 %
    Favored  : 81.27 %
  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:  1.76 (0.24), residues: 1325
  helix:  2.41 (0.19), residues: 823
  sheet: -1.10 (0.50), residues: 92
  loop : -0.93 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  90 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.011   0.001   PHE D 481 
 TRP   0.007   0.001   TRP D  14 
 HIS   0.007   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (10705)
  covalent geometry    : angle       0.56117 (14513)
  hydrogen bonds       : bond        0.04302 (  637)
  hydrogen bonds       : angle       3.49602 ( 1872)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8864 (tttp) cc_final: 0.8466 (ttpp)
REVERT: D   57 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7663 (mp0)
REVERT: F   70 GLN cc_start: 0.9105 (mp10) cc_final: 0.8771 (pm20)
  outliers start: 21
  outliers final: 20
  residues processed: 74
  average time/residue: 0.0930
  time to fit residues: 10.6136
Evaluate side-chains
  79 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain C residue   50 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  532 ILE
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain D residue  608 MET
Chi-restraints excluded: chain E residue   74 LEU
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue  153 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 22 optimal weight:    0.0050
   chunk 77 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0670
   chunk 28 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.4138

-------------------------------------------------------------------------------
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 = 0.3315 r_free = 0.3315 target = 0.064023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.045894 restraints weight = 37892.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 3.09
r_work: 0.2680 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10705  Z= 0.180
  Angle     :  0.567   9.875  14513  Z= 0.281
  Chirality :  0.040   0.163   1721
  Planarity :  0.004   0.075   1805
  Dihedral  :  3.530  17.073   1429
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.04 %
    Favored  : 81.09 %
  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:  1.76 (0.24), residues: 1325
  helix:  2.41 (0.19), residues: 823
  sheet: -1.11 (0.50), residues: 92
  loop : -0.92 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  90 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.022   0.001   PHE B  66 
 TRP   0.007   0.001   TRP D  14 
 HIS   0.007   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (10705)
  covalent geometry    : angle       0.56680 (14513)
  hydrogen bonds       : bond        0.04319 (  637)
  hydrogen bonds       : angle       3.50012 ( 1872)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2607.41 seconds
wall clock time: 45 minutes 32.61 seconds (2732.61 seconds total)