Starting phenix.real_space_refine
on Tue May 13 02:35:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jl0_36385/05_2025/8jl0_36385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jl0_36385/05_2025/8jl0_36385.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jl0_36385/05_2025/8jl0_36385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jl0_36385/05_2025/8jl0_36385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jl0_36385/05_2025/8jl0_36385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jl0_36385/05_2025/8jl0_36385.cif"
  }
  resolution = 3.1
  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=   0.002 sd=   0.033
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: 5
    Type Number    sf(0)   Gaussians
     P      46      5.49       5
     S      33      5.16       5
     C    5757      2.51       5
     N    1583      2.21       5
     O    1825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9244
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4572
          Classifications: {'peptide': 573}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 3712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3712
          Classifications: {'peptide': 469}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 28, 'TRANS': 440}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 450
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "C"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 466
          Classifications: {'RNA': 22}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 2, 'rna3p': 19}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.74, per 1000 atoms: 0.62
  Number of scatterers: 9244
  At special positions: 0
  Unit cell: (84.84, 115.08, 112.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     P      46     15.00
     O    1825      8.00
     N    1583      7.00
     C    5757      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: 2.36
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 9 sheets defined
      41.2% alpha, 17.9% beta
      18 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 3.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 16
      removed outlier: 3.816A  pdb=" N   GLN A  11 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   HIS A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   TYR A  13 " --> pdb=" O   PHE A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 31
      removed outlier: 4.281A  pdb=" N   SER A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 50
    Processing helix  chain 'A' and resid 67 through 79
    Processing helix  chain 'A' and resid 87 through 98
      removed outlier: 3.515A  pdb=" N   PHE A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 109
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 169 through 176
    Processing helix  chain 'A' and resid 200 through 219
      removed outlier: 3.712A  pdb=" N   ASN A 204 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 213 " --> pdb=" O   HIS A 209 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ALA A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 243
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 3.518A  pdb=" N   LYS A 260 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 276
    Processing helix  chain 'A' and resid 286 through 297
      removed outlier: 3.851A  pdb=" N   GLN A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 310
      removed outlier: 3.528A  pdb=" N   ALA A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 366
      removed outlier: 3.607A  pdb=" N   LYS A 366 " --> pdb=" O   ARG A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 391
    Processing helix  chain 'A' and resid 406 through 414
    Processing helix  chain 'A' and resid 414 through 431
      removed outlier: 3.804A  pdb=" N   LYS A 418 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 465
    Processing helix  chain 'A' and resid 513 through 519
      removed outlier: 3.575A  pdb=" N   ARG A 517 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   GLU A 518 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLU A 519 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 528
    Processing helix  chain 'A' and resid 532 through 549
    Processing helix  chain 'B' and resid 29 through 37
    Processing helix  chain 'B' and resid 39 through 43
      removed outlier: 3.506A  pdb=" N   CYS B  43 " --> pdb=" O   TYR B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 59
      No H-bonds generated for 'chain 'B' and resid 57 through 59'
    Processing helix  chain 'B' and resid 60 through 71
      removed outlier: 3.762A  pdb=" N   LEU B  64 " --> pdb=" O   HIS B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 94
    Processing helix  chain 'B' and resid 102 through 104
      No H-bonds generated for 'chain 'B' and resid 102 through 104'
    Processing helix  chain 'B' and resid 109 through 119
      removed outlier: 4.128A  pdb=" N   HIS B 114 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   GLY B 115 " --> pdb=" O   ASP B 111 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   VAL B 116 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 134
    Processing helix  chain 'B' and resid 135 through 137
      No H-bonds generated for 'chain 'B' and resid 135 through 137'
    Processing helix  chain 'B' and resid 154 through 159
      removed outlier: 3.950A  pdb=" N   GLU B 159 " --> pdb=" O   LYS B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 174
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 192 through 209
      removed outlier: 3.802A  pdb=" N   VAL B 196 " --> pdb=" O   CYS B 192 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   VAL B 202 " --> pdb=" O   TRP B 198 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA B 203 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY B 209 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 295
    Processing helix  chain 'B' and resid 312 through 321
      removed outlier: 3.615A  pdb=" N   GLN B 317 " --> pdb=" O   GLU B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 430
      removed outlier: 4.206A  pdb=" N   THR B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LYS B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 458
      removed outlier: 4.069A  pdb=" N   GLN B 458 " --> pdb=" O   ASP B 454 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 162
      removed outlier: 7.227A  pdb=" N   MET A  20 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 8.547A  pdb=" N   PHE A 139 " --> pdb=" O   MET A  20 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   TRP A  22 " --> pdb=" O   PHE A 139 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU A 221 " --> pdb=" O   TYR A 252 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   THR A 254 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL A 223 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 355 through 356
      removed outlier: 3.537A  pdb=" N   GLY A 582 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   SER A 580 " --> pdb=" O   PRO A 329 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   PHE A 579 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ALA B  10 " --> pdb=" O   PHE A 579 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU A 581 " --> pdb=" O   ALA B  10 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   SER B  12 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
      removed outlier: 12.386A  pdb=" N   LEU B   8 " --> pdb=" O   THR B 370 " (cutoff:3.500A)
      removed outlier: 8.585A  pdb=" N   THR B 370 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ALA B  10 " --> pdb=" O   PRO B 368 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   GLU B 373 " --> pdb=" O   LEU B 369 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ILE B 303 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   VAL B 332 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   ILE B 305 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   ILE B 334 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LYS B 307 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ALA B 223 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   HIS B 306 " --> pdb=" O   ALA B 223 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ILE B 225 " --> pdb=" O   HIS B 306 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLY B 226 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLN B 246 " --> pdb=" O   GLY B 226 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   SER B 228 " --> pdb=" O   CYS B 244 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER B 245 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 258 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE B 257 " --> pdb=" O   TYR B 467 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 338
      removed outlier: 4.571A  pdb=" N   LEU A 501 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   HIS A 444 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG A 438 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338
      removed outlier: 4.571A  pdb=" N   LEU A 501 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374
      removed outlier: 4.932A  pdb=" N   VAL A 378 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE A 343 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 404 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER A 398 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 561
    Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 27
    Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 99
      removed outlier: 6.511A  pdb=" N   VAL B  50 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 8.837A  pdb=" N   CYS B 107 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   TYR B  54 " --> pdb=" O   CYS B 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99
      removed outlier: 6.511A  pdb=" N   VAL B  50 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ARG B  51 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   LEU B 147 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   ALA B  53 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   TYR B 149 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   LEU B  55 " --> pdb=" O   TYR B 149 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    960 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      43 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1410
        1.31 -     1.43: 2851
        1.43 -     1.56: 5155
        1.56 -     1.69: 94
        1.69 -     1.81: 51
  Bond restraints: 9561
  Sorted by residual:
  bond pdb=" C2D NAD A 601 "
       pdb=" C3D NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.531  1.247  0.284 2.00e-02 2.50e+03 2.02e+02
  bond pdb=" C4B NAD A 601 "
       pdb=" O4B NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.433  1.678 -0.245 2.00e-02 2.50e+03 1.50e+02
  bond pdb=" C3B NAD A 601 "
       pdb=" C4B NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.523  1.280  0.243 2.00e-02 2.50e+03 1.48e+02
  bond pdb=" C4D NAD A 601 "
       pdb=" O4D NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.445  1.268  0.177 2.00e-02 2.50e+03 7.84e+01
  bond pdb=" C7N NAD A 601 "
       pdb=" N7N NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.328  1.473 -0.145 2.00e-02 2.50e+03 5.24e+01
  ... (remaining 9556 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 12969
        2.58 -     5.17: 173
        5.17 -     7.75: 20
        7.75 -    10.33: 2
       10.33 -    12.91: 4
  Bond angle restraints: 13168
  Sorted by residual:
  angle pdb=" N   PRO A 329 "
        pdb=" CA  PRO A 329 "
        pdb=" C   PRO A 329 "
      ideal   model   delta    sigma   weight residual
     112.47  100.45   12.02 2.06e+00 2.36e-01 3.41e+01
  angle pdb=" C3'   A C   1 "
        pdb=" O3'   A C   1 "
        pdb=" P     U C   2 "
      ideal   model   delta    sigma   weight residual
     120.20  113.69    6.51 1.50e+00 4.44e-01 1.89e+01
  angle pdb=" O1A NAD A 601 "
        pdb=" PA  NAD A 601 "
        pdb=" O2A NAD A 601 "
      ideal   model   delta    sigma   weight residual
     122.64  109.73   12.91 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" N   THR A 176 "
        pdb=" CA  THR A 176 "
        pdb=" C   THR A 176 "
      ideal   model   delta    sigma   weight residual
     113.20  108.19    5.01 1.21e+00 6.83e-01 1.72e+01
  angle pdb=" CA  SER A 327 "
        pdb=" C   SER A 327 "
        pdb=" O   SER A 327 "
      ideal   model   delta    sigma   weight residual
     121.87  117.38    4.49 1.10e+00 8.26e-01 1.67e+01
  ... (remaining 13163 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.70: 5099
       27.70 -    55.41: 521
       55.41 -    83.11: 87
       83.11 -   110.81: 5
      110.81 -   138.51: 2
  Dihedral angle restraints: 5714
    sinusoidal: 2674
      harmonic: 3040
  Sorted by residual:
  dihedral pdb=" O4'   C C  17 "
           pdb=" C1'   C C  17 "
           pdb=" N1    C C  17 "
           pdb=" C2    C C  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -21.49 -138.51     1      1.50e+01 4.44e-03 7.46e+01
  dihedral pdb=" CA  LYS A 260 "
           pdb=" C   LYS A 260 "
           pdb=" N   SER A 261 "
           pdb=" CA  SER A 261 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.77  -18.23     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" C4'  DC D   2 "
           pdb=" C3'  DC D   2 "
           pdb=" O3'  DC D   2 "
           pdb=" P    DG D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   -7.37 -132.63     1      3.50e+01 8.16e-04 1.31e+01
  ... (remaining 5711 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 1401
       0.109 -    0.217: 58
       0.217 -    0.326: 2
       0.326 -    0.434: 2
       0.434 -    0.543: 1
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" P     A C   1 "
            pdb=" OP1   A C   1 "
            pdb=" OP2   A C   1 "
            pdb=" O5'   A C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.95   -0.54 2.00e-01 2.50e+01 7.36e+00
  chirality pdb=" P     U C   2 "
            pdb=" OP1   U C   2 "
            pdb=" OP2   U C   2 "
            pdb=" O5'   U C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.79   -0.38 2.00e-01 2.50e+01 3.58e+00
  chirality pdb=" C3D NAD A 601 "
            pdb=" C2D NAD A 601 "
            pdb=" C4D NAD A 601 "
            pdb=" O3D NAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.38   -0.35 2.00e-01 2.50e+01 2.99e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 344 "    0.444 9.50e-02 1.11e+02   1.99e-01 2.43e+01
        pdb=" NE  ARG A 344 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 344 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 344 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 344 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 414 "    0.016 2.00e-02 2.50e+03   3.00e-02 9.00e+00
        pdb=" C   SER A 414 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   SER A 414 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR A 415 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C   4 "   -0.033 2.00e-02 2.50e+03   1.48e-02 6.04e+00
        pdb=" N9    A C   4 "    0.035 2.00e-02 2.50e+03
        pdb=" C8    A C   4 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A C   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A C   4 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A C   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6    A C   4 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    A C   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A C   4 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A C   4 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A C   4 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1523 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1543
        2.77 -     3.30: 8321
        3.30 -     3.83: 15661
        3.83 -     4.37: 18393
        4.37 -     4.90: 30818
  Nonbonded interactions: 74736
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 435 "
            pdb=" OG1 THR B 437 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   ALA A 578 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ARG A 440 "
            pdb=" OG1 THR A 443 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O2D NAD A 601 "
            pdb=" O3D NAD A 601 "
     model   vdw
     2.257 2.432
  nonbonded pdb=" OD1 ASN B 436 "
            pdb=" O2'   A C   3 "
     model   vdw
     2.273 3.040
  ... (remaining 74731 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:             0.680
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.030
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
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      :  0.008   0.284   9561  Z= 0.417
  Angle     :  0.728  12.913  13168  Z= 0.418
  Chirality :  0.051   0.543   1464
  Planarity :  0.006   0.199   1526
  Dihedral  : 20.611 138.513   3760
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.30 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 29.73 %
    Favored  : 69.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.51 (0.25), residues: 1036
  helix:  0.82 (0.28), residues: 358
  sheet: -1.02 (0.37), residues: 199
  loop : -2.50 (0.25), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 377 
 HIS   0.006   0.001   HIS A 441 
 PHE   0.015   0.001   PHE A  91 
 TYR   0.015   0.002   TYR B 341 
 ARG   0.010   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17908 (  365)
  hydrogen bonds       : angle       6.51777 ( 1046)
  covalent geometry    : bond        0.00766 ( 9561)
  covalent geometry    : angle       0.72762 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.945 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 98
  average time/residue: 0.2733
  time to fit residues: 36.6436
Evaluate side-chains
  89 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0470
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 54 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A 441 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.168583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.128620 restraints weight = 10966.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.92
r_work: 0.3183 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.0837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9561  Z= 0.116
  Angle     :  0.533   7.198  13168  Z= 0.289
  Chirality :  0.041   0.211   1464
  Planarity :  0.004   0.036   1526
  Dihedral  : 17.170 135.335   1788
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.34 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 29.28 %
    Favored  : 67.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.00 (0.26), residues: 1036
  helix:  1.18 (0.28), residues: 378
  sheet: -0.66 (0.37), residues: 199
  loop : -2.33 (0.25), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 377 
 HIS   0.004   0.001   HIS A 441 
 PHE   0.012   0.001   PHE A  80 
 TYR   0.016   0.001   TYR A  74 
 ARG   0.006   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  365)
  hydrogen bonds       : angle       4.93383 ( 1046)
  covalent geometry    : bond        0.00242 ( 9561)
  covalent geometry    : angle       0.53296 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A  115 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.5994 (ptm160)
REVERT: A  260 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7776 (mmtp)
REVERT: A  426 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7713 (mp)
REVERT: B  149 TYR cc_start: 0.8595 (t80) cc_final: 0.8289 (t80)
REVERT: B  221 ASP cc_start: 0.7731 (p0) cc_final: 0.7509 (p0)
REVERT: B  279 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7944 (mt-10)
  outliers start: 29
  outliers final: 8
  residues processed: 116
  average time/residue: 0.2391
  time to fit residues: 37.7638
Evaluate side-chains
  97 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 55 optimal weight:    0.0010
   chunk 6 optimal weight:    9.9990
   chunk 47 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0770
   chunk 50 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.4944

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A 245 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.170305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.132977 restraints weight = 11058.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.00
r_work: 0.3061 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9561  Z= 0.105
  Angle     :  0.496   7.087  13168  Z= 0.269
  Chirality :  0.040   0.183   1464
  Planarity :  0.004   0.029   1526
  Dihedral  : 17.009 135.137   1787
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.85 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 28.38 %
    Favored  : 67.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.79 (0.26), residues: 1036
  helix:  1.37 (0.28), residues: 378
  sheet: -0.51 (0.37), residues: 202
  loop : -2.26 (0.25), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 340 
 HIS   0.003   0.001   HIS A 441 
 PHE   0.009   0.001   PHE A  80 
 TYR   0.012   0.001   TYR A  74 
 ARG   0.007   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03540 (  365)
  hydrogen bonds       : angle       4.58076 ( 1046)
  covalent geometry    : bond        0.00223 ( 9561)
  covalent geometry    : angle       0.49575 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 96
  time to evaluate  : 1.049 
Fit side-chains
REVERT: A  115 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.6055 (ptm160)
REVERT: A  260 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7705 (mmtp)
REVERT: A  426 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7690 (mp)
REVERT: B  221 ASP cc_start: 0.7742 (p0) cc_final: 0.7461 (p0)
  outliers start: 36
  outliers final: 16
  residues processed: 127
  average time/residue: 0.2388
  time to fit residues: 41.0288
Evaluate side-chains
  106 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  192 GLN
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  264 GLU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 64 optimal weight:    0.3980
   chunk 55 optimal weight:    5.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.163538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.124889 restraints weight = 10991.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.08
r_work: 0.3059 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9561  Z= 0.173
  Angle     :  0.569   7.827  13168  Z= 0.303
  Chirality :  0.042   0.216   1464
  Planarity :  0.004   0.043   1526
  Dihedral  : 17.139 141.694   1786
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.53 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 28.15 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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 (0.26), residues: 1036
  helix:  1.20 (0.28), residues: 377
  sheet: -0.76 (0.39), residues: 186
  loop : -2.31 (0.24), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 377 
 HIS   0.004   0.001   HIS B  29 
 PHE   0.018   0.002   PHE A   9 
 TYR   0.017   0.002   TYR B 341 
 ARG   0.004   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04268 (  365)
  hydrogen bonds       : angle       4.69711 ( 1046)
  covalent geometry    : bond        0.00402 ( 9561)
  covalent geometry    : angle       0.56906 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 89
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5785 (OUTLIER) cc_final: 0.5059 (t70)
REVERT: A  115 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.5936 (ptm160)
REVERT: A  133 ASN cc_start: 0.7517 (m-40) cc_final: 0.7183 (m-40)
REVERT: A  260 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7645 (mmtp)
REVERT: A  426 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7714 (mp)
REVERT: A  572 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7987 (tm-30)
REVERT: B  221 ASP cc_start: 0.7683 (p0) cc_final: 0.7383 (p0)
  outliers start: 36
  outliers final: 19
  residues processed: 118
  average time/residue: 0.2478
  time to fit residues: 39.7817
Evaluate side-chains
  109 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 MET
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  264 GLU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  401 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 58 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.163412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.122600 restraints weight = 11018.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.29
r_work: 0.3072 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9561  Z= 0.205
  Angle     :  0.606   8.085  13168  Z= 0.322
  Chirality :  0.044   0.228   1464
  Planarity :  0.005   0.048   1526
  Dihedral  : 17.265 143.789   1786
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.53 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 27.93 %
    Favored  : 67.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.16 (0.26), residues: 1036
  helix:  0.98 (0.28), residues: 379
  sheet: -0.80 (0.39), residues: 186
  loop : -2.31 (0.25), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 377 
 HIS   0.005   0.001   HIS B  29 
 PHE   0.018   0.002   PHE A   9 
 TYR   0.020   0.002   TYR B 341 
 ARG   0.007   0.001   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04584 (  365)
  hydrogen bonds       : angle       4.80269 ( 1046)
  covalent geometry    : bond        0.00486 ( 9561)
  covalent geometry    : angle       0.60602 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 85
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5768 (OUTLIER) cc_final: 0.5388 (t70)
REVERT: A  115 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.5965 (ptm160)
REVERT: A  133 ASN cc_start: 0.7841 (m-40) cc_final: 0.7508 (m-40)
REVERT: A  262 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5444 (mp0)
REVERT: A  331 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8835 (tp)
REVERT: A  426 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7726 (mp)
REVERT: A  572 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7919 (tm-30)
REVERT: B  214 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8612 (mtpt)
REVERT: B  221 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7583 (p0)
  outliers start: 40
  outliers final: 17
  residues processed: 117
  average time/residue: 0.2418
  time to fit residues: 38.5405
Evaluate side-chains
  108 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  264 GLU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  379 GLN
Chi-restraints excluded: chain B residue  401 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0070
   chunk 43 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.9802

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.164368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.124926 restraints weight = 11014.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.20
r_work: 0.3050 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9561  Z= 0.128
  Angle     :  0.529   6.786  13168  Z= 0.285
  Chirality :  0.041   0.168   1464
  Planarity :  0.004   0.037   1526
  Dihedral  : 17.086 138.244   1786
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.34 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 28.49 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.90 (0.26), residues: 1036
  helix:  1.19 (0.28), residues: 379
  sheet: -0.56 (0.40), residues: 183
  loop : -2.18 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 377 
 HIS   0.003   0.001   HIS B  29 
 PHE   0.012   0.001   PHE A 328 
 TYR   0.014   0.001   TYR B 341 
 ARG   0.007   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03717 (  365)
  hydrogen bonds       : angle       4.57601 ( 1046)
  covalent geometry    : bond        0.00286 ( 9561)
  covalent geometry    : angle       0.52871 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5750 (OUTLIER) cc_final: 0.5396 (t70)
REVERT: A  115 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5931 (ptm160)
REVERT: A  133 ASN cc_start: 0.7510 (m-40) cc_final: 0.7203 (m-40)
REVERT: A  260 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7594 (mmtp)
REVERT: A  331 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8663 (tp)
REVERT: A  426 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7651 (mp)
REVERT: A  572 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7976 (tm-30)
REVERT: B  176 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7305 (mp)
REVERT: B  214 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8550 (mtpt)
REVERT: B  221 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7350 (p0)
  outliers start: 34
  outliers final: 17
  residues processed: 114
  average time/residue: 0.2501
  time to fit residues: 38.7873
Evaluate side-chains
  110 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  264 GLU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  401 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 68 optimal weight:   20.0000
   chunk 11 optimal weight:    0.6980
   chunk 60 optimal weight:    0.3980
   chunk 74 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.164966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.125447 restraints weight = 11031.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.92
r_work: 0.2984 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9561  Z= 0.167
  Angle     :  0.566   7.980  13168  Z= 0.302
  Chirality :  0.042   0.205   1464
  Planarity :  0.004   0.040   1526
  Dihedral  : 17.150 141.472   1786
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.72 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 28.04 %
    Favored  : 67.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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 (0.26), residues: 1036
  helix:  1.14 (0.28), residues: 378
  sheet: -0.70 (0.39), residues: 186
  loop : -2.22 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 377 
 HIS   0.005   0.001   HIS B  29 
 PHE   0.013   0.001   PHE A   9 
 TYR   0.017   0.002   TYR B 341 
 ARG   0.009   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04102 (  365)
  hydrogen bonds       : angle       4.62024 ( 1046)
  covalent geometry    : bond        0.00390 ( 9561)
  covalent geometry    : angle       0.56556 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 88
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5733 (OUTLIER) cc_final: 0.5377 (t70)
REVERT: A  115 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5816 (ptm160)
REVERT: A  133 ASN cc_start: 0.7578 (m-40) cc_final: 0.7269 (m-40)
REVERT: A  260 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7591 (mmtp)
REVERT: A  331 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8762 (tp)
REVERT: A  426 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7638 (mp)
REVERT: A  572 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7851 (tm-30)
REVERT: B  176 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7250 (mp)
REVERT: B  214 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8539 (mtpt)
REVERT: B  221 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7372 (p0)
  outliers start: 41
  outliers final: 23
  residues processed: 120
  average time/residue: 0.2378
  time to fit residues: 39.0171
Evaluate side-chains
  116 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 84
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  264 GLU
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  379 GLN
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.164880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.126359 restraints weight = 11174.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.75
r_work: 0.3055 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9561  Z= 0.135
  Angle     :  0.534   6.720  13168  Z= 0.287
  Chirality :  0.041   0.157   1464
  Planarity :  0.004   0.039   1526
  Dihedral  : 17.052 138.597   1786
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.63 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 28.60 %
    Favored  : 67.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.84 (0.26), residues: 1036
  helix:  1.22 (0.28), residues: 379
  sheet: -0.50 (0.40), residues: 183
  loop : -2.15 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 377 
 HIS   0.003   0.001   HIS B  29 
 PHE   0.015   0.001   PHE A 328 
 TYR   0.014   0.001   TYR B 341 
 ARG   0.008   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  365)
  hydrogen bonds       : angle       4.52508 ( 1046)
  covalent geometry    : bond        0.00306 ( 9561)
  covalent geometry    : angle       0.53379 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 87
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5722 (OUTLIER) cc_final: 0.5391 (t70)
REVERT: A  115 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.5858 (ptm160)
REVERT: A  133 ASN cc_start: 0.7635 (m-40) cc_final: 0.7326 (m-40)
REVERT: A  260 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7575 (mmtp)
REVERT: A  262 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5130 (mp0)
REVERT: A  331 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8728 (tp)
REVERT: A  426 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7668 (mp)
REVERT: A  572 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7980 (tm-30)
REVERT: B  176 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7332 (mp)
REVERT: B  214 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8565 (mtpt)
REVERT: B  221 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7563 (p0)
  outliers start: 38
  outliers final: 22
  residues processed: 120
  average time/residue: 0.2329
  time to fit residues: 38.6119
Evaluate side-chains
  116 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 84
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  264 GLU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0060
   chunk 42 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.6596

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.167278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.127846 restraints weight = 10911.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.11
r_work: 0.3029 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9561  Z= 0.114
  Angle     :  0.520   6.187  13168  Z= 0.281
  Chirality :  0.040   0.155   1464
  Planarity :  0.004   0.044   1526
  Dihedral  : 17.005 137.086   1786
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.53 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 28.72 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.74 (0.26), residues: 1036
  helix:  1.29 (0.28), residues: 380
  sheet: -0.42 (0.39), residues: 186
  loop : -2.10 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 377 
 HIS   0.004   0.001   HIS A 437 
 PHE   0.010   0.001   PHE A 143 
 TYR   0.013   0.001   TYR B 341 
 ARG   0.009   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03493 (  365)
  hydrogen bonds       : angle       4.46202 ( 1046)
  covalent geometry    : bond        0.00249 ( 9561)
  covalent geometry    : angle       0.52017 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5701 (OUTLIER) cc_final: 0.5353 (t70)
REVERT: A  115 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.5849 (ptm160)
REVERT: A  133 ASN cc_start: 0.7463 (m-40) cc_final: 0.7159 (m-40)
REVERT: A  260 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7611 (mmtp)
REVERT: A  262 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.4962 (mp0)
REVERT: A  331 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8672 (tp)
REVERT: A  426 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7574 (mp)
REVERT: A  572 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7944 (tm-30)
REVERT: B  214 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8526 (mtpt)
REVERT: B  221 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7331 (p0)
  outliers start: 32
  outliers final: 22
  residues processed: 118
  average time/residue: 0.2360
  time to fit residues: 38.0895
Evaluate side-chains
  118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 87
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  264 GLU
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  379 GLN
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 87 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 96 optimal weight:    0.1980
   chunk 34 optimal weight:    6.9990
   chunk 81 optimal weight:    0.2980
   chunk 67 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.169308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.129813 restraints weight = 11125.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.92
r_work: 0.3164 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9561  Z= 0.106
  Angle     :  0.502   5.816  13168  Z= 0.271
  Chirality :  0.040   0.146   1464
  Planarity :  0.004   0.047   1526
  Dihedral  : 16.842 134.421   1786
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.14 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 28.94 %
    Favored  : 67.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.58 (0.27), residues: 1036
  helix:  1.46 (0.29), residues: 379
  sheet: -0.30 (0.39), residues: 190
  loop : -2.06 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 340 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.011   0.001   PHE A 328 
 TYR   0.016   0.001   TYR A  74 
 ARG   0.010   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03184 (  365)
  hydrogen bonds       : angle       4.30157 ( 1046)
  covalent geometry    : bond        0.00230 ( 9561)
  covalent geometry    : angle       0.50156 (13168)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5692 (OUTLIER) cc_final: 0.4921 (t70)
REVERT: A  115 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5790 (ptm160)
REVERT: A  244 ASN cc_start: 0.6942 (p0) cc_final: 0.6564 (p0)
REVERT: A  260 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7643 (mmtp)
REVERT: A  331 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8643 (tp)
REVERT: A  426 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7693 (mp)
REVERT: A  572 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7980 (tm-30)
REVERT: B  176 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7314 (mp)
REVERT: B  214 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8558 (mtpt)
REVERT: B  221 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7416 (p0)
REVERT: B  240 TYR cc_start: 0.7239 (m-80) cc_final: 0.6922 (m-80)
  outliers start: 32
  outliers final: 20
  residues processed: 119
  average time/residue: 0.2329
  time to fit residues: 37.8687
Evaluate side-chains
  119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  260 LYS
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  258 VAL
Chi-restraints excluded: chain B residue  264 GLU
Chi-restraints excluded: chain B residue  279 GLU
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  379 GLN
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  426 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0970
   chunk 55 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0670
   chunk 34 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   overall best weight:    1.4120

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.164097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.121002 restraints weight = 11015.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.91
r_work: 0.3037 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9561  Z= 0.154
  Angle     :  0.550   6.746  13168  Z= 0.293
  Chirality :  0.042   0.156   1464
  Planarity :  0.004   0.046   1526
  Dihedral  : 16.925 139.135   1786
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.43 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 28.94 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.74 (0.26), residues: 1036
  helix:  1.29 (0.28), residues: 380
  sheet: -0.43 (0.40), residues: 189
  loop : -2.10 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 377 
 HIS   0.004   0.001   HIS B  29 
 PHE   0.013   0.001   PHE A  91 
 TYR   0.016   0.001   TYR B 341 
 ARG   0.010   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03816 (  365)
  hydrogen bonds       : angle       4.42569 ( 1046)
  covalent geometry    : bond        0.00359 ( 9561)
  covalent geometry    : angle       0.54953 (13168)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5019.24 seconds
wall clock time: 87 minutes 38.13 seconds (5258.13 seconds total)