Starting phenix.real_space_refine
on Sun Dec 29 02:30:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jl0_36385/12_2024/8jl0_36385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jl0_36385/12_2024/8jl0_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_36385/12_2024/8jl0_36385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jl0_36385/12_2024/8jl0_36385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jl0_36385/12_2024/8jl0_36385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jl0_36385/12_2024/8jl0_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.31, per 1000 atoms: 0.68
  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: 2.75
  Conformation dependent library (CDL) restraints added in 1.2 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: 3.80
  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: 3.57

  Time building geometry restraints manager: 3.00 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:             1.420
  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:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.940
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.120
-------------------------------------------------------------------------------
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= 0.457
  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 

*********************** 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  : 1.211 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 98
  average time/residue: 0.2775
  time to fit residues: 36.9368
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  : 0.965 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
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= 0.154
  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 

*********************** 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  : 1.018 
Fit side-chains
REVERT: A  426 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7924 (mp)
REVERT: B  149 TYR cc_start: 0.8373 (t80) cc_final: 0.8102 (t80)
REVERT: B  221 ASP cc_start: 0.7428 (p0) cc_final: 0.7186 (p0)
REVERT: B  279 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7745 (mt-10)
  outliers start: 29
  outliers final: 8
  residues processed: 116
  average time/residue: 0.2546
  time to fit residues: 40.2346
Evaluate side-chains
  95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  132 MET
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 54 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0970
   chunk 33 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.8982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1024

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= 0.177
  Angle     :  0.522   7.512  13168  Z= 0.282
  Chirality :  0.041   0.211   1464
  Planarity :  0.004   0.029   1526
  Dihedral  : 17.087 137.751   1787
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.34 %
    Favored  : 92.47 %
  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: -0.94 (0.26), residues: 1036
  helix:  1.27 (0.28), residues: 378
  sheet: -0.60 (0.39), residues: 183
  loop : -2.29 (0.24), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 377 
 HIS   0.003   0.001   HIS B  29 
 PHE   0.009   0.001   PHE A  80 
 TYR   0.015   0.001   TYR B 341 
 ARG   0.007   0.000   ARG B 168 

*********************** 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
  128 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A  426 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7930 (mp)
REVERT: B  149 TYR cc_start: 0.8395 (t80) cc_final: 0.8127 (t80)
REVERT: B  221 ASP cc_start: 0.7449 (p0) cc_final: 0.7149 (p0)
  outliers start: 36
  outliers final: 18
  residues processed: 121
  average time/residue: 0.2409
  time to fit residues: 40.2707
Evaluate side-chains
  104 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
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  154 ILE
Chi-restraints excluded: chain A residue  192 GLN
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  347 VAL
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   96 VAL
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  354 VAL
Chi-restraints excluded: chain B residue  401 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0050
   chunk 27 optimal weight:    0.0670
   overall best weight:    1.5736

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9561  Z= 0.254
  Angle     :  0.564   7.920  13168  Z= 0.301
  Chirality :  0.042   0.213   1464
  Planarity :  0.004   0.032   1526
  Dihedral  : 17.143 141.103   1787
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.14 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 28.27 %
    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: -1.05 (0.26), residues: 1036
  helix:  1.17 (0.28), residues: 377
  sheet: -0.76 (0.39), residues: 186
  loop : -2.31 (0.25), 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   0.015   0.002   PHE A   9 
 TYR   0.017   0.002   TYR B 341 
 ARG   0.007   0.000   ARG B 168 

*********************** 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: 35
    poor density    : 90
  time to evaluate  : 1.433 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5980 (OUTLIER) cc_final: 0.5170 (t70)
REVERT: A  133 ASN cc_start: 0.7278 (m-40) cc_final: 0.6953 (m-40)
REVERT: A  328 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6278 (t80)
REVERT: A  426 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7935 (mp)
REVERT: A  572 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8161 (tm-30)
REVERT: B  221 ASP cc_start: 0.7479 (p0) cc_final: 0.7167 (p0)
  outliers start: 35
  outliers final: 18
  residues processed: 119
  average time/residue: 0.2809
  time to fit residues: 46.6869
Evaluate side-chains
  107 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
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  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  347 VAL
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  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  354 VAL
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 86 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1160

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= 0.212
  Angle     :  0.541   7.572  13168  Z= 0.290
  Chirality :  0.041   0.190   1464
  Planarity :  0.004   0.037   1526
  Dihedral  : 17.084 139.215   1787
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.34 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 27.93 %
    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: -0.93 (0.26), residues: 1036
  helix:  1.21 (0.28), residues: 378
  sheet: -0.58 (0.39), residues: 183
  loop : -2.23 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 377 
 HIS   0.004   0.001   HIS B  29 
 PHE   0.011   0.001   PHE A 328 
 TYR   0.016   0.001   TYR B 341 
 ARG   0.007   0.000   ARG B 168 

*********************** 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
  130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 88
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5967 (OUTLIER) cc_final: 0.5162 (t70)
REVERT: A  133 ASN cc_start: 0.7264 (m-40) cc_final: 0.6949 (m-40)
REVERT: A  262 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5484 (mp0)
REVERT: A  328 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5979 (t80)
REVERT: A  331 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8695 (tp)
REVERT: A  426 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7931 (mp)
REVERT: A  572 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8184 (tm-30)
REVERT: B  214 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8595 (mtpt)
REVERT: B  221 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7220 (p0)
  outliers start: 42
  outliers final: 21
  residues processed: 121
  average time/residue: 0.2342
  time to fit residues: 39.3064
Evaluate side-chains
  115 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
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  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  328 PHE
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  127 ASP
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  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  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 34 optimal weight:    5.9990
   chunk 93 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    2.3588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
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      :  0.005   0.055   9561  Z= 0.353
  Angle     :  0.622   8.598  13168  Z= 0.330
  Chirality :  0.045   0.226   1464
  Planarity :  0.005   0.044   1526
  Dihedral  : 17.344 145.268   1786
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.11 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 27.93 %
    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: -1.12 (0.26), residues: 1036
  helix:  0.98 (0.28), residues: 378
  sheet: -0.67 (0.40), residues: 175
  loop : -2.26 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 377 
 HIS   0.006   0.001   HIS B  29 
 PHE   0.019   0.002   PHE A   9 
 TYR   0.020   0.002   TYR B 469 
 ARG   0.007   0.000   ARG A 105 

*********************** 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
  126 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 85
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5980 (OUTLIER) cc_final: 0.5564 (t70)
REVERT: A  133 ASN cc_start: 0.7465 (m-40) cc_final: 0.7162 (m-40)
REVERT: A  262 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5670 (mp0)
REVERT: A  331 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8871 (tp)
REVERT: A  426 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8020 (mp)
REVERT: A  572 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8169 (tm-30)
REVERT: B  214 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8569 (mtpt)
REVERT: B  221 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7253 (p0)
  outliers start: 41
  outliers final: 21
  residues processed: 117
  average time/residue: 0.2447
  time to fit residues: 39.5994
Evaluate side-chains
  112 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
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  154 ILE
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  182 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 103 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1327

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= 0.182
  Angle     :  0.528   6.694  13168  Z= 0.285
  Chirality :  0.041   0.163   1464
  Planarity :  0.004   0.041   1526
  Dihedral  : 17.105 138.042   1786
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.24 %
    Favored  : 92.66 %
  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: -0.87 (0.26), residues: 1036
  helix:  1.18 (0.28), residues: 381
  sheet: -0.52 (0.40), residues: 183
  loop : -2.16 (0.25), residues: 472

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   0.014   0.001   PHE A 328 
 TYR   0.014   0.001   TYR B 341 
 ARG   0.009   0.000   ARG A 105 

*********************** 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
  119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 87
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5962 (OUTLIER) cc_final: 0.5555 (t70)
REVERT: A  133 ASN cc_start: 0.7302 (m-40) cc_final: 0.7025 (m-40)
REVERT: A  331 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8727 (tp)
REVERT: A  426 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7963 (mp)
REVERT: A  572 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8242 (tm-30)
REVERT: B  176 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7343 (mp)
REVERT: B  214 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8597 (mtpt)
REVERT: B  221 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7233 (p0)
  outliers start: 32
  outliers final: 19
  residues processed: 115
  average time/residue: 0.2441
  time to fit residues: 38.5962
Evaluate side-chains
  111 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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  217 ILE
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  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 61 optimal weight:   10.0000
   chunk 31 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0770
   chunk 81 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.5738

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1497

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= 0.146
  Angle     :  0.501   6.366  13168  Z= 0.271
  Chirality :  0.040   0.146   1464
  Planarity :  0.004   0.047   1526
  Dihedral  : 16.899 134.636   1786
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.43 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 29.28 %
    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: -0.68 (0.26), residues: 1036
  helix:  1.40 (0.28), residues: 380
  sheet: -0.44 (0.39), residues: 190
  loop : -2.11 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 377 
 HIS   0.003   0.001   HIS B 166 
 PHE   0.012   0.001   PHE A 328 
 TYR   0.013   0.001   TYR A  74 
 ARG   0.009   0.000   ARG B 168 

*********************** 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
  127 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5897 (OUTLIER) cc_final: 0.5060 (t70)
REVERT: A  133 ASN cc_start: 0.7073 (m-40) cc_final: 0.6816 (m-40)
REVERT: A  262 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.4956 (mp0)
REVERT: A  331 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8689 (tp)
REVERT: A  426 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7959 (mp)
REVERT: A  572 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7924 (tm-30)
REVERT: B  176 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7308 (mp)
REVERT: B  214 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8607 (mtpt)
REVERT: B  221 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7314 (p0)
  outliers start: 32
  outliers final: 19
  residues processed: 121
  average time/residue: 0.2493
  time to fit residues: 41.5444
Evaluate side-chains
  114 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  291 LEU
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  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  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 90 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 95 optimal weight:    0.2980
   chunk 63 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1505

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= 0.170
  Angle     :  0.514   5.973  13168  Z= 0.277
  Chirality :  0.040   0.157   1464
  Planarity :  0.004   0.045   1526
  Dihedral  : 16.871 136.301   1786
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.85 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 28.94 %
    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: -0.63 (0.27), residues: 1036
  helix:  1.39 (0.28), residues: 381
  sheet: -0.34 (0.39), residues: 190
  loop : -2.08 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 377 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.015   0.001   PHE A  91 
 TYR   0.013   0.001   TYR A  74 
 ARG   0.009   0.000   ARG A 105 

*********************** 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: 30
    poor density    : 94
  time to evaluate  : 1.073 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5854 (OUTLIER) cc_final: 0.5006 (t70)
REVERT: A  244 ASN cc_start: 0.6832 (p0) cc_final: 0.6399 (p0)
REVERT: A  331 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8712 (tp)
REVERT: A  426 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7961 (mp)
REVERT: A  572 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8218 (tm-30)
REVERT: B  176 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7235 (mp)
REVERT: B  214 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8626 (mtpt)
REVERT: B  221 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7288 (p0)
  outliers start: 30
  outliers final: 22
  residues processed: 119
  average time/residue: 0.2428
  time to fit residues: 40.1310
Evaluate side-chains
  120 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
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  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  279 GLU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  358 SER
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 62 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0770
   chunk 106 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 84 optimal weight:    0.3980
   chunk 8 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 67 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1531

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= 0.146
  Angle     :  0.509   5.782  13168  Z= 0.274
  Chirality :  0.040   0.145   1464
  Planarity :  0.004   0.046   1526
  Dihedral  : 16.854 135.455   1786
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.85 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 29.17 %
    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: -0.58 (0.27), residues: 1036
  helix:  1.41 (0.28), residues: 381
  sheet: -0.28 (0.40), residues: 190
  loop : -2.05 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 377 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.012   0.001   PHE A 328 
 TYR   0.012   0.001   TYR A  74 
 ARG   0.010   0.000   ARG A 105 

********************** 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
  121 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A   46 HIS cc_start: 0.5840 (OUTLIER) cc_final: 0.4997 (t70)
REVERT: A  244 ASN cc_start: 0.6848 (p0) cc_final: 0.6427 (p0)
REVERT: A  331 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8736 (tp)
REVERT: A  426 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7969 (mp)
REVERT: A  572 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7907 (tm-30)
REVERT: B  176 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7287 (mp)
REVERT: B  214 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8601 (mtpt)
REVERT: B  221 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7322 (p0)
  outliers start: 28
  outliers final: 21
  residues processed: 115
  average time/residue: 0.2398
  time to fit residues: 38.1970
Evaluate side-chains
  120 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  217 ILE
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  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  279 GLU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  358 SER
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 26 optimal weight:    0.3980
   chunk 78 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0370
   chunk 87 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.167894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.125955 restraints weight = 10970.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.95
r_work: 0.3097 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1686

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= 0.145
  Angle     :  0.498   5.487  13168  Z= 0.269
  Chirality :  0.040   0.143   1464
  Planarity :  0.004   0.049   1526
  Dihedral  : 16.756 133.720   1786
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.95 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 28.94 %
    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: -0.51 (0.27), residues: 1036
  helix:  1.48 (0.28), residues: 380
  sheet: -0.18 (0.40), residues: 190
  loop : -2.05 (0.26), residues: 466

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   0.017   0.001   PHE A  91 
 TYR   0.017   0.001   TYR A  74 
 ARG   0.009   0.000   ARG A 105 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2159.76 seconds
wall clock time: 40 minutes 18.57 seconds (2418.57 seconds total)