Starting phenix.real_space_refine
on Sun May  3 16:49:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ta2_41126/05_2026/8ta2_41126_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ta2_41126/05_2026/8ta2_41126.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ta2_41126/05_2026/8ta2_41126_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ta2_41126/05_2026/8ta2_41126_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ta2_41126/05_2026/8ta2_41126.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ta2_41126/05_2026/8ta2_41126.map"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.153
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: 6
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     Cl      6      4.86       5
     C    4774      2.51       5
     N    1168      2.21       5
     O    1202      1.98       5
     H    7411      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14605
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 7231
          Classifications: {'peptide': 460}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 437}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 7320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 466, 7320
          Classifications: {'peptide': 466}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 443}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 27
          Unusual residues: {' CL': 1, 'GH6': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 27
          Unusual residues: {' CL': 1, 'GH6': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.97, per 1000 atoms: 0.20
  Number of scatterers: 14605
  At special positions: 0
  Unit cell: (81.356, 78.518, 118.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      6     17.00
     S      44     16.00
     O    1202      8.00
     N    1168      7.00
     C    4774      6.00
     H    7411      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 434.3 milliseconds
  

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 1 sheets defined
      79.5% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 125
      removed outlier: 3.580A  pdb=" N   ILE A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA A 102 " --> pdb=" O   GLY A  98 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLN A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 156
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 181 through 197
    Processing helix  chain 'A' and resid 204 through 223
    Processing helix  chain 'A' and resid 232 through 253
      removed outlier: 3.654A  pdb=" N   ALA A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 267
    Processing helix  chain 'A' and resid 272 through 296
      removed outlier: 3.708A  pdb=" N   ARG A 277 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 320 through 352
      removed outlier: 3.808A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 362
      removed outlier: 3.534A  pdb=" N   LYS A 362 " --> pdb=" O   PHE A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 379
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 3.753A  pdb=" N   ALA A 388 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 401
    Processing helix  chain 'A' and resid 419 through 425
    Processing helix  chain 'A' and resid 430 through 450
      removed outlier: 3.589A  pdb=" N   TRP A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 481
      removed outlier: 3.658A  pdb=" N   VAL A 462 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 3.893A  pdb=" N   TYR A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 526
      removed outlier: 3.678A  pdb=" N   PHE A 522 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 547
      removed outlier: 3.854A  pdb=" N   SER A 547 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'B' and resid 89 through 126
      removed outlier: 3.803A  pdb=" N   VAL B  95 " --> pdb=" O   TRP B  91 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN B 119 " --> pdb=" O   CYS B 115 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLN B 120 " --> pdb=" O   LEU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 156
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 157 through 160
      removed outlier: 3.944A  pdb=" N   VAL B 160 " --> pdb=" O   PRO B 157 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 157 through 160'
    Processing helix  chain 'B' and resid 163 through 171
      removed outlier: 4.040A  pdb=" N   THR B 169 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 198
      removed outlier: 3.634A  pdb=" N   THR B 193 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 223
      removed outlier: 3.518A  pdb=" N   LYS B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 253
      removed outlier: 3.708A  pdb=" N   ALA B 242 " --> pdb=" O   GLU B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 267
      removed outlier: 4.090A  pdb=" N   VAL B 259 " --> pdb=" O   PRO B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 296
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 317 through 319
      No H-bonds generated for 'chain 'B' and resid 317 through 319'
    Processing helix  chain 'B' and resid 320 through 352
      removed outlier: 3.529A  pdb=" N   PHE B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 362
    Processing helix  chain 'B' and resid 364 through 379
      removed outlier: 3.806A  pdb=" N   ALA B 368 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 392 through 401
    Processing helix  chain 'B' and resid 420 through 424
    Processing helix  chain 'B' and resid 430 through 450
      removed outlier: 3.927A  pdb=" N   TRP B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 481
      removed outlier: 3.809A  pdb=" N   VAL B 462 " --> pdb=" O   ALA B 458 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE B 465 " --> pdb=" O   PRO B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 3.949A  pdb=" N   TYR B 499 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL B 501 " --> pdb=" O   GLY B 497 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL B 502 " --> pdb=" O   GLY B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 526
      removed outlier: 3.530A  pdb=" N   PHE B 522 " --> pdb=" O   ALA B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 546
    Processing helix  chain 'B' and resid 551 through 561
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271

    528 hydrogen bonds defined for protein.
    1551 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.17

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        0.93 -     1.11: 7397
        1.11 -     1.29: 1070
        1.29 -     1.47: 2629
        1.47 -     1.64: 3612
        1.64 -     1.82: 78
  Bond restraints: 14786
  Sorted by residual:
  bond pdb=" N   LEU B 472 "
       pdb=" H   LEU B 472 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   ALA B 449 "
       pdb=" H   ALA B 449 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   ALA B 388 "
       pdb=" H   ALA B 388 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   LEU B 144 "
       pdb=" H   LEU B 144 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CZ  PHE A 316 "
       pdb=" HZ  PHE A 316 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 14781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 23195
        2.87 -     5.73: 2761
        5.73 -     8.60: 788
        8.60 -    11.46: 12
       11.46 -    14.33: 13
  Bond angle restraints: 26769
  Sorted by residual:
  angle pdb=" CA  PHE A 270 "
        pdb=" CB  PHE A 270 "
        pdb=" CG  PHE A 270 "
      ideal   model   delta    sigma   weight residual
     113.80  123.19   -9.39 1.00e+00 1.00e+00 8.82e+01
  angle pdb=" CA  ASP A 402 "
        pdb=" CB  ASP A 402 "
        pdb=" CG  ASP A 402 "
      ideal   model   delta    sigma   weight residual
     112.60  118.36   -5.76 1.00e+00 1.00e+00 3.31e+01
  angle pdb=" CD  ARG B 235 "
        pdb=" NE  ARG B 235 "
        pdb=" CZ  ARG B 235 "
      ideal   model   delta    sigma   weight residual
     124.40  132.36   -7.96 1.40e+00 5.10e-01 3.23e+01
  angle pdb=" CB  HIS B 513 "
        pdb=" CG  HIS B 513 "
        pdb=" CD2 HIS B 513 "
      ideal   model   delta    sigma   weight residual
     131.20  124.14    7.06 1.30e+00 5.92e-01 2.95e+01
  angle pdb=" CA  PHE B 306 "
        pdb=" CB  PHE B 306 "
        pdb=" CG  PHE B 306 "
      ideal   model   delta    sigma   weight residual
     113.80  119.13   -5.33 1.00e+00 1.00e+00 2.84e+01
  ... (remaining 26764 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 6266
       17.74 -    35.47: 340
       35.47 -    53.21: 148
       53.21 -    70.94: 185
       70.94 -    88.67: 10
  Dihedral angle restraints: 6949
    sinusoidal: 3704
      harmonic: 3245
  Sorted by residual:
  dihedral pdb=" CA  PHE B 222 "
           pdb=" C   PHE B 222 "
           pdb=" N   LEU B 223 "
           pdb=" CA  LEU B 223 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.05   28.95     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  GLU B 178 "
           pdb=" C   GLU B 178 "
           pdb=" N   TYR B 179 "
           pdb=" CA  TYR B 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.58  -28.42     0      5.00e+00 4.00e-02 3.23e+01
  dihedral pdb=" CA  LEU B 176 "
           pdb=" C   LEU B 176 "
           pdb=" N   LYS B 177 "
           pdb=" CA  LYS B 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.80  -26.20     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 6946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 777
       0.082 -    0.164: 310
       0.164 -    0.246: 75
       0.246 -    0.329: 11
       0.329 -    0.411: 2
  Chirality restraints: 1175
  Sorted by residual:
  chirality pdb=" CA  PRO B 380 "
            pdb=" N   PRO B 380 "
            pdb=" C   PRO B 380 "
            pdb=" CB  PRO B 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.41 2.00e-01 2.50e+01 4.22e+00
  chirality pdb=" CA  PRO A 380 "
            pdb=" N   PRO A 380 "
            pdb=" C   PRO A 380 "
            pdb=" CB  PRO A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.34    0.38 2.00e-01 2.50e+01 3.66e+00
  chirality pdb=" CA  PRO A 453 "
            pdb=" N   PRO A 453 "
            pdb=" C   PRO A 453 "
            pdb=" CB  PRO A 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.43e+00
  ... (remaining 1172 not shown)

  Planarity restraints: 2105
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 GH6 B 601 "   -0.004 2.00e-02 2.50e+03   7.85e-02 1.54e+02
        pdb=" C12 GH6 B 601 "   -0.026 2.00e-02 2.50e+03
        pdb=" C14 GH6 B 601 "   -0.070 2.00e-02 2.50e+03
        pdb=" C15 GH6 B 601 "   -0.063 2.00e-02 2.50e+03
        pdb=" C16 GH6 B 601 "   -0.049 2.00e-02 2.50e+03
        pdb=" C25 GH6 B 601 "   -0.041 2.00e-02 2.50e+03
        pdb=" N10 GH6 B 601 "    0.042 2.00e-02 2.50e+03
        pdb=" O17 GH6 B 601 "    0.183 2.00e-02 2.50e+03
        pdb="CL1  GH6 B 601 "    0.093 2.00e-02 2.50e+03
        pdb="CL2  GH6 B 601 "   -0.064 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 406 "    0.142 2.00e-02 2.50e+03   6.14e-02 1.51e+02
        pdb=" CG  TRP A 406 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 406 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 406 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 406 "   -0.059 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 406 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 406 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 406 "    0.044 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 406 "   -0.030 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 406 "    0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 406 "   -0.009 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 406 "   -0.105 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 406 "   -0.060 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 406 "    0.123 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 406 "   -0.046 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 406 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 444 "    0.140 2.00e-02 2.50e+03   5.55e-02 1.23e+02
        pdb=" CG  TRP B 444 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 444 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 444 "   -0.013 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 444 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 444 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 444 "   -0.042 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 444 "    0.042 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 444 "   -0.022 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 444 "    0.033 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 444 "   -0.015 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 444 "   -0.083 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 444 "   -0.071 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 444 "    0.061 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 444 "   -0.046 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 444 "    0.051 2.00e-02 2.50e+03
  ... (remaining 2102 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 779
        2.20 -     2.80: 26495
        2.80 -     3.40: 41439
        3.40 -     4.00: 56050
        4.00 -     4.60: 79699
  Nonbonded interactions: 204462
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 166 "
            pdb=" HH  TYR A 179 "
     model   vdw
     1.602 2.450
  nonbonded pdb=" OE1 GLU B 166 "
            pdb=" HH  TYR B 179 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OE1 GLU B 320 "
            pdb=" HH  TYR B 499 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" OE2 GLU A 264 "
            pdb=" HG  SER A 516 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" HG  SER A 392 "
            pdb=" O03 GH6 A 601 "
     model   vdw
     1.621 2.450
  ... (remaining 204457 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 88 through 297 or resid 304 through 602))
}

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:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.080
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.110
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
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      :  0.013   0.095   7375  Z= 0.786
  Angle     :  1.847  14.326  10033  Z= 1.259
  Chirality :  0.091   0.411   1175
  Planarity :  0.016   0.145   1230
  Dihedral  : 13.743  88.674   2571
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 0.07
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.74 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  3.88 %
    Favored  : 94.39 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.25), residues: 912
  helix: -0.82 (0.17), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.34 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 273 
 TYR   0.089   0.021   TYR A 134 
 PHE   0.070   0.013   PHE B 386 
 TRP   0.088   0.020   TRP A 106 
 HIS   0.015   0.005   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.01312 ( 7375)
  covalent geometry    : angle       1.84671 (10033)
  hydrogen bonds       : bond        0.21017 (  528)
  hydrogen bonds       : angle       6.56584 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.7816 (tp) cc_final: 0.7529 (tt)
REVERT: A  121 TRP cc_start: 0.8224 (t60) cc_final: 0.7750 (t-100)
REVERT: A  122 MET cc_start: 0.8587 (ttm) cc_final: 0.8352 (ttp)
REVERT: A  214 MET cc_start: 0.7986 (mtm) cc_final: 0.7783 (mtm)
REVERT: A  535 MET cc_start: 0.7441 (mtm) cc_final: 0.7232 (mtp)
REVERT: B  183 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6892 (mttp)
REVERT: B  200 MET cc_start: 0.7979 (mmp) cc_final: 0.7602 (mmp)
REVERT: B  295 TRP cc_start: 0.7100 (t-100) cc_final: 0.6359 (t60)
REVERT: B  307 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7183 (pttt)
REVERT: B  363 ARG cc_start: 0.6489 (pmt170) cc_final: 0.5911 (pmt-80)
REVERT: B  433 LEU cc_start: 0.7691 (tp) cc_final: 0.7397 (tt)
REVERT: B  558 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7448 (mtp-110)
  outliers start: 13
  outliers final: 4
  residues processed: 120
  average time/residue: 1.1306
  time to fit residues: 143.9316
Evaluate side-chains
  91 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  326 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
B 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.157684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.123171 restraints weight = 20013.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.75
r_work: 0.3343 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7375  Z= 0.184
  Angle     :  0.673  11.334  10033  Z= 0.370
  Chirality :  0.040   0.153   1175
  Planarity :  0.006   0.065   1230
  Dihedral  :  8.496  69.181   1016
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  6.42 %
    Favored  : 92.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.27), residues: 912
  helix:  0.90 (0.18), residues: 699
  sheet:  None (None), residues: 0
  loop : -1.64 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 297 
 TYR   0.017   0.002   TYR A 564 
 PHE   0.018   0.002   PHE B 280 
 TRP   0.017   0.001   TRP A 444 
 HIS   0.008   0.002   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7375)
  covalent geometry    : angle       0.67267 (10033)
  hydrogen bonds       : bond        0.07958 (  528)
  hydrogen bonds       : angle       4.56271 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.7713 (tpt) cc_final: 0.7377 (tpt)
REVERT: A  121 TRP cc_start: 0.7320 (t60) cc_final: 0.7055 (t60)
REVERT: A  314 PHE cc_start: 0.6393 (t80) cc_final: 0.5816 (m-80)
REVERT: A  321 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7348 (mm)
REVERT: A  349 MET cc_start: 0.6423 (ptp) cc_final: 0.5711 (mmt)
REVERT: B  183 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5999 (mttp)
REVERT: B  295 TRP cc_start: 0.6753 (t-100) cc_final: 0.6542 (t60)
REVERT: B  307 LYS cc_start: 0.7242 (ttmt) cc_final: 0.7019 (tttp)
REVERT: B  363 ARG cc_start: 0.6263 (pmt170) cc_final: 0.5527 (pmt-80)
REVERT: B  433 LEU cc_start: 0.7611 (tp) cc_final: 0.7400 (tt)
REVERT: B  561 LYS cc_start: 0.6429 (mttt) cc_final: 0.5737 (mtmt)
  outliers start: 11
  outliers final: 4
  residues processed: 104
  average time/residue: 1.1333
  time to fit residues: 125.1092
Evaluate side-chains
  90 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  344 LYS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  305 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0270
   chunk 19 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.9242

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.157399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.121115 restraints weight = 20020.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.86
r_work: 0.3337 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7375  Z= 0.146
  Angle     :  0.566  11.439  10033  Z= 0.306
  Chirality :  0.038   0.135   1175
  Planarity :  0.005   0.060   1230
  Dihedral  :  7.940  68.607   1014
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  7.09 %
    Favored  : 91.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.27), residues: 912
  helix:  1.46 (0.19), residues: 698
  sheet:  None (None), residues: 0
  loop : -1.78 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 471 
 TYR   0.015   0.002   TYR B 140 
 PHE   0.014   0.001   PHE A 280 
 TRP   0.014   0.001   TRP A 444 
 HIS   0.005   0.002   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7375)
  covalent geometry    : angle       0.56649 (10033)
  hydrogen bonds       : bond        0.06570 (  528)
  hydrogen bonds       : angle       4.19528 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.7247 (t60) cc_final: 0.6906 (t60)
REVERT: A  239 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6677 (ptp)
REVERT: A  314 PHE cc_start: 0.6427 (t80) cc_final: 0.5777 (m-80)
REVERT: A  344 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7625 (mmtm)
REVERT: A  349 MET cc_start: 0.6501 (ptp) cc_final: 0.5778 (mmt)
REVERT: B  183 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5919 (mttp)
REVERT: B  295 TRP cc_start: 0.6691 (t-100) cc_final: 0.6416 (t60)
REVERT: B  307 LYS cc_start: 0.7402 (ttmt) cc_final: 0.6943 (pttt)
REVERT: B  363 ARG cc_start: 0.6276 (pmt170) cc_final: 0.5377 (pmt-80)
REVERT: B  433 LEU cc_start: 0.7598 (tp) cc_final: 0.7377 (tt)
REVERT: B  523 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7426 (mt-10)
REVERT: B  561 LYS cc_start: 0.6266 (mttt) cc_final: 0.5583 (mtmt)
  outliers start: 10
  outliers final: 4
  residues processed: 93
  average time/residue: 0.9273
  time to fit residues: 92.8725
Evaluate side-chains
  90 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  344 LYS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  274 ASN
Chi-restraints excluded: chain B residue  305 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.156679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.120550 restraints weight = 20022.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.87
r_work: 0.3329 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7375  Z= 0.148
  Angle     :  0.542  11.028  10033  Z= 0.292
  Chirality :  0.038   0.133   1175
  Planarity :  0.005   0.055   1230
  Dihedral  :  7.723  68.293   1014
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  7.89 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.28), residues: 912
  helix:  1.63 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.81 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 471 
 TYR   0.013   0.002   TYR B 140 
 PHE   0.013   0.001   PHE B 279 
 TRP   0.014   0.001   TRP A 444 
 HIS   0.006   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7375)
  covalent geometry    : angle       0.54220 (10033)
  hydrogen bonds       : bond        0.06298 (  528)
  hydrogen bonds       : angle       4.03589 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.7187 (t60) cc_final: 0.6845 (t60)
REVERT: A  313 ASP cc_start: 0.7736 (p0) cc_final: 0.7257 (p0)
REVERT: A  314 PHE cc_start: 0.6535 (t80) cc_final: 0.5949 (m-80)
REVERT: A  349 MET cc_start: 0.6384 (ptp) cc_final: 0.5708 (mmt)
REVERT: B  183 LYS cc_start: 0.6076 (OUTLIER) cc_final: 0.5839 (mttp)
REVERT: B  295 TRP cc_start: 0.6677 (t-100) cc_final: 0.6389 (t60)
REVERT: B  307 LYS cc_start: 0.7434 (ttmt) cc_final: 0.6954 (pttt)
REVERT: B  363 ARG cc_start: 0.6336 (pmt170) cc_final: 0.5491 (pmt-80)
REVERT: B  433 LEU cc_start: 0.7658 (tp) cc_final: 0.7439 (tt)
  outliers start: 10
  outliers final: 6
  residues processed: 91
  average time/residue: 0.9240
  time to fit residues: 90.7617
Evaluate side-chains
  88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  483 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.155734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.120512 restraints weight = 20036.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.79
r_work: 0.3332 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7375  Z= 0.150
  Angle     :  0.536  11.120  10033  Z= 0.286
  Chirality :  0.038   0.140   1175
  Planarity :  0.005   0.056   1230
  Dihedral  :  7.673  67.514   1014
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  9.36 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.28), residues: 912
  helix:  1.70 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -1.82 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 471 
 TYR   0.013   0.002   TYR B 140 
 PHE   0.014   0.001   PHE B 279 
 TRP   0.013   0.001   TRP A 444 
 HIS   0.005   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7375)
  covalent geometry    : angle       0.53555 (10033)
  hydrogen bonds       : bond        0.06173 (  528)
  hydrogen bonds       : angle       3.97024 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8283 (mtp) cc_final: 0.8033 (ttm)
REVERT: A  121 TRP cc_start: 0.7149 (t60) cc_final: 0.6787 (t60)
REVERT: A  313 ASP cc_start: 0.7765 (p0) cc_final: 0.7413 (p0)
REVERT: A  314 PHE cc_start: 0.6565 (t80) cc_final: 0.5983 (m-80)
REVERT: A  349 MET cc_start: 0.6292 (ptp) cc_final: 0.5638 (mmt)
REVERT: B  183 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5814 (mttp)
REVERT: B  295 TRP cc_start: 0.6731 (t-100) cc_final: 0.6464 (t60)
REVERT: B  307 LYS cc_start: 0.7450 (ttmt) cc_final: 0.6963 (pttt)
REVERT: B  363 ARG cc_start: 0.6282 (pmt170) cc_final: 0.5463 (pmt-80)
REVERT: B  386 PHE cc_start: 0.7053 (m-80) cc_final: 0.6823 (m-10)
REVERT: B  433 LEU cc_start: 0.7672 (tp) cc_final: 0.7455 (tt)
REVERT: B  523 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7523 (mt-10)
  outliers start: 11
  outliers final: 5
  residues processed: 94
  average time/residue: 0.8702
  time to fit residues: 88.7101
Evaluate side-chains
  88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  483 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0970
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.156654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.121563 restraints weight = 20109.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.79
r_work: 0.3343 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7375  Z= 0.137
  Angle     :  0.515  11.100  10033  Z= 0.275
  Chirality :  0.037   0.138   1175
  Planarity :  0.005   0.053   1230
  Dihedral  :  7.567  66.810   1014
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.96 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.28), residues: 912
  helix:  1.85 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -1.77 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 471 
 TYR   0.014   0.001   TYR B 140 
 PHE   0.012   0.001   PHE B 279 
 TRP   0.015   0.001   TRP B 121 
 HIS   0.004   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7375)
  covalent geometry    : angle       0.51492 (10033)
  hydrogen bonds       : bond        0.05824 (  528)
  hydrogen bonds       : angle       3.90576 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8290 (mtp) cc_final: 0.8033 (ttm)
REVERT: A  121 TRP cc_start: 0.7114 (t60) cc_final: 0.6747 (t60)
REVERT: A  266 THR cc_start: 0.8002 (p) cc_final: 0.7768 (t)
REVERT: A  313 ASP cc_start: 0.7885 (p0) cc_final: 0.7554 (p0)
REVERT: A  314 PHE cc_start: 0.6567 (t80) cc_final: 0.5994 (m-80)
REVERT: A  349 MET cc_start: 0.6220 (ptp) cc_final: 0.5575 (mmt)
REVERT: B  183 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5759 (mttp)
REVERT: B  295 TRP cc_start: 0.6779 (t-100) cc_final: 0.6510 (t60)
REVERT: B  307 LYS cc_start: 0.7443 (ttmt) cc_final: 0.6959 (pttt)
REVERT: B  347 GLN cc_start: 0.6402 (mt0) cc_final: 0.6099 (tp40)
REVERT: B  363 ARG cc_start: 0.6263 (pmt170) cc_final: 0.5454 (pmt-80)
  outliers start: 10
  outliers final: 6
  residues processed: 91
  average time/residue: 0.8836
  time to fit residues: 86.9416
Evaluate side-chains
  90 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  483 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.153358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.117666 restraints weight = 20011.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.84
r_work: 0.3297 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7375  Z= 0.187
  Angle     :  0.572  11.142  10033  Z= 0.307
  Chirality :  0.040   0.186   1175
  Planarity :  0.006   0.054   1230
  Dihedral  :  7.831  67.562   1014
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 11.23 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.28), residues: 912
  helix:  1.52 (0.19), residues: 695
  sheet:  None (None), residues: 0
  loop : -2.01 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 471 
 TYR   0.018   0.002   TYR A 499 
 PHE   0.019   0.002   PHE B 438 
 TRP   0.014   0.001   TRP B 121 
 HIS   0.006   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7375)
  covalent geometry    : angle       0.57217 (10033)
  hydrogen bonds       : bond        0.06705 (  528)
  hydrogen bonds       : angle       4.00463 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8370 (mtp) cc_final: 0.8105 (ttm)
REVERT: A  121 TRP cc_start: 0.7138 (t60) cc_final: 0.6749 (t60)
REVERT: A  313 ASP cc_start: 0.7964 (p0) cc_final: 0.7642 (p0)
REVERT: A  314 PHE cc_start: 0.6534 (t80) cc_final: 0.6032 (m-80)
REVERT: B  183 LYS cc_start: 0.6096 (OUTLIER) cc_final: 0.5798 (mttp)
REVERT: B  295 TRP cc_start: 0.6770 (t-100) cc_final: 0.6512 (t60)
REVERT: B  307 LYS cc_start: 0.7500 (ttmt) cc_final: 0.7009 (pttt)
REVERT: B  363 ARG cc_start: 0.6225 (pmt170) cc_final: 0.5440 (pmt-80)
  outliers start: 11
  outliers final: 8
  residues processed: 87
  average time/residue: 0.8638
  time to fit residues: 81.5493
Evaluate side-chains
  89 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  483 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0000
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.156634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.121105 restraints weight = 20030.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.84
r_work: 0.3338 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7375  Z= 0.128
  Angle     :  0.511  11.106  10033  Z= 0.273
  Chirality :  0.037   0.138   1175
  Planarity :  0.005   0.052   1230
  Dihedral  :  7.574  65.794   1014
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.17 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.28), residues: 912
  helix:  1.89 (0.19), residues: 697
  sheet:  None (None), residues: 0
  loop : -1.77 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 471 
 TYR   0.012   0.001   TYR B 140 
 PHE   0.012   0.001   PHE A 280 
 TRP   0.015   0.001   TRP B 121 
 HIS   0.004   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7375)
  covalent geometry    : angle       0.51133 (10033)
  hydrogen bonds       : bond        0.05654 (  528)
  hydrogen bonds       : angle       3.88429 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8303 (mtp) cc_final: 0.8024 (ttm)
REVERT: A  121 TRP cc_start: 0.7106 (t60) cc_final: 0.6712 (t60)
REVERT: A  266 THR cc_start: 0.8022 (p) cc_final: 0.7773 (t)
REVERT: A  313 ASP cc_start: 0.7933 (p0) cc_final: 0.7575 (p0)
REVERT: B  183 LYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5765 (mttp)
REVERT: B  295 TRP cc_start: 0.6768 (t-100) cc_final: 0.6518 (t60)
REVERT: B  307 LYS cc_start: 0.7477 (ttmt) cc_final: 0.6993 (pttt)
REVERT: B  363 ARG cc_start: 0.6311 (pmt170) cc_final: 0.5507 (pmt-80)
  outliers start: 9
  outliers final: 4
  residues processed: 88
  average time/residue: 0.9009
  time to fit residues: 85.7959
Evaluate side-chains
  86 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  312 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 83 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN
B 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.158751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.123022 restraints weight = 20051.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.85
r_work: 0.3366 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7375  Z= 0.116
  Angle     :  0.496  11.069  10033  Z= 0.262
  Chirality :  0.036   0.146   1175
  Planarity :  0.005   0.054   1230
  Dihedral  :  7.350  67.645   1014
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 13.24 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.29), residues: 912
  helix:  2.13 (0.19), residues: 698
  sheet:  None (None), residues: 0
  loop : -1.69 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 471 
 TYR   0.010   0.001   TYR A 275 
 PHE   0.012   0.001   PHE A 279 
 TRP   0.016   0.001   TRP B 121 
 HIS   0.010   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7375)
  covalent geometry    : angle       0.49613 (10033)
  hydrogen bonds       : bond        0.05061 (  528)
  hydrogen bonds       : angle       3.78209 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8293 (mtp) cc_final: 0.8006 (ttm)
REVERT: A  121 TRP cc_start: 0.7085 (t60) cc_final: 0.6691 (t60)
REVERT: A  266 THR cc_start: 0.7989 (p) cc_final: 0.7762 (t)
REVERT: A  313 ASP cc_start: 0.7933 (p0) cc_final: 0.7576 (p0)
REVERT: A  349 MET cc_start: 0.6292 (ptp) cc_final: 0.5647 (mmt)
REVERT: B  183 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5748 (mttm)
REVERT: B  295 TRP cc_start: 0.6607 (t-100) cc_final: 0.6363 (t60)
REVERT: B  307 LYS cc_start: 0.7436 (ttmt) cc_final: 0.6970 (pttt)
REVERT: B  347 GLN cc_start: 0.6279 (mt0) cc_final: 0.6007 (tp40)
REVERT: B  363 ARG cc_start: 0.6410 (pmt170) cc_final: 0.5561 (pmt-80)
  outliers start: 6
  outliers final: 3
  residues processed: 91
  average time/residue: 0.9889
  time to fit residues: 96.9559
Evaluate side-chains
  90 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  312 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0670
   chunk 43 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.7724

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN
B 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.158493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.122790 restraints weight = 19957.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 1.85
r_work: 0.3363 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7375  Z= 0.121
  Angle     :  0.495  11.075  10033  Z= 0.261
  Chirality :  0.037   0.163   1175
  Planarity :  0.005   0.050   1230
  Dihedral  :  7.363  65.856   1014
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 13.77 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.29), residues: 912
  helix:  2.16 (0.19), residues: 698
  sheet:  None (None), residues: 0
  loop : -1.68 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 471 
 TYR   0.011   0.001   TYR B 179 
 PHE   0.011   0.001   PHE A 279 
 TRP   0.014   0.001   TRP B 121 
 HIS   0.006   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7375)
  covalent geometry    : angle       0.49506 (10033)
  hydrogen bonds       : bond        0.05151 (  528)
  hydrogen bonds       : angle       3.75038 ( 1551)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8308 (mtp) cc_final: 0.8021 (ttm)
REVERT: A  121 TRP cc_start: 0.7055 (t60) cc_final: 0.6675 (t60)
REVERT: A  266 THR cc_start: 0.8026 (p) cc_final: 0.7763 (t)
REVERT: A  349 MET cc_start: 0.6290 (ptp) cc_final: 0.5651 (mmt)
REVERT: B  183 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5697 (mttm)
REVERT: B  295 TRP cc_start: 0.6598 (t-100) cc_final: 0.6355 (t60)
REVERT: B  307 LYS cc_start: 0.7443 (ttmt) cc_final: 0.6981 (pttt)
REVERT: B  347 GLN cc_start: 0.6237 (mt0) cc_final: 0.5964 (tp40)
REVERT: B  363 ARG cc_start: 0.6362 (pmt170) cc_final: 0.5554 (pmt-80)
  outliers start: 5
  outliers final: 3
  residues processed: 87
  average time/residue: 1.0308
  time to fit residues: 96.2225
Evaluate side-chains
  88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  312 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN
B 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.157437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.121465 restraints weight = 20057.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.86
r_work: 0.3345 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7375  Z= 0.132
  Angle     :  0.506  11.103  10033  Z= 0.268
  Chirality :  0.037   0.146   1175
  Planarity :  0.005   0.052   1230
  Dihedral  :  7.396  65.357   1014
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 13.50 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.28), residues: 912
  helix:  2.08 (0.19), residues: 698
  sheet:  None (None), residues: 0
  loop : -1.73 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 471 
 TYR   0.010   0.001   TYR A 275 
 PHE   0.013   0.001   PHE B 279 
 TRP   0.021   0.001   TRP B 121 
 HIS   0.005   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7375)
  covalent geometry    : angle       0.50623 (10033)
  hydrogen bonds       : bond        0.05418 (  528)
  hydrogen bonds       : angle       3.75711 ( 1551)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4809.08 seconds
wall clock time: 81 minutes 58.88 seconds (4918.88 seconds total)