Starting phenix.real_space_refine
on Wed Sep 17 05:49:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5ttp_8467/09_2025/5ttp_8467.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5ttp_8467/09_2025/5ttp_8467.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5ttp_8467/09_2025/5ttp_8467.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5ttp_8467/09_2025/5ttp_8467.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5ttp_8467/09_2025/5ttp_8467.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5ttp_8467/09_2025/5ttp_8467.map"
  }
  resolution = 4.8
  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=   0.000 sd=   0.004
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: 3
    Type Number    sf(0)   Gaussians
     C    3340      2.51       5
     N    1138      2.21       5
     O    1138      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5616
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 2808
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 484}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
          Unresolved chain link angles: 13
          Unresolved non-hydrogen bonds: 1665
          Unresolved non-hydrogen angles: 2123
          Unresolved non-hydrogen dihedrals: 1347
          Unresolved non-hydrogen chiralities: 188
          Planarities with less than four sites: {'GLN:plan1': 24, 'PHE:plan': 22, 'ARG:plan': 38, 'TRP:plan': 4, 'ASN:plan1': 20, 'ASP:plan': 28, 'TYR:plan': 13, 'HIS:plan': 8, 'GLU:plan': 28}
          Unresolved non-hydrogen planarities: 841
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.22, per 1000 atoms: 0.40
  Number of scatterers: 5616
  At special positions: 0
  Unit cell: (77.49, 71.34, 135.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1138      8.00
     N    1138      7.00
     C    3340      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: 0.66
  Conformation dependent library (CDL) restraints added in 484.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 2 sheets defined
      67.8% alpha, 2.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 17
    Processing helix  chain 'A' and resid 20 through 54
      removed outlier: 3.872A  pdb=" N   LYS A  24 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   SER A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP A  41 " --> pdb=" O   ASN A  37 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 58 through 109
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.790A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 130
      removed outlier: 4.035A  pdb=" N   ARG A 127 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ILE A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 161
      removed outlier: 3.807A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLU A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLY A 150 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA A 151 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 214
      Proline residue:  A 176  - end of helix
      removed outlier: 4.388A  pdb=" N   GLN A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   VAL A 203 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   HIS A 214 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 221
    Processing helix  chain 'A' and resid 223 through 276
      removed outlier: 4.593A  pdb=" N   THR A 227 " --> pdb=" O   GLN A 223 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      Proline residue:  A 273  - end of helix
    Processing helix  chain 'A' and resid 280 through 296
      removed outlier: 4.380A  pdb=" N   ILE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   VAL A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE A 288 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER A 289 " --> pdb=" O   THR A 285 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER A 290 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 321
      removed outlier: 3.686A  pdb=" N   LEU A 301 " --> pdb=" O   PRO A 297 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ARG A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLY A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   MET A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   CYS A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 4.191A  pdb=" N   SER A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.871A  pdb=" N   TYR A 410 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 417
    Processing helix  chain 'A' and resid 446 through 455
    Processing helix  chain 'A' and resid 456 through 458
      No H-bonds generated for 'chain 'A' and resid 456 through 458'
    Processing helix  chain 'A' and resid 483 through 497
      removed outlier: 4.940A  pdb=" N   ALA A 494 " --> pdb=" O   ALA A 490 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 495 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A 496 " --> pdb=" O   ALA A 492 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ARG A 497 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 527
    Processing helix  chain 'A' and resid 538 through 545
      removed outlier: 4.571A  pdb=" N   ILE A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU A 543 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   LYS A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 569
      removed outlier: 4.444A  pdb=" N   GLU A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 579
      removed outlier: 4.198A  pdb=" N   ALA A 573 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 17
    Processing helix  chain 'B' and resid 20 through 54
      removed outlier: 3.872A  pdb=" N   LYS B  24 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   SER B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP B  41 " --> pdb=" O   ASN B  37 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 58 through 109
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 3.790A  pdb=" N   PHE B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 130
      removed outlier: 4.035A  pdb=" N   ARG B 127 " --> pdb=" O   THR B 123 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ILE B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 161
      removed outlier: 3.807A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLU B 149 " --> pdb=" O   THR B 145 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLY B 150 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B 151 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 214
      Proline residue:  B 176  - end of helix
      removed outlier: 4.387A  pdb=" N   GLN B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   VAL B 203 " --> pdb=" O   THR B 199 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   HIS B 214 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 221
    Processing helix  chain 'B' and resid 223 through 276
      removed outlier: 4.594A  pdb=" N   THR B 227 " --> pdb=" O   GLN B 223 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
      Proline residue:  B 273  - end of helix
    Processing helix  chain 'B' and resid 280 through 296
      removed outlier: 4.380A  pdb=" N   ILE B 284 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   VAL B 286 " --> pdb=" O   GLY B 282 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL B 287 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE B 288 " --> pdb=" O   ILE B 284 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER B 289 " --> pdb=" O   THR B 285 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER B 290 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 321
      removed outlier: 3.686A  pdb=" N   LEU B 301 " --> pdb=" O   PRO B 297 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   THR B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG B 310 " --> pdb=" O   ALA B 306 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLY B 311 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   MET B 312 " --> pdb=" O   PHE B 308 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   CYS B 315 " --> pdb=" O   GLY B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 4.191A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
      removed outlier: 3.871A  pdb=" N   TYR B 410 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 446 through 455
    Processing helix  chain 'B' and resid 456 through 458
      No H-bonds generated for 'chain 'B' and resid 456 through 458'
    Processing helix  chain 'B' and resid 483 through 497
      removed outlier: 4.940A  pdb=" N   ALA B 494 " --> pdb=" O   ALA B 490 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU B 495 " --> pdb=" O   ILE B 491 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU B 496 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ARG B 497 " --> pdb=" O   ARG B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 527
    Processing helix  chain 'B' and resid 538 through 545
      removed outlier: 4.572A  pdb=" N   ILE B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU B 543 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LYS B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 569
      removed outlier: 4.445A  pdb=" N   GLU B 567 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 579
      removed outlier: 4.199A  pdb=" N   ALA B 573 " --> pdb=" O   ARG B 569 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 375
      removed outlier: 5.555A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   VAL A 375 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ILE A 548 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ARG A 559 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 372 through 375
      removed outlier: 5.555A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)

    508 hydrogen bonds defined for protein.
    1512 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: 0.79

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 1138
        1.29 -     1.36: 1136
        1.36 -     1.43: 1
        1.43 -     1.50: 1147
        1.50 -     1.57: 2192
  Bond restraints: 5614
  Sorted by residual:
  bond pdb=" CA  LEU B  36 "
       pdb=" C   LEU B  36 "
    ideal  model  delta    sigma   weight residual
    1.522  1.574 -0.051 1.37e-02 5.33e+03 1.41e+01
  bond pdb=" CA  LEU A  36 "
       pdb=" C   LEU A  36 "
    ideal  model  delta    sigma   weight residual
    1.522  1.573 -0.051 1.37e-02 5.33e+03 1.39e+01
  bond pdb=" CA  GLN B 326 "
       pdb=" C   GLN B 326 "
    ideal  model  delta    sigma   weight residual
    1.525  1.492  0.033 1.28e-02 6.10e+03 6.53e+00
  bond pdb=" CA  GLN A 326 "
       pdb=" C   GLN A 326 "
    ideal  model  delta    sigma   weight residual
    1.525  1.492  0.033 1.28e-02 6.10e+03 6.52e+00
  bond pdb=" CA  LEU B 211 "
       pdb=" C   LEU B 211 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.027 1.28e-02 6.10e+03 4.35e+00
  ... (remaining 5609 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 7347
        2.59 -     5.19: 413
        5.19 -     7.78: 35
        7.78 -    10.37: 15
       10.37 -    12.97: 2
  Bond angle restraints: 7812
  Sorted by residual:
  angle pdb=" C   ILE A  20 "
        pdb=" N   ALA A  21 "
        pdb=" CA  ALA A  21 "
      ideal   model   delta    sigma   weight residual
     119.78  129.54   -9.76 1.24e+00 6.50e-01 6.20e+01
  angle pdb=" C   ILE B  20 "
        pdb=" N   ALA B  21 "
        pdb=" CA  ALA B  21 "
      ideal   model   delta    sigma   weight residual
     119.78  129.48   -9.70 1.24e+00 6.50e-01 6.12e+01
  angle pdb=" N   VAL A 173 "
        pdb=" CA  VAL A 173 "
        pdb=" C   VAL A 173 "
      ideal   model   delta    sigma   weight residual
     111.00  103.01    7.99 1.09e+00 8.42e-01 5.37e+01
  angle pdb=" N   VAL B 173 "
        pdb=" CA  VAL B 173 "
        pdb=" C   VAL B 173 "
      ideal   model   delta    sigma   weight residual
     111.00  103.04    7.96 1.09e+00 8.42e-01 5.34e+01
  angle pdb=" N   GLN A 326 "
        pdb=" CA  GLN A 326 "
        pdb=" C   GLN A 326 "
      ideal   model   delta    sigma   weight residual
     108.20   98.07   10.13 1.71e+00 3.42e-01 3.51e+01
  ... (remaining 7807 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.35: 2934
       11.35 -    22.70: 268
       22.70 -    34.04: 46
       34.04 -    45.39: 14
       45.39 -    56.74: 2
  Dihedral angle restraints: 3264
    sinusoidal: 0
      harmonic: 3264
  Sorted by residual:
  dihedral pdb=" CA  MET B 111 "
           pdb=" C   MET B 111 "
           pdb=" N   PRO B 112 "
           pdb=" CA  PRO B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -123.26  -56.74     0      5.00e+00 4.00e-02 1.29e+02
  dihedral pdb=" CA  MET A 111 "
           pdb=" C   MET A 111 "
           pdb=" N   PRO A 112 "
           pdb=" CA  PRO A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -123.31  -56.69     0      5.00e+00 4.00e-02 1.29e+02
  dihedral pdb=" CA  GLU A 325 "
           pdb=" C   GLU A 325 "
           pdb=" N   GLN A 326 "
           pdb=" CA  GLN A 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.29   44.71     0      5.00e+00 4.00e-02 7.99e+01
  ... (remaining 3261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 667
       0.054 -    0.108: 309
       0.108 -    0.162: 75
       0.162 -    0.217: 9
       0.217 -    0.271: 4
  Chirality restraints: 1064
  Sorted by residual:
  chirality pdb=" CA  PRO B 112 "
            pdb=" N   PRO B 112 "
            pdb=" C   PRO B 112 "
            pdb=" CB  PRO B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  PRO A 112 "
            pdb=" N   PRO A 112 "
            pdb=" C   PRO A 112 "
            pdb=" CB  PRO A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CA  GLU A 325 "
            pdb=" N   GLU A 325 "
            pdb=" C   GLU A 325 "
            pdb=" CB  GLU A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1061 not shown)

  Planarity restraints: 1136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 100 "   -0.014 2.00e-02 2.50e+03   2.84e-02 8.08e+00
        pdb=" C   MET A 100 "    0.049 2.00e-02 2.50e+03
        pdb=" O   MET A 100 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ARG A 101 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 100 "    0.014 2.00e-02 2.50e+03   2.83e-02 8.00e+00
        pdb=" C   MET B 100 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   MET B 100 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ARG B 101 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 303 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.82e+00
        pdb=" C   ASN A 303 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ASN A 303 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A 304 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1133 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 268
        2.65 -     3.21: 7019
        3.21 -     3.77: 8714
        3.77 -     4.34: 10473
        4.34 -     4.90: 14646
  Nonbonded interactions: 41120
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 435 "
            pdb=" N   TYR A 439 "
     model   vdw
     2.086 3.120
  nonbonded pdb=" O   ASN B 435 "
            pdb=" N   TYR B 439 "
     model   vdw
     2.087 3.120
  nonbonded pdb=" O   PHE A  56 "
            pdb=" N   ARG A  61 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" O   PHE B  56 "
            pdb=" N   ARG B  61 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" O   MET B 196 "
            pdb=" N   THR B 199 "
     model   vdw
     2.227 3.120
  ... (remaining 41115 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.290
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6012
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      :  0.006   0.051   5614  Z= 0.463
  Angle     :  1.358  12.968   7812  Z= 0.898
  Chirality :  0.063   0.271   1064
  Planarity :  0.006   0.028   1136
  Dihedral  : 11.703  56.740   1136
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 24.92
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 14.11 %
    Favored  : 85.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 1.62 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.87 (0.16), residues: 1134
  helix: -4.21 (0.10), residues: 630
  sheet: -3.46 (0.39), residues: 44
  loop : -3.22 (0.23), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00630 ( 5614)
  covalent geometry    : angle       1.35844 ( 7812)
  hydrogen bonds       : bond        0.23360 (  508)
  hydrogen bonds       : angle      12.70726 ( 1512)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.094 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0139
  time to fit residues: 0.7445
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:   50.0000
   chunk 49 optimal weight:    0.0980
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:   50.0000
   chunk 5 optimal weight:   30.0000
   chunk 33 optimal weight:   30.0000
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:   30.0000
   chunk 100 optimal weight:   40.0000
   chunk 106 optimal weight:   30.0000
   overall best weight:   13.6192
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.060651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.051843 restraints weight = 31935.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.051931 restraints weight = 30469.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.051931 restraints weight = 29555.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.051931 restraints weight = 29555.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.051931 restraints weight = 29555.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   5614  Z= 0.367
  Angle     :  0.908   9.903   7812  Z= 0.559
  Chirality :  0.047   0.202   1064
  Planarity :  0.006   0.021   1136
  Dihedral  :  9.069  41.515   1136
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 10.58 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 1.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.17 (0.22), residues: 1134
  helix: -1.51 (0.17), residues: 686
  sheet: -3.39 (0.59), residues: 44
  loop : -2.81 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 5614)
  covalent geometry    : angle       0.90783 ( 7812)
  hydrogen bonds       : bond        0.06588 (  508)
  hydrogen bonds       : angle       6.66432 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.092 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0134
  time to fit residues: 0.7282
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:   30.0000
   chunk 74 optimal weight:   30.0000
   chunk 87 optimal weight:   20.0000
   chunk 21 optimal weight:    0.5980
   chunk 95 optimal weight:    5.9990
   chunk 31 optimal weight:   20.0000
   chunk 67 optimal weight:    1.9990
   chunk 99 optimal weight:   30.0000
   chunk 38 optimal weight:   30.0000
   chunk 102 optimal weight:    0.0980
   chunk 111 optimal weight:    4.9990
   overall best weight:    2.7386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.064927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.055479 restraints weight = 30962.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.055717 restraints weight = 29006.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.055864 restraints weight = 27433.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.056030 restraints weight = 26314.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.056109 restraints weight = 25370.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.6237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.009   5614  Z= 0.119
  Angle     :  0.543   6.608   7812  Z= 0.318
  Chirality :  0.043   0.200   1064
  Planarity :  0.002   0.010   1136
  Dihedral  :  5.814  34.588   1136
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  9.17 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.25), residues: 1134
  helix:  0.92 (0.19), residues: 720
  sheet: -3.60 (0.58), residues: 44
  loop : -2.35 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00158 ( 5614)
  covalent geometry    : angle       0.54278 ( 7812)
  hydrogen bonds       : bond        0.03732 (  508)
  hydrogen bonds       : angle       4.36902 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.090 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0128
  time to fit residues: 0.7063
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:   30.0000
   chunk 39 optimal weight:    0.0670
   chunk 41 optimal weight:   20.0000
   chunk 88 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 91 optimal weight:   30.0000
   chunk 55 optimal weight:    8.9990
   chunk 110 optimal weight:   30.0000
   chunk 43 optimal weight:   40.0000
   chunk 95 optimal weight:    0.0670
   chunk 0 optimal weight:   30.0000
   overall best weight:    3.5860
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.064020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.055184 restraints weight = 30011.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.055411 restraints weight = 27684.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.055660 restraints weight = 26049.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.055837 restraints weight = 24682.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.055912 restraints weight = 23567.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.7067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   5614  Z= 0.134
  Angle     :  0.508   6.765   7812  Z= 0.299
  Chirality :  0.042   0.197   1064
  Planarity :  0.002   0.010   1136
  Dihedral  :  5.096  31.055   1136
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  9.52 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.26), residues: 1134
  helix:  1.90 (0.19), residues: 718
  sheet: -3.02 (0.58), residues: 64
  loop : -1.92 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00179 ( 5614)
  covalent geometry    : angle       0.50798 ( 7812)
  hydrogen bonds       : bond        0.03624 (  508)
  hydrogen bonds       : angle       3.98539 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.100 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0139
  time to fit residues: 0.7707
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 38 optimal weight:   30.0000
   chunk 75 optimal weight:    5.9990
   chunk 99 optimal weight:   30.0000
   chunk 33 optimal weight:   30.0000
   chunk 103 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 108 optimal weight:   50.0000
   chunk 102 optimal weight:    0.0170
   chunk 93 optimal weight:    1.9990
   overall best weight:    4.2026
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.063684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.054824 restraints weight = 29399.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.055067 restraints weight = 27445.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.055261 restraints weight = 25842.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.055425 restraints weight = 24575.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.055495 restraints weight = 23678.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.7957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   5614  Z= 0.126
  Angle     :  0.492   6.345   7812  Z= 0.290
  Chirality :  0.041   0.177   1064
  Planarity :  0.002   0.011   1136
  Dihedral  :  4.794  26.613   1136
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.11 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.27), residues: 1134
  helix:  2.29 (0.19), residues: 710
  sheet: -3.99 (0.53), residues: 24
  loop : -2.37 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00168 ( 5614)
  covalent geometry    : angle       0.49233 ( 7812)
  hydrogen bonds       : bond        0.03448 (  508)
  hydrogen bonds       : angle       3.70217 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.100 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0133
  time to fit residues: 0.7428
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 40 optimal weight:   30.0000
   chunk 50 optimal weight:   30.0000
   chunk 86 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:   20.0000
   chunk 98 optimal weight:   20.0000
   chunk 75 optimal weight:    1.9990
   chunk 31 optimal weight:   20.0000
   chunk 104 optimal weight:   30.0000
   chunk 48 optimal weight:   30.0000
   overall best weight:    6.3388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.061038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.048970 restraints weight = 31008.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.049209 restraints weight = 29026.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.049208 restraints weight = 27176.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.049208 restraints weight = 27175.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.049208 restraints weight = 27175.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.8706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   5614  Z= 0.178
  Angle     :  0.553   6.713   7812  Z= 0.331
  Chirality :  0.042   0.199   1064
  Planarity :  0.002   0.013   1136
  Dihedral  :  5.481  27.330   1136
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 12.70 %
    Favored  : 87.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.25), residues: 1134
  helix:  1.67 (0.19), residues: 708
  sheet: -4.21 (0.38), residues: 44
  loop : -2.67 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5614)
  covalent geometry    : angle       0.55268 ( 7812)
  hydrogen bonds       : bond        0.04147 (  508)
  hydrogen bonds       : angle       4.32133 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.097 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0139
  time to fit residues: 0.7954
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:   20.0000
   chunk 59 optimal weight:   30.0000
   chunk 55 optimal weight:    0.3980
   chunk 41 optimal weight:   30.0000
   chunk 26 optimal weight:   30.0000
   chunk 68 optimal weight:   20.0000
   chunk 48 optimal weight:   30.0000
   chunk 42 optimal weight:   20.0000
   chunk 4 optimal weight:   30.0000
   chunk 108 optimal weight:   20.0000
   overall best weight:   13.6794
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.054208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.042789 restraints weight = 33049.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.043057 restraints weight = 30018.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 15)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.043275 restraints weight = 27780.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.043510 restraints weight = 26354.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.043635 restraints weight = 25075.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.9779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   5614  Z= 0.343
  Angle     :  0.754   8.861   7812  Z= 0.469
  Chirality :  0.044   0.218   1064
  Planarity :  0.004   0.017   1136
  Dihedral  :  7.349  36.594   1136
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 16.05 %
    Favored  : 83.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 0.54 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.24 (0.23), residues: 1134
  helix: -0.34 (0.18), residues: 704
  sheet: -4.71 (0.46), residues: 40
  loop : -3.24 (0.27), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 5614)
  covalent geometry    : angle       0.75387 ( 7812)
  hydrogen bonds       : bond        0.06000 (  508)
  hydrogen bonds       : angle       5.76322 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.095 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0140
  time to fit residues: 0.8179
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 92 optimal weight:   30.0000
   chunk 18 optimal weight:   30.0000
   chunk 67 optimal weight:    5.9990
   chunk 105 optimal weight:   30.0000
   chunk 91 optimal weight:    0.0040
   chunk 47 optimal weight:   30.0000
   chunk 97 optimal weight:   30.0000
   chunk 64 optimal weight:    9.9990
   chunk 40 optimal weight:   30.0000
   chunk 72 optimal weight:   20.0000
   chunk 70 optimal weight:    7.9990
   overall best weight:    8.8002
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.055651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.044215 restraints weight = 34191.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 14)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.044507 restraints weight = 31015.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.044767 restraints weight = 28811.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.045003 restraints weight = 27088.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.045156 restraints weight = 25752.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          1.0154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   5614  Z= 0.225
  Angle     :  0.619   8.118   7812  Z= 0.376
  Chirality :  0.043   0.202   1064
  Planarity :  0.003   0.013   1136
  Dihedral  :  6.290  30.342   1136
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 14.64 %
    Favored  : 85.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.24), residues: 1134
  helix:  0.41 (0.18), residues: 714
  sheet: -4.55 (0.39), residues: 44
  loop : -3.48 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5614)
  covalent geometry    : angle       0.61915 ( 7812)
  hydrogen bonds       : bond        0.04745 (  508)
  hydrogen bonds       : angle       4.74180 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.103 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0139
  time to fit residues: 0.7720
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:   20.0000
   chunk 84 optimal weight:   30.0000
   chunk 31 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 109 optimal weight:   50.0000
   chunk 14 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 47 optimal weight:   30.0000
   chunk 51 optimal weight:   30.0000
   overall best weight:    5.5388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.057502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.046390 restraints weight = 34750.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 13)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.046640 restraints weight = 31789.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.046937 restraints weight = 29602.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.047101 restraints weight = 28016.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.047302 restraints weight = 26741.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          1.0438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   5614  Z= 0.152
  Angle     :  0.522   6.650   7812  Z= 0.310
  Chirality :  0.042   0.158   1064
  Planarity :  0.002   0.011   1136
  Dihedral  :  5.533  30.390   1136
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 13.93 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.25), residues: 1134
  helix:  1.35 (0.19), residues: 728
  sheet: -4.74 (0.35), residues: 44
  loop : -3.10 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 5614)
  covalent geometry    : angle       0.52244 ( 7812)
  hydrogen bonds       : bond        0.03878 (  508)
  hydrogen bonds       : angle       3.99502 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.106 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0138
  time to fit residues: 0.7770
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 45 optimal weight:   30.0000
   chunk 110 optimal weight:    6.9990
   chunk 106 optimal weight:   30.0000
   chunk 44 optimal weight:   30.0000
   chunk 20 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 21 optimal weight:    0.3980
   chunk 108 optimal weight:   50.0000
   chunk 93 optimal weight:    0.8980
   overall best weight:    4.2586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.058406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.046897 restraints weight = 34383.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.047222 restraints weight = 31442.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.047424 restraints weight = 29192.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.047676 restraints weight = 27664.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.047701 restraints weight = 26309.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          1.0772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   5614  Z= 0.130
  Angle     :  0.473   5.835   7812  Z= 0.281
  Chirality :  0.042   0.140   1064
  Planarity :  0.002   0.012   1136
  Dihedral  :  4.877  29.010   1136
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.58 %
    Favored  : 86.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.27), residues: 1134
  helix:  1.96 (0.19), residues: 742
  sheet: -4.88 (0.32), residues: 44
  loop : -3.20 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00174 ( 5614)
  covalent geometry    : angle       0.47297 ( 7812)
  hydrogen bonds       : bond        0.03487 (  508)
  hydrogen bonds       : angle       3.56089 ( 1512)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.111 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0130
  time to fit residues: 0.7606
Evaluate side-chains
  25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 85 optimal weight:   20.0000
   chunk 62 optimal weight:    0.7980
   chunk 93 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 97 optimal weight:   20.0000
   chunk 94 optimal weight:   20.0000
   chunk 57 optimal weight:   20.0000
   chunk 42 optimal weight:   20.0000
   chunk 109 optimal weight:   50.0000
   overall best weight:    4.8788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.057715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.046578 restraints weight = 33529.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.046855 restraints weight = 31080.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.047091 restraints weight = 29223.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.047251 restraints weight = 27744.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.047453 restraints weight = 26536.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          1.1026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   5614  Z= 0.141
  Angle     :  0.489   6.352   7812  Z= 0.290
  Chirality :  0.041   0.137   1064
  Planarity :  0.002   0.011   1136
  Dihedral  :  5.020  29.067   1136
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.23 %
    Favored  : 86.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.26), residues: 1134
  helix:  1.96 (0.19), residues: 728
  sheet: -5.17 (0.26), residues: 44
  loop : -3.10 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  83 
 PHE   0.000   0.000   PHE A  13 
 TRP   0.000   0.000   TRP A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 5614)
  covalent geometry    : angle       0.48891 ( 7812)
  hydrogen bonds       : bond        0.03663 (  508)
  hydrogen bonds       : angle       3.80525 ( 1512)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 649.34 seconds
wall clock time: 11 minutes 50.33 seconds (710.33 seconds total)