Starting phenix.real_space_refine
on Thu Mar  6 08:37:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5ttp_8467/03_2025/5ttp_8467.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5ttp_8467/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5ttp_8467/03_2025/5ttp_8467.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5ttp_8467/03_2025/5ttp_8467.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5ttp_8467/03_2025/5ttp_8467.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5ttp_8467/03_2025/5ttp_8467.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'HIS:plan': 8, 'TYR:plan': 13, 'ASN:plan1': 20, 'TRP:plan': 4, 'ASP:plan': 28, 'PHE:plan': 22, 'GLU:plan': 28, 'ARG:plan': 38}
          Unresolved non-hydrogen planarities: 841
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.79, per 1000 atoms: 0.85
  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: 1.93
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 0.64
  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: 1.94

  Time building geometry restraints manager: 2.19 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: 0.04
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:             0.490
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.900
  Find NCS groups from input model:        0.120
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.480
-------------------------------------------------------------------------------
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= 0.459
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.000   0.000   TRP A  17 
 PHE   0.000   0.000   PHE A  13 
 TYR   0.000   0.000   TYR A  83 

*********************** 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  : 0.298 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0317
  time to fit residues: 1.8229
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  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.0770
   chunk 84 optimal weight:   30.0000
   chunk 47 optimal weight:   40.0000
   chunk 28 optimal weight:   30.0000
   chunk 57 optimal weight:    0.0870
   chunk 45 optimal weight:   30.0000
   chunk 87 optimal weight:    0.0980
   chunk 33 optimal weight:   30.0000
   chunk 53 optimal weight:   50.0000
   chunk 65 optimal weight:    9.9990
   chunk 101 optimal weight:   30.0000
   overall best weight:    8.0522
-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.064801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.055115 restraints weight = 30796.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.055338 restraints weight = 28935.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.055338 restraints weight = 27547.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.4506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   5614  Z= 0.242
  Angle     :  0.750   7.501   7812  Z= 0.457
  Chirality :  0.045   0.175   1064
  Planarity :  0.004   0.018   1136
  Dihedral  :  7.611  34.629   1136
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.23 %
    Favored  : 92.42 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.23), residues: 1134
  helix: -0.87 (0.17), residues: 686
  sheet: -3.71 (0.49), residues: 44
  loop : -2.29 (0.31), residues: 404

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

*********************** 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  : 0.300 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0286
  time to fit residues: 1.7065
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  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    8.9990
   chunk 57 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 98 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:   30.0000
   chunk 111 optimal weight:    6.9990
   chunk 100 optimal weight:    8.9990
   chunk 59 optimal weight:   20.0000
   overall best weight:    7.3992
-------------------------------------------------------------------------------
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 = 0.3275 r_free = 0.3275 target = 0.061955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.053138 restraints weight = 30197.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.053365 restraints weight = 28120.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.053488 restraints weight = 26451.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.6616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.013   5614  Z= 0.207
  Angle     :  0.643   8.130   7812  Z= 0.384
  Chirality :  0.044   0.230   1064
  Planarity :  0.003   0.012   1136
  Dihedral  :  6.308  36.687   1136
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 10.76 %
    Favored  : 88.54 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.24), residues: 1134
  helix:  0.25 (0.19), residues: 700
  sheet: -3.65 (0.48), residues: 64
  loop : -2.52 (0.32), residues: 370

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

*********************** 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  : 0.292 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0283
  time to fit residues: 1.7008
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  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:   30.0000
   chunk 78 optimal weight:   20.0000
   chunk 109 optimal weight:   40.0000
   chunk 46 optimal weight:    6.9990
   chunk 96 optimal weight:   30.0000
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 4 optimal weight:   20.0000
   chunk 93 optimal weight:    4.9990
   chunk 83 optimal weight:    0.0030
   chunk 98 optimal weight:   20.0000
   overall best weight:    5.1998
-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.062885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.054116 restraints weight = 29948.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.054320 restraints weight = 27759.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.054560 restraints weight = 26208.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.7473

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= 0.149
  Angle     :  0.535   6.736   7812  Z= 0.318
  Chirality :  0.042   0.188   1064
  Planarity :  0.002   0.010   1136
  Dihedral  :  5.466  31.000   1136
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 10.41 %
    Favored  : 89.07 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.26), residues: 1134
  helix:  1.58 (0.19), residues: 712
  sheet: -3.69 (0.52), residues: 64
  loop : -2.32 (0.33), residues: 358

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

*********************** 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  : 0.300 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0289
  time to fit residues: 1.7225
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  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:   20.0000
   chunk 60 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 71 optimal weight:   20.0000
   chunk 91 optimal weight:    9.9990
   chunk 58 optimal weight:    0.8980
   chunk 100 optimal weight:   20.0000
   chunk 9 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 98 optimal weight:   20.0000
   chunk 13 optimal weight:    4.9990
   overall best weight:    6.7788
-------------------------------------------------------------------------------
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 = 0.3254 r_free = 0.3254 target = 0.060978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.049058 restraints weight = 31976.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.049349 restraints weight = 29696.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.049605 restraints weight = 27953.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.8340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.011   5614  Z= 0.185
  Angle     :  0.570   6.568   7812  Z= 0.341
  Chirality :  0.043   0.203   1064
  Planarity :  0.002   0.013   1136
  Dihedral  :  5.773  32.613   1136
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.92
  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 : 7.69 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.25), residues: 1134
  helix:  1.39 (0.19), residues: 690
  sheet: -3.00 (0.97), residues: 20
  loop : -2.57 (0.30), residues: 424

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

*********************** 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  : 0.295 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0287
  time to fit residues: 1.7152
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  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 25 optimal weight:   30.0000
   chunk 82 optimal weight:   30.0000
   chunk 23 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 4 optimal weight:   30.0000
   chunk 5 optimal weight:   40.0000
   chunk 62 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 99 optimal weight:   30.0000
   chunk 58 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    7.3992
-------------------------------------------------------------------------------
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 = 0.3233 r_free = 0.3233 target = 0.060004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.048320 restraints weight = 32876.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.048651 restraints weight = 30163.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.048831 restraints weight = 28125.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.9290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   5614  Z= 0.191
  Angle     :  0.564   6.413   7812  Z= 0.342
  Chirality :  0.043   0.191   1064
  Planarity :  0.002   0.012   1136
  Dihedral  :  5.814  29.150   1136
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 13.23 %
    Favored  : 86.42 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.25), residues: 1134
  helix:  1.19 (0.19), residues: 710
  sheet: -4.45 (0.51), residues: 40
  loop : -3.00 (0.29), residues: 384

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

*********************** 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  : 0.302 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0297
  time to fit residues: 1.8064
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  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 73 optimal weight:   30.0000
   chunk 63 optimal weight:   30.0000
   chunk 6 optimal weight:    7.9990
   chunk 102 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 103 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   chunk 106 optimal weight:   30.0000
   chunk 27 optimal weight:    0.0370
   overall best weight:    6.9666
-------------------------------------------------------------------------------
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 = 0.3185 r_free = 0.3185 target = 0.056800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.045944 restraints weight = 34786.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.046196 restraints weight = 32126.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.046465 restraints weight = 30087.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          1.0007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.012   5614  Z= 0.189
  Angle     :  0.559   6.651   7812  Z= 0.338
  Chirality :  0.043   0.171   1064
  Planarity :  0.002   0.013   1136
  Dihedral  :  5.595  30.414   1136
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 12.35 %
    Favored  : 87.30 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.25), residues: 1134
  helix:  1.24 (0.19), residues: 714
  sheet: -4.64 (0.38), residues: 44
  loop : -3.00 (0.30), residues: 376

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

*********************** 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  : 0.293 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0285
  time to fit residues: 1.7092
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  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 77 optimal weight:   20.0000
   chunk 69 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 108 optimal weight:   50.0000
   chunk 49 optimal weight:   30.0000
   chunk 62 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 102 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   overall best weight:    4.9188
-------------------------------------------------------------------------------
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 = 0.3205 r_free = 0.3205 target = 0.057740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.046527 restraints weight = 33961.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.046814 restraints weight = 30905.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.047110 restraints weight = 28782.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          1.0231

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= 0.137
  Angle     :  0.494   5.927   7812  Z= 0.295
  Chirality :  0.042   0.150   1064
  Planarity :  0.002   0.011   1136
  Dihedral  :  5.173  29.183   1136
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 13.05 %
    Favored  : 86.77 %
  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 : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.26), residues: 1134
  helix:  1.74 (0.19), residues: 722
  sheet: -5.07 (0.31), residues: 44
  loop : -3.11 (0.30), residues: 368

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

*********************** 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  : 0.301 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0310
  time to fit residues: 1.8502
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  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    0.0570
   chunk 56 optimal weight:   30.0000
   chunk 20 optimal weight:    0.1980
   chunk 64 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 40 optimal weight:   30.0000
   chunk 90 optimal weight:   20.0000
   chunk 102 optimal weight:    0.0170
   chunk 7 optimal weight:   30.0000
   chunk 49 optimal weight:   30.0000
   chunk 94 optimal weight:   30.0000
   overall best weight:    3.2542
-------------------------------------------------------------------------------
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 = 0.3232 r_free = 0.3232 target = 0.058992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.047734 restraints weight = 33529.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.047951 restraints weight = 31273.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.048187 restraints weight = 29613.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          1.0426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.011   5614  Z= 0.103
  Angle     :  0.444   5.768   7812  Z= 0.262
  Chirality :  0.041   0.131   1064
  Planarity :  0.002   0.010   1136
  Dihedral  :  4.581  28.008   1136
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.64 %
    Favored  : 88.18 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.27), residues: 1134
  helix:  2.20 (0.19), residues: 742
  sheet: -5.20 (0.29), residues: 44
  loop : -3.06 (0.32), residues: 348

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

*********************** 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  : 0.307 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0280
  time to fit residues: 1.6933
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  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 7 optimal weight:   30.0000
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   chunk 84 optimal weight:   30.0000
   chunk 95 optimal weight:    0.0270
   chunk 28 optimal weight:   30.0000
   chunk 31 optimal weight:   20.0000
   chunk 57 optimal weight:   20.0000
   chunk 52 optimal weight:   30.0000
   chunk 39 optimal weight:    0.0270
   chunk 15 optimal weight:   20.0000
   overall best weight:    8.4106
-------------------------------------------------------------------------------
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 = 0.3177 r_free = 0.3177 target = 0.056318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.045400 restraints weight = 34687.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.045675 restraints weight = 32198.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.045853 restraints weight = 30204.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          1.0727

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= 0.210
  Angle     :  0.554   6.314   7812  Z= 0.337
  Chirality :  0.042   0.151   1064
  Planarity :  0.002   0.012   1136
  Dihedral  :  5.423  29.216   1136
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.65
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.25), residues: 1134
  helix:  1.28 (0.18), residues: 726
  sheet: -5.59 (0.24), residues: 40
  loop : -3.32 (0.31), residues: 368

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

********************** 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  : 0.290 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0279
  time to fit residues: 1.6895
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  : 0.293 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 68 optimal weight:   20.0000
   chunk 21 optimal weight:   20.0000
   chunk 65 optimal weight:    7.9990
   chunk 7 optimal weight:   30.0000
   chunk 74 optimal weight:   30.0000
   chunk 38 optimal weight:   30.0000
   chunk 19 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   chunk 79 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    6.9990
-------------------------------------------------------------------------------
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 = 0.3170 r_free = 0.3170 target = 0.055896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.044676 restraints weight = 33182.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.044989 restraints weight = 30381.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.045203 restraints weight = 28245.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          1.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   5614  Z= 0.183
  Angle     :  0.536   6.557   7812  Z= 0.325
  Chirality :  0.042   0.151   1064
  Planarity :  0.002   0.013   1136
  Dihedral  :  5.369  29.701   1136
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 15.34 %
    Favored  : 84.48 %
  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 : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.26), residues: 1134
  helix:  1.39 (0.19), residues: 726
  sheet: -5.49 (0.33), residues: 24
  loop : -3.52 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  17 
 PHE   0.000   0.000   PHE A  13 
 TYR   0.000   0.000   TYR A  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1118.06 seconds
wall clock time: 19 minutes 56.03 seconds (1196.03 seconds total)