Starting phenix.real_space_refine
on Fri Mar 14 01:05:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x0z_32930/03_2025/7x0z_32930.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x0z_32930/03_2025/7x0z_32930.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x0z_32930/03_2025/7x0z_32930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x0z_32930/03_2025/7x0z_32930.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x0z_32930/03_2025/7x0z_32930.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x0z_32930/03_2025/7x0z_32930.cif"
  }
  resolution = 2.96
  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=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C    5946      2.51       5
     N    1638      2.21       5
     O    1649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9285
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 576, 4597
          Classifications: {'peptide': 576}
          Link IDs: {'PTRANS': 22, 'TRANS': 553}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4624
          Classifications: {'peptide': 580}
          Link IDs: {'PTRANS': 22, 'TRANS': 557}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.04, per 1000 atoms: 0.65
  Number of scatterers: 9285
  At special positions: 0
  Unit cell: (83.83, 78.85, 131.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      44     16.00
     P       6     15.00
     Mg      2     11.99
     O    1649      8.00
     N    1638      7.00
     C    5946      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.11
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      69.1% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 83
      removed outlier: 3.544A  pdb=" N   LEU A  72 " --> pdb=" O   ASN A  68 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU A  81 " --> pdb=" O   TRP A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 124
    Processing helix  chain 'A' and resid 128 through 175
      removed outlier: 3.929A  pdb=" N   LEU A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      Proline residue:  A 143  - end of helix
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 4.040A  pdb=" N   SER A 184 " --> pdb=" O   TYR A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 236
      removed outlier: 4.049A  pdb=" N   ASP A 200 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL A 202 " --> pdb=" O   THR A 198 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      Proline residue:  A 218  - end of helix
      removed outlier: 3.743A  pdb=" N   ARG A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 262
      removed outlier: 4.031A  pdb=" N   ALA A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE A 246 " --> pdb=" O   TRP A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 289
    Processing helix  chain 'A' and resid 289 through 297
    Processing helix  chain 'A' and resid 298 through 335
      removed outlier: 3.614A  pdb=" N   GLN A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 346
    Processing helix  chain 'A' and resid 380 through 404
    Processing helix  chain 'A' and resid 405 through 431
      removed outlier: 3.579A  pdb=" N   GLU A 411 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 521
      removed outlier: 3.572A  pdb=" N   PHE A 517 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 558
    Processing helix  chain 'A' and resid 562 through 569
      removed outlier: 3.534A  pdb=" N   LYS A 569 " --> pdb=" O   ASP A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 581
      removed outlier: 3.518A  pdb=" N   LEU A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 591
      removed outlier: 3.744A  pdb=" N   GLN A 590 " --> pdb=" O   HIS A 586 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 586 through 591'
    Processing helix  chain 'A' and resid 600 through 605
    Processing helix  chain 'A' and resid 606 through 621
      removed outlier: 3.832A  pdb=" N   GLN A 611 " --> pdb=" O   GLY A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 650
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 4.154A  pdb=" N   LYS A 665 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TYR A 666 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   HIS A 667 " --> pdb=" O   TRP A 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 83
    Processing helix  chain 'B' and resid 88 through 123
      removed outlier: 3.978A  pdb=" N   VAL B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 140
      removed outlier: 3.507A  pdb=" N   ILE B 140 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 175
      removed outlier: 3.607A  pdb=" N   THR B 145 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 186
      removed outlier: 4.184A  pdb=" N   SER B 184 " --> pdb=" O   TYR B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 235
      removed outlier: 3.717A  pdb=" N   ASP B 200 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   VAL B 201 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL B 202 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   SER B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      Proline residue:  B 218  - end of helix
    Processing helix  chain 'B' and resid 240 through 262
    Processing helix  chain 'B' and resid 264 through 289
    Processing helix  chain 'B' and resid 289 through 297
    Processing helix  chain 'B' and resid 298 through 335
    Processing helix  chain 'B' and resid 337 through 347
      removed outlier: 3.741A  pdb=" N   VAL B 347 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 404
    Processing helix  chain 'B' and resid 405 through 431
      removed outlier: 3.536A  pdb=" N   ARG B 431 " --> pdb=" O   GLU B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 521
      removed outlier: 3.542A  pdb=" N   LEU B 516 " --> pdb=" O   GLY B 512 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE B 517 " --> pdb=" O   LYS B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 558
    Processing helix  chain 'B' and resid 562 through 569
      removed outlier: 3.787A  pdb=" N   LYS B 569 " --> pdb=" O   ASP B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 583
      removed outlier: 3.548A  pdb=" N   LEU B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 591
      removed outlier: 3.621A  pdb=" N   ARG B 591 " --> pdb=" O   ILE B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 605
    Processing helix  chain 'B' and resid 608 through 621
    Processing helix  chain 'B' and resid 636 through 650
    Processing helix  chain 'B' and resid 660 through 667
      removed outlier: 4.323A  pdb=" N   LYS B 665 " --> pdb=" O   SER B 662 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR B 666 " --> pdb=" O   LEU B 663 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   HIS B 667 " --> pdb=" O   TRP B 664 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469
      removed outlier: 6.827A  pdb=" N   GLN A 466 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   LYS A 533 " --> pdb=" O   GLN A 466 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   VAL A 468 " --> pdb=" O   LYS A 533 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   LEU A 493 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ALA A 491 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   VAL A 482 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL A 489 " --> pdb=" O   VAL A 482 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 503 through 504
      removed outlier: 6.862A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ALA A 626 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   ILE A 657 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A 628 " --> pdb=" O   ILE A 657 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE A 540 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ASP A 629 " --> pdb=" O   PHE A 540 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   ILE A 542 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 467 through 469
      removed outlier: 6.203A  pdb=" N   VAL B 468 " --> pdb=" O   LYS B 533 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ILE B 475 " --> pdb=" O   ILE B 495 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE B 495 " --> pdb=" O   ILE B 475 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLU B 477 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU B 493 " --> pdb=" O   GLU B 477 " (cutoff:3.500A)
      removed outlier: 5.843A  pdb=" N   ILE B 479 " --> pdb=" O   ALA B 491 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   ALA B 491 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE B 481 " --> pdb=" O   VAL B 489 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 503 through 504
      removed outlier: 6.990A  pdb=" N   LEU B 503 " --> pdb=" O   SER B 656 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ALA B 626 " --> pdb=" O   LEU B 655 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   ILE B 657 " --> pdb=" O   ALA B 626 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU B 628 " --> pdb=" O   ILE B 657 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   PHE B 540 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   ASP B 629 " --> pdb=" O   PHE B 540 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ILE B 542 " --> pdb=" O   ASP B 629 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    592 hydrogen bonds defined for protein.
    1749 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: 2.45

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3022
        1.34 -     1.46: 1449
        1.46 -     1.57: 4935
        1.57 -     1.69: 13
        1.69 -     1.81: 74
  Bond restraints: 9493
  Sorted by residual:
  bond pdb=" C3' ATP A 802 "
       pdb=" C4' ATP A 802 "
    ideal  model  delta    sigma   weight residual
    1.526  1.306  0.220 1.10e-02 8.26e+03 3.99e+02
  bond pdb=" C3' ATP B 802 "
       pdb=" C4' ATP B 802 "
    ideal  model  delta    sigma   weight residual
    1.526  1.309  0.217 1.10e-02 8.26e+03 3.89e+02
  bond pdb=" C1' ATP A 802 "
       pdb=" C2' ATP A 802 "
    ideal  model  delta    sigma   weight residual
    1.531  1.335  0.196 1.20e-02 6.94e+03 2.68e+02
  bond pdb=" C1' ATP B 802 "
       pdb=" C2' ATP B 802 "
    ideal  model  delta    sigma   weight residual
    1.531  1.336  0.195 1.20e-02 6.94e+03 2.63e+02
  bond pdb=" C4' ATP B 802 "
       pdb=" O4' ATP B 802 "
    ideal  model  delta    sigma   weight residual
    1.444  1.577 -0.133 1.10e-02 8.26e+03 1.46e+02
  ... (remaining 9488 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.07: 12804
        4.07 -     8.15: 53
        8.15 -    12.22: 11
       12.22 -    16.29: 3
       16.29 -    20.36: 1
  Bond angle restraints: 12872
  Sorted by residual:
  angle pdb=" PA  ATP A 802 "
        pdb=" O3A ATP A 802 "
        pdb=" PB  ATP A 802 "
      ideal   model   delta    sigma   weight residual
     136.83  116.47   20.36 1.00e+00 1.00e+00 4.15e+02
  angle pdb=" PB  ATP A 802 "
        pdb=" O3B ATP A 802 "
        pdb=" PG  ATP A 802 "
      ideal   model   delta    sigma   weight residual
     139.87  124.27   15.60 1.00e+00 1.00e+00 2.43e+02
  angle pdb=" PB  ATP B 802 "
        pdb=" O3B ATP B 802 "
        pdb=" PG  ATP B 802 "
      ideal   model   delta    sigma   weight residual
     139.87  125.96   13.91 1.00e+00 1.00e+00 1.93e+02
  angle pdb=" PA  ATP B 802 "
        pdb=" O3A ATP B 802 "
        pdb=" PB  ATP B 802 "
      ideal   model   delta    sigma   weight residual
     136.83  125.53   11.30 1.00e+00 1.00e+00 1.28e+02
  angle pdb=" C5  ATP B 802 "
        pdb=" C4  ATP B 802 "
        pdb=" N3  ATP B 802 "
      ideal   model   delta    sigma   weight residual
     126.80  118.06    8.74 1.00e+00 1.00e+00 7.65e+01
  ... (remaining 12867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5094
       17.99 -    35.98: 491
       35.98 -    53.97: 79
       53.97 -    71.96: 14
       71.96 -    89.95: 14
  Dihedral angle restraints: 5692
    sinusoidal: 2338
      harmonic: 3354
  Sorted by residual:
  dihedral pdb=" CA  ILE B 558 "
           pdb=" C   ILE B 558 "
           pdb=" N   TYR B 559 "
           pdb=" CA  TYR B 559 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.55  -23.45     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  ILE A 558 "
           pdb=" C   ILE A 558 "
           pdb=" N   TYR A 559 "
           pdb=" CA  TYR A 559 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.81  -21.19     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  HIS A 669 "
           pdb=" C   HIS A 669 "
           pdb=" N   LEU A 670 "
           pdb=" CA  LEU A 670 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.42  -19.58     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 5689 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1114
       0.047 -    0.094: 250
       0.094 -    0.141: 61
       0.141 -    0.188: 3
       0.188 -    0.235: 3
  Chirality restraints: 1431
  Sorted by residual:
  chirality pdb=" C2' ATP A 802 "
            pdb=" C1' ATP A 802 "
            pdb=" C3' ATP A 802 "
            pdb=" O2' ATP A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.44   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" C3' ATP A 802 "
            pdb=" C2' ATP A 802 "
            pdb=" C4' ATP A 802 "
            pdb=" O3' ATP A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  ILE A 505 "
            pdb=" CA  ILE A 505 "
            pdb=" CG1 ILE A 505 "
            pdb=" CG2 ILE A 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.42e-01
  ... (remaining 1428 not shown)

  Planarity restraints: 1622
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 535 "   -0.055 5.00e-02 4.00e+02   8.33e-02 1.11e+01
        pdb=" N   PRO A 536 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 536 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 536 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 507 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.12e+00
        pdb=" N   PRO A 508 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 508 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 508 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 106 "    0.014 2.00e-02 2.50e+03   1.13e-02 2.23e+00
        pdb=" CG  PHE A 106 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 106 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 106 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 106 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 106 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1619 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 56
        2.56 -     3.14: 7320
        3.14 -     3.73: 14915
        3.73 -     4.31: 20506
        4.31 -     4.90: 34928
  Nonbonded interactions: 77725
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 514 "
            pdb="MG    MG A 801 "
     model   vdw
     1.974 2.170
  nonbonded pdb=" OG  SER B 514 "
            pdb="MG    MG B 801 "
     model   vdw
     2.050 2.170
  nonbonded pdb=" OE1 GLN B 544 "
            pdb="MG    MG B 801 "
     model   vdw
     2.074 2.170
  nonbonded pdb=" O   MET A 548 "
            pdb=" NH2 ARG B 285 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" O   THR B 632 "
            pdb=" NH1 ARG B 660 "
     model   vdw
     2.190 3.120
  ... (remaining 77720 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 64 through 351 or resid 379 through 685 or resid 801 throu \ 
gh 802))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.830
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
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      :  0.007   0.220   9493  Z= 0.451
  Angle     :  0.792  20.362  12872  Z= 0.533
  Chirality :  0.042   0.235   1431
  Planarity :  0.004   0.083   1622
  Dihedral  : 14.783  89.948   3536
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.45 (0.25), residues: 1144
  helix:  1.50 (0.19), residues: 737
  sheet: -0.80 (0.70), residues: 60
  loop : -2.21 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 326 
 HIS   0.008   0.001   HIS B 210 
 PHE   0.025   0.001   PHE A 106 
 TYR   0.025   0.002   TYR A 110 
 ARG   0.003   0.000   ARG A 163 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8671 (tp) cc_final: 0.8471 (tp)
REVERT: A   89 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6940 (ttt180)
REVERT: A  598 MET cc_start: 0.7980 (mtt) cc_final: 0.7734 (mtp)
REVERT: B  421 GLU cc_start: 0.7681 (tp30) cc_final: 0.7280 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 1.4464
  time to fit residues: 196.1750
Evaluate side-chains
  105 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 87 optimal weight:    9.9990
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
A 586 HIS
B 148 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.164793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.130910 restraints weight = 9312.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.61
r_work: 0.3323 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9493  Z= 0.261
  Angle     :  0.579  10.606  12872  Z= 0.295
  Chirality :  0.041   0.157   1431
  Planarity :  0.004   0.067   1622
  Dihedral  :  8.649  85.339   1358
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  8.63 %
    Favored  : 89.72 %
  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:  0.75 (0.25), residues: 1144
  helix:  1.83 (0.19), residues: 738
  sheet: -1.16 (0.63), residues: 67
  loop : -2.25 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 326 
 HIS   0.007   0.001   HIS B 210 
 PHE   0.018   0.001   PHE A 106 
 TYR   0.016   0.002   TYR B 310 
 ARG   0.005   0.000   ARG B 436 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8659 (tp) cc_final: 0.8440 (tp)
REVERT: A  272 GLU cc_start: 0.8226 (tt0) cc_final: 0.7963 (tt0)
REVERT: A  335 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8195 (mtt)
REVERT: A  598 MET cc_start: 0.8489 (mtt) cc_final: 0.8179 (mtp)
REVERT: B  421 GLU cc_start: 0.8330 (tp30) cc_final: 0.7364 (pt0)
  outliers start: 16
  outliers final: 4
  residues processed: 118
  average time/residue: 1.6160
  time to fit residues: 201.1138
Evaluate side-chains
  110 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  672 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 22 optimal weight:    0.0870
   chunk 23 optimal weight:    0.5980
   chunk 98 optimal weight:    0.0970
   chunk 107 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 111 optimal weight:    0.4980
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
A 210 HIS
A 586 HIS
B 502 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.167966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.134301 restraints weight = 9387.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.50
r_work: 0.3348 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9493  Z= 0.182
  Angle     :  0.514   9.318  12872  Z= 0.262
  Chirality :  0.039   0.153   1431
  Planarity :  0.004   0.058   1622
  Dihedral  :  8.011  80.335   1358
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.20 %
    Favored  : 87.26 %
  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:  1.00 (0.25), residues: 1144
  helix:  2.10 (0.18), residues: 738
  sheet: -2.04 (0.59), residues: 69
  loop : -2.12 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 326 
 HIS   0.007   0.001   HIS B 210 
 PHE   0.014   0.001   PHE A 106 
 TYR   0.013   0.001   TYR B 310 
 ARG   0.004   0.000   ARG B 660 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8604 (tp) cc_final: 0.8403 (tp)
REVERT: A  155 GLU cc_start: 0.8067 (tt0) cc_final: 0.7790 (tt0)
REVERT: A  272 GLU cc_start: 0.8290 (tt0) cc_final: 0.8026 (tt0)
REVERT: A  598 MET cc_start: 0.8485 (mtt) cc_final: 0.8180 (mtp)
REVERT: B  421 GLU cc_start: 0.8300 (tp30) cc_final: 0.7306 (pt0)
  outliers start: 15
  outliers final: 5
  residues processed: 122
  average time/residue: 1.4776
  time to fit residues: 190.7797
Evaluate side-chains
  112 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  250 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    0.0030
   chunk 51 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
A 210 HIS
A 586 HIS
B 502 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.167759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.133832 restraints weight = 9291.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 1.67
r_work: 0.3322 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9493  Z= 0.209
  Angle     :  0.524   9.766  12872  Z= 0.265
  Chirality :  0.039   0.153   1431
  Planarity :  0.004   0.055   1622
  Dihedral  :  7.663  80.447   1358
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.64 %
    Favored  : 85.71 %
  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:  1.13 (0.25), residues: 1144
  helix:  2.19 (0.18), residues: 739
  sheet: -1.99 (0.59), residues: 69
  loop : -2.05 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 326 
 HIS   0.006   0.001   HIS B 210 
 PHE   0.010   0.001   PHE A 252 
 TYR   0.014   0.001   TYR B 310 
 ARG   0.003   0.000   ARG B 660 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 1.166 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.7132 (ttt180)
REVERT: A  155 GLU cc_start: 0.8142 (tt0) cc_final: 0.7856 (tt0)
REVERT: A  272 GLU cc_start: 0.8426 (tt0) cc_final: 0.8107 (tt0)
REVERT: A  312 ASP cc_start: 0.8197 (m-30) cc_final: 0.7757 (m-30)
REVERT: A  403 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8354 (mtt)
REVERT: A  498 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7914 (mp0)
REVERT: A  598 MET cc_start: 0.8544 (mtt) cc_final: 0.8237 (mtp)
REVERT: B  421 GLU cc_start: 0.8363 (tp30) cc_final: 0.7424 (pt0)
REVERT: B  487 GLU cc_start: 0.6572 (tt0) cc_final: 0.6330 (tt0)
  outliers start: 16
  outliers final: 7
  residues processed: 125
  average time/residue: 1.9589
  time to fit residues: 260.0629
Evaluate side-chains
  113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  410 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0670
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
A 210 HIS
A 586 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.167066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.133047 restraints weight = 9249.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.74
r_work: 0.3327 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9493  Z= 0.221
  Angle     :  0.528   9.872  12872  Z= 0.267
  Chirality :  0.039   0.155   1431
  Planarity :  0.004   0.053   1622
  Dihedral  :  7.586  80.909   1358
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.26 %
    Favored  : 83.97 %
  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:  1.13 (0.25), residues: 1144
  helix:  2.19 (0.18), residues: 740
  sheet: -2.03 (0.59), residues: 70
  loop : -2.05 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 326 
 HIS   0.006   0.001   HIS B 210 
 PHE   0.010   0.001   PHE A 252 
 TYR   0.014   0.001   TYR B 310 
 ARG   0.004   0.000   ARG B 172 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 1.292 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.7412 (ttm-80) cc_final: 0.7171 (ttt180)
REVERT: A  155 GLU cc_start: 0.8198 (tt0) cc_final: 0.7975 (tt0)
REVERT: A  272 GLU cc_start: 0.8414 (tt0) cc_final: 0.8077 (tt0)
REVERT: A  403 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8384 (mtt)
REVERT: A  498 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7999 (mp0)
REVERT: A  598 MET cc_start: 0.8549 (mtt) cc_final: 0.8235 (mtp)
REVERT: B  421 GLU cc_start: 0.8382 (tp30) cc_final: 0.7436 (pt0)
REVERT: B  672 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8018 (tp40)
  outliers start: 27
  outliers final: 9
  residues processed: 131
  average time/residue: 1.5692
  time to fit residues: 218.8651
Evaluate side-chains
  114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  672 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0980
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   chunk 111 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
A 210 HIS
A 472 GLN
A 586 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.166685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.132678 restraints weight = 9197.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.74
r_work: 0.3282 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9493  Z= 0.231
  Angle     :  0.533  10.134  12872  Z= 0.269
  Chirality :  0.040   0.156   1431
  Planarity :  0.004   0.052   1622
  Dihedral  :  7.579  82.023   1358
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 14.08 %
    Favored  : 82.53 %
  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:  1.14 (0.25), residues: 1144
  helix:  2.23 (0.18), residues: 738
  sheet: -2.07 (0.59), residues: 70
  loop : -2.08 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 326 
 HIS   0.005   0.001   HIS B 210 
 PHE   0.009   0.001   PHE A 252 
 TYR   0.014   0.001   TYR B 310 
 ARG   0.003   0.000   ARG B 660 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.7173 (ttt180)
REVERT: A  155 GLU cc_start: 0.8203 (tt0) cc_final: 0.7970 (tt0)
REVERT: A  272 GLU cc_start: 0.8425 (tt0) cc_final: 0.8110 (tt0)
REVERT: A  311 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6901 (tp40)
REVERT: A  312 ASP cc_start: 0.8187 (m-30) cc_final: 0.7827 (m-30)
REVERT: A  498 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7808 (mp0)
REVERT: A  598 MET cc_start: 0.8547 (mtt) cc_final: 0.8219 (mtp)
REVERT: B  421 GLU cc_start: 0.8406 (tp30) cc_final: 0.7439 (pt0)
REVERT: B  659 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.6804 (p90)
  outliers start: 33
  outliers final: 12
  residues processed: 133
  average time/residue: 1.3829
  time to fit residues: 195.4746
Evaluate side-chains
  118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  311 GLN
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  659 HIS
Chi-restraints excluded: chain B residue  668 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
A 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.165409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.131166 restraints weight = 9304.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.72
r_work: 0.3271 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9493  Z= 0.258
  Angle     :  0.566  10.882  12872  Z= 0.283
  Chirality :  0.041   0.211   1431
  Planarity :  0.004   0.052   1622
  Dihedral  :  7.662  84.095   1358
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.52 %
    Favored  : 81.81 %
  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:  1.02 (0.25), residues: 1144
  helix:  2.12 (0.18), residues: 746
  sheet: -2.05 (0.60), residues: 70
  loop : -2.24 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 326 
 HIS   0.007   0.001   HIS B 210 
 PHE   0.008   0.001   PHE A 252 
 TYR   0.015   0.001   TYR B 310 
 ARG   0.003   0.000   ARG B 660 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 1.312 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7184 (ttt180)
REVERT: A  155 GLU cc_start: 0.8210 (tt0) cc_final: 0.7976 (tt0)
REVERT: A  272 GLU cc_start: 0.8428 (tt0) cc_final: 0.8097 (tt0)
REVERT: A  311 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6918 (tp40)
REVERT: A  312 ASP cc_start: 0.8222 (m-30) cc_final: 0.7800 (m-30)
REVERT: A  498 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7848 (mp0)
REVERT: A  574 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7137 (mp10)
REVERT: A  598 MET cc_start: 0.8543 (mtt) cc_final: 0.8214 (mtp)
REVERT: A  659 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7586 (p90)
REVERT: A  684 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7338 (tp)
REVERT: B  421 GLU cc_start: 0.8430 (tp30) cc_final: 0.7467 (pt0)
REVERT: B  602 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8186 (ptmm)
  outliers start: 26
  outliers final: 11
  residues processed: 123
  average time/residue: 1.4157
  time to fit residues: 185.1944
Evaluate side-chains
  117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  311 GLN
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  574 GLN
Chi-restraints excluded: chain A residue  659 HIS
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  602 LYS
Chi-restraints excluded: chain B residue  668 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 56 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 70 optimal weight:    0.3980
   chunk 109 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
A 210 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.167019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.133020 restraints weight = 9439.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.74
r_work: 0.3325 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9493  Z= 0.218
  Angle     :  0.542  10.492  12872  Z= 0.272
  Chirality :  0.040   0.222   1431
  Planarity :  0.004   0.050   1622
  Dihedral  :  7.494  83.320   1358
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.83 %
    Favored  : 81.40 %
  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:  1.11 (0.25), residues: 1144
  helix:  2.20 (0.18), residues: 746
  sheet: -2.03 (0.61), residues: 70
  loop : -2.21 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 326 
 HIS   0.008   0.001   HIS B 210 
 PHE   0.006   0.001   PHE A 252 
 TYR   0.014   0.001   TYR B 310 
 ARG   0.003   0.000   ARG B 163 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 1.045 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.7171 (ttt180)
REVERT: A  155 GLU cc_start: 0.8161 (tt0) cc_final: 0.7922 (tt0)
REVERT: A  272 GLU cc_start: 0.8394 (tt0) cc_final: 0.8057 (tt0)
REVERT: A  311 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6902 (tp40)
REVERT: A  312 ASP cc_start: 0.8161 (m-30) cc_final: 0.7757 (m-30)
REVERT: A  598 MET cc_start: 0.8548 (mtt) cc_final: 0.8218 (mtp)
REVERT: B  421 GLU cc_start: 0.8414 (tp30) cc_final: 0.7451 (pt0)
REVERT: B  432 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7881 (m)
REVERT: B  487 GLU cc_start: 0.6457 (tt0) cc_final: 0.6183 (tt0)
REVERT: B  602 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8109 (ptmm)
  outliers start: 27
  outliers final: 11
  residues processed: 122
  average time/residue: 1.4204
  time to fit residues: 184.5689
Evaluate side-chains
  115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  311 GLN
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  602 LYS
Chi-restraints excluded: chain B residue  668 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 13 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.166550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.131575 restraints weight = 9261.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.64
r_work: 0.3297 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9493  Z= 0.226
  Angle     :  0.551  10.763  12872  Z= 0.276
  Chirality :  0.040   0.231   1431
  Planarity :  0.004   0.050   1622
  Dihedral  :  7.497  82.666   1358
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.44 %
    Favored  : 81.29 %
  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:  1.11 (0.25), residues: 1144
  helix:  2.20 (0.18), residues: 748
  sheet: -1.99 (0.62), residues: 70
  loop : -2.24 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 326 
 HIS   0.008   0.001   HIS B 210 
 PHE   0.006   0.001   PHE A 252 
 TYR   0.014   0.001   TYR B 310 
 ARG   0.006   0.000   ARG B 518 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.933 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7186 (ttt180)
REVERT: A  155 GLU cc_start: 0.8169 (tt0) cc_final: 0.7925 (tt0)
REVERT: A  272 GLU cc_start: 0.8425 (tt0) cc_final: 0.8081 (tt0)
REVERT: A  311 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6894 (tp40)
REVERT: A  312 ASP cc_start: 0.8218 (m-30) cc_final: 0.7806 (m-30)
REVERT: A  335 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.6936 (mpp)
REVERT: A  427 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7821 (mp0)
REVERT: A  598 MET cc_start: 0.8568 (mtt) cc_final: 0.8254 (mtp)
REVERT: A  659 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7015 (p90)
REVERT: B  421 GLU cc_start: 0.8441 (tp30) cc_final: 0.7443 (pt0)
REVERT: B  432 CYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7890 (m)
REVERT: B  462 LYS cc_start: 0.7366 (tmtt) cc_final: 0.7094 (tptp)
REVERT: B  487 GLU cc_start: 0.6454 (tt0) cc_final: 0.6194 (tt0)
REVERT: B  602 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8185 (ptmm)
  outliers start: 22
  outliers final: 14
  residues processed: 122
  average time/residue: 1.5549
  time to fit residues: 201.8007
Evaluate side-chains
  122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  311 GLN
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  659 HIS
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  602 LYS
Chi-restraints excluded: chain B residue  668 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 93 optimal weight:    0.4980
   chunk 100 optimal weight:    0.3980
   chunk 5 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.166245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131402 restraints weight = 9340.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.71
r_work: 0.3287 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9493  Z= 0.249
  Angle     :  0.568  11.467  12872  Z= 0.285
  Chirality :  0.041   0.261   1431
  Planarity :  0.004   0.051   1622
  Dihedral  :  7.582  83.576   1358
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.44 %
    Favored  : 81.29 %
  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:  1.02 (0.25), residues: 1144
  helix:  2.16 (0.18), residues: 746
  sheet: -2.16 (0.66), residues: 58
  loop : -2.33 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 326 
 HIS   0.008   0.001   HIS B 210 
 PHE   0.007   0.001   PHE A 252 
 TYR   0.015   0.001   TYR B 310 
 ARG   0.006   0.000   ARG B 518 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7180 (ttt180)
REVERT: A  155 GLU cc_start: 0.8200 (tt0) cc_final: 0.7916 (tt0)
REVERT: A  199 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7522 (mp0)
REVERT: A  272 GLU cc_start: 0.8415 (tt0) cc_final: 0.8089 (tt0)
REVERT: A  311 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6911 (tp40)
REVERT: A  312 ASP cc_start: 0.8240 (m-30) cc_final: 0.7827 (m-30)
REVERT: A  335 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.6968 (mpp)
REVERT: A  427 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7817 (mp0)
REVERT: A  574 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7164 (mp10)
REVERT: A  598 MET cc_start: 0.8565 (mtt) cc_final: 0.8240 (mtp)
REVERT: A  659 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.6970 (p90)
REVERT: B  421 GLU cc_start: 0.8454 (tp30) cc_final: 0.7491 (pt0)
REVERT: B  432 CYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7881 (m)
REVERT: B  602 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8131 (ptmm)
  outliers start: 22
  outliers final: 13
  residues processed: 119
  average time/residue: 1.4506
  time to fit residues: 183.5257
Evaluate side-chains
  121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  199 GLU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  311 GLN
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  574 GLN
Chi-restraints excluded: chain A residue  659 HIS
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  432 CYS
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  602 LYS
Chi-restraints excluded: chain B residue  668 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 113 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.165978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131219 restraints weight = 9276.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.68
r_work: 0.3286 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9493  Z= 0.252
  Angle     :  0.563  11.345  12872  Z= 0.283
  Chirality :  0.041   0.247   1431
  Planarity :  0.004   0.051   1622
  Dihedral  :  7.601  84.776   1358
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.65 %
    Favored  : 81.09 %
  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:  1.03 (0.25), residues: 1144
  helix:  2.14 (0.18), residues: 748
  sheet: -2.24 (0.70), residues: 48
  loop : -2.27 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 326 
 HIS   0.008   0.001   HIS B 210 
 PHE   0.007   0.001   PHE A 540 
 TYR   0.015   0.001   TYR B 310 
 ARG   0.006   0.000   ARG B 518 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6739.17 seconds
wall clock time: 118 minutes 58.69 seconds (7138.69 seconds total)