Starting phenix.real_space_refine
on Mon Nov 17 20:26:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5z1f_6875/11_2025/5z1f_6875.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5z1f_6875/11_2025/5z1f_6875.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5z1f_6875/11_2025/5z1f_6875.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5z1f_6875/11_2025/5z1f_6875.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5z1f_6875/11_2025/5z1f_6875.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5z1f_6875/11_2025/5z1f_6875.map"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.009
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    5604      2.51       5
     N    1364      2.21       5
     O    1488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8480
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 601, 4240
          Classifications: {'peptide': 601}
          Incomplete info: {'truncation_to_alanine': 145}
          Link IDs: {'PTRANS': 27, 'TRANS': 573}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 634
          Unresolved non-hydrogen angles: 792
          Unresolved non-hydrogen dihedrals: 548
          Unresolved non-hydrogen chiralities: 38
          Planarities with less than four sites: {'PHE:plan': 10, 'TRP:plan': 4, 'ARG:plan': 17, 'TYR:plan': 8, 'ASN:plan1': 5, 'GLU:plan': 21, 'GLN:plan1': 9, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 384
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.40, per 1000 atoms: 0.40
  Number of scatterers: 8480
  At special positions: 0
  Unit cell: (127.655, 81.235, 91.785, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1488      8.00
     N    1364      7.00
     C    5604      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 364.6 milliseconds
  

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2296

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 2 sheets defined
      70.9% alpha, 2.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 24
      removed outlier: 3.532A  pdb=" N   LEU A  22 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 41
    Processing helix  chain 'A' and resid 61 through 68
    Processing helix  chain 'A' and resid 69 through 77
      removed outlier: 3.507A  pdb=" N   VAL A  73 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   ASN A  75 " --> pdb=" O   GLN A  71 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A  77 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 97
      removed outlier: 3.503A  pdb=" N   ALA A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 107
      Proline residue:  A 104  - end of helix
    Processing helix  chain 'A' and resid 151 through 184
    Processing helix  chain 'A' and resid 188 through 191
      removed outlier: 3.632A  pdb=" N   GLN A 191 " --> pdb=" O   LYS A 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 188 through 191'
    Processing helix  chain 'A' and resid 207 through 220
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 240 through 247
    Processing helix  chain 'A' and resid 290 through 295
      removed outlier: 3.949A  pdb=" N   LYS A 294 " --> pdb=" O   GLU A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 317 through 327
      removed outlier: 3.548A  pdb=" N   SER A 327 " --> pdb=" O   SER A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 377
      removed outlier: 4.070A  pdb=" N   ILE A 361 " --> pdb=" O   PHE A 357 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA A 371 " --> pdb=" O   TYR A 367 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU A 375 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 386
      removed outlier: 4.340A  pdb=" N   ILE A 381 " --> pdb=" O   TYR A 377 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 427
      Proline residue:  A 418  - end of helix
    Processing helix  chain 'A' and resid 428 through 438
    Processing helix  chain 'A' and resid 444 through 463
      removed outlier: 3.759A  pdb=" N   ARG A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA A 451 " --> pdb=" O   HIS A 447 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   TYR A 458 " --> pdb=" O   GLY A 454 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   PHE A 462 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ASN A 463 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 475
    Processing helix  chain 'A' and resid 489 through 523
      Proline residue:  A 499  - end of helix
      removed outlier: 3.643A  pdb=" N   ILE A 515 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLY A 516 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLY A 518 " --> pdb=" O   PHE A 514 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A 522 " --> pdb=" O   GLY A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 537
      removed outlier: 3.684A  pdb=" N   HIS A 531 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 576
      Proline residue:  A 560  - end of helix
      removed outlier: 4.041A  pdb=" N   ILE A 565 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   VAL A 574 " --> pdb=" O   PHE A 570 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   ILE A 575 " --> pdb=" O   CYS A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 599
      removed outlier: 3.587A  pdb=" N   ILE A 581 " --> pdb=" O   PRO A 577 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR A 586 " --> pdb=" O   PHE A 582 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE A 587 " --> pdb=" O   GLY A 583 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LEU A 592 " --> pdb=" O   GLY A 588 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG A 595 " --> pdb=" O   TRP A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 639
      removed outlier: 4.274A  pdb=" N   HIS A 615 " --> pdb=" O   ARG A 611 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA A 637 " --> pdb=" O   GLY A 633 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS A 638 " --> pdb=" O   TYR A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 662
      Proline residue:  A 648  - end of helix
    Processing helix  chain 'A' and resid 664 through 670
      removed outlier: 4.005A  pdb=" N   HIS A 670 " --> pdb=" O   GLY A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 680
    Processing helix  chain 'A' and resid 686 through 691
      removed outlier: 3.887A  pdb=" N   PHE A 690 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ARG A 691 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 686 through 691'
    Processing helix  chain 'B' and resid 4 through 24
      removed outlier: 3.532A  pdb=" N   LEU B  22 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 41
    Processing helix  chain 'B' and resid 61 through 68
    Processing helix  chain 'B' and resid 69 through 77
      removed outlier: 3.507A  pdb=" N   VAL B  73 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL B  74 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   ASN B  75 " --> pdb=" O   GLN B  71 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER B  77 " --> pdb=" O   VAL B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 97
      removed outlier: 3.503A  pdb=" N   ALA B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 107
      Proline residue:  B 104  - end of helix
    Processing helix  chain 'B' and resid 151 through 184
    Processing helix  chain 'B' and resid 188 through 191
      removed outlier: 3.631A  pdb=" N   GLN B 191 " --> pdb=" O   LYS B 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 188 through 191'
    Processing helix  chain 'B' and resid 207 through 220
    Processing helix  chain 'B' and resid 233 through 239
    Processing helix  chain 'B' and resid 240 through 247
    Processing helix  chain 'B' and resid 290 through 295
      removed outlier: 3.949A  pdb=" N   LYS B 294 " --> pdb=" O   GLU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 305
    Processing helix  chain 'B' and resid 317 through 327
      removed outlier: 3.548A  pdb=" N   SER B 327 " --> pdb=" O   SER B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 377
      removed outlier: 4.070A  pdb=" N   ILE B 361 " --> pdb=" O   PHE B 357 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA B 371 " --> pdb=" O   TYR B 367 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU B 375 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 386
      removed outlier: 4.341A  pdb=" N   ILE B 381 " --> pdb=" O   TYR B 377 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA B 386 " --> pdb=" O   ALA B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 427
      Proline residue:  B 418  - end of helix
    Processing helix  chain 'B' and resid 428 through 438
    Processing helix  chain 'B' and resid 444 through 463
      removed outlier: 3.759A  pdb=" N   ARG B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA B 451 " --> pdb=" O   HIS B 447 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   TYR B 458 " --> pdb=" O   GLY B 454 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   PHE B 462 " --> pdb=" O   TYR B 458 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ASN B 463 " --> pdb=" O   PHE B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 475
    Processing helix  chain 'B' and resid 489 through 523
      Proline residue:  B 499  - end of helix
      removed outlier: 3.643A  pdb=" N   ILE B 515 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLY B 516 " --> pdb=" O   LYS B 512 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLY B 518 " --> pdb=" O   PHE B 514 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER B 522 " --> pdb=" O   GLY B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 537
      removed outlier: 3.684A  pdb=" N   HIS B 531 " --> pdb=" O   LEU B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 576
      Proline residue:  B 560  - end of helix
      removed outlier: 4.041A  pdb=" N   ILE B 565 " --> pdb=" O   GLY B 561 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   VAL B 574 " --> pdb=" O   PHE B 570 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   ILE B 575 " --> pdb=" O   CYS B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 599
      removed outlier: 3.587A  pdb=" N   ILE B 581 " --> pdb=" O   PRO B 577 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR B 586 " --> pdb=" O   PHE B 582 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE B 587 " --> pdb=" O   GLY B 583 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LEU B 592 " --> pdb=" O   GLY B 588 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG B 595 " --> pdb=" O   TRP B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 611 through 639
      removed outlier: 4.274A  pdb=" N   HIS B 615 " --> pdb=" O   ARG B 611 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA B 637 " --> pdb=" O   GLY B 633 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS B 638 " --> pdb=" O   TYR B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 662
      Proline residue:  B 648  - end of helix
    Processing helix  chain 'B' and resid 664 through 670
      removed outlier: 4.005A  pdb=" N   HIS B 670 " --> pdb=" O   GLY B 666 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 680
    Processing helix  chain 'B' and resid 686 through 691
      removed outlier: 3.887A  pdb=" N   PHE B 690 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ARG B 691 " --> pdb=" O   GLU B 687 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 686 through 691'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 229
      removed outlier: 3.992A  pdb=" N   ARG A 226 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 229
      removed outlier: 3.992A  pdb=" N   ARG B 226 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1590 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: 1.15

  Time building geometry restraints manager: 1.16 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: 2588
        1.34 -     1.46: 2128
        1.46 -     1.58: 3940
        1.58 -     1.70: 2
        1.70 -     1.82: 36
  Bond restraints: 8694
  Sorted by residual:
  bond pdb=" C   ALA A  34 "
       pdb=" N   PRO A  35 "
    ideal  model  delta    sigma   weight residual
    1.334  1.594 -0.260 2.34e-02 1.83e+03 1.23e+02
  bond pdb=" C   ALA B  34 "
       pdb=" N   PRO B  35 "
    ideal  model  delta    sigma   weight residual
    1.334  1.593 -0.259 2.34e-02 1.83e+03 1.23e+02
  bond pdb=" C   PRO B 202 "
       pdb=" O   PRO B 202 "
    ideal  model  delta    sigma   weight residual
    1.243  1.231  0.013 8.50e-03 1.38e+04 2.18e+00
  bond pdb=" C   PRO A 202 "
       pdb=" O   PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.243  1.231  0.012 8.50e-03 1.38e+04 1.96e+00
  bond pdb=" CG  LEU A 422 "
       pdb=" CD2 LEU A 422 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.91e+00
  ... (remaining 8689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 11576
        2.10 -     4.19: 301
        4.19 -     6.29: 57
        6.29 -     8.38: 10
        8.38 -    10.48: 4
  Bond angle restraints: 11948
  Sorted by residual:
  angle pdb=" N   GLU B 305 "
        pdb=" CA  GLU B 305 "
        pdb=" C   GLU B 305 "
      ideal   model   delta    sigma   weight residual
     107.67  118.15  -10.48 2.09e+00 2.29e-01 2.51e+01
  angle pdb=" N   GLU A 305 "
        pdb=" CA  GLU A 305 "
        pdb=" C   GLU A 305 "
      ideal   model   delta    sigma   weight residual
     107.67  118.13  -10.46 2.09e+00 2.29e-01 2.51e+01
  angle pdb=" O   PRO A 202 "
        pdb=" C   PRO A 202 "
        pdb=" N   PRO A 203 "
      ideal   model   delta    sigma   weight residual
     121.15  123.42   -2.27 4.70e-01 4.53e+00 2.32e+01
  angle pdb=" O   PRO B 202 "
        pdb=" C   PRO B 202 "
        pdb=" N   PRO B 203 "
      ideal   model   delta    sigma   weight residual
     121.15  123.39   -2.24 4.70e-01 4.53e+00 2.26e+01
  angle pdb=" N   THR A 297 "
        pdb=" CA  THR A 297 "
        pdb=" C   THR A 297 "
      ideal   model   delta    sigma   weight residual
     111.07  115.54   -4.47 1.07e+00 8.73e-01 1.75e+01
  ... (remaining 11943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 4640
       17.03 -    34.07: 262
       34.07 -    51.10: 88
       51.10 -    68.14: 10
       68.14 -    85.17: 2
  Dihedral angle restraints: 5002
    sinusoidal: 1472
      harmonic: 3530
  Sorted by residual:
  dihedral pdb=" CA  LEU B  46 "
           pdb=" C   LEU B  46 "
           pdb=" N   GLU B  47 "
           pdb=" CA  GLU B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.39  -29.61     0      5.00e+00 4.00e-02 3.51e+01
  dihedral pdb=" CA  LEU A  46 "
           pdb=" C   LEU A  46 "
           pdb=" N   GLU A  47 "
           pdb=" CA  GLU A  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.45  -29.55     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  THR A  55 "
           pdb=" C   THR A  55 "
           pdb=" N   ARG A  56 "
           pdb=" CA  ARG A  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.98   25.02     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 4999 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1096
       0.051 -    0.103: 298
       0.103 -    0.154: 70
       0.154 -    0.205: 14
       0.205 -    0.257: 4
  Chirality restraints: 1482
  Sorted by residual:
  chirality pdb=" CA  GLU B 305 "
            pdb=" N   GLU B 305 "
            pdb=" C   GLU B 305 "
            pdb=" CB  GLU B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  GLU A 305 "
            pdb=" N   GLU A 305 "
            pdb=" C   GLU A 305 "
            pdb=" CB  GLU A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  LYS B 300 "
            pdb=" N   LYS B 300 "
            pdb=" C   LYS B 300 "
            pdb=" CB  LYS B 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1479 not shown)

  Planarity restraints: 1484
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 107 "    0.059 5.00e-02 4.00e+02   8.87e-02 1.26e+01
        pdb=" N   PRO B 108 "   -0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO B 108 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B 108 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 107 "   -0.059 5.00e-02 4.00e+02   8.86e-02 1.26e+01
        pdb=" N   PRO A 108 "    0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO A 108 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 108 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 202 "   -0.056 5.00e-02 4.00e+02   8.59e-02 1.18e+01
        pdb=" N   PRO A 203 "    0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO A 203 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 203 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 1481 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1312
        2.75 -     3.29: 9749
        3.29 -     3.83: 14301
        3.83 -     4.36: 16456
        4.36 -     4.90: 25235
  Nonbonded interactions: 67053
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 492 "
            pdb=" OG1 THR B 496 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   ASN A 492 "
            pdb=" OG1 THR A 496 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   GLU A 232 "
            pdb=" CD  GLU A 232 "
     model   vdw
     2.214 3.270
  nonbonded pdb=" O   GLU B 232 "
            pdb=" CD  GLU B 232 "
     model   vdw
     2.214 3.270
  nonbonded pdb=" O   LEU A 635 "
            pdb=" OH  TYR A 642 "
     model   vdw
     2.223 3.040
  ... (remaining 67048 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.950
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
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   0.260   8694  Z= 0.276
  Angle     :  0.868  10.477  11948  Z= 0.490
  Chirality :  0.052   0.257   1482
  Planarity :  0.008   0.089   1484
  Dihedral  : 13.130  85.173   2706
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 25.30
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  9.81 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 12.73 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.90 (0.19), residues: 1182
  helix: -3.32 (0.13), residues: 750
  sheet: -2.20 (0.75), residues: 46
  loop : -2.77 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 178 
 TYR   0.019   0.002   TYR A 609 
 PHE   0.014   0.002   PHE A 668 
 TRP   0.017   0.002   TRP A  61 
 HIS   0.006   0.002   HIS B  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 ( 8694)
  covalent geometry    : angle       0.86799 (11948)
  hydrogen bonds       : bond        0.16906 (  536)
  hydrogen bonds       : angle      10.58532 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ARG cc_start: 0.9138 (ttt90) cc_final: 0.8859 (ttt-90)
REVERT: A  180 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8904 (tp40)
REVERT: A  209 LYS cc_start: 0.9324 (tttt) cc_final: 0.8936 (tppt)
REVERT: A  315 PHE cc_start: 0.9415 (m-80) cc_final: 0.9046 (m-10)
REVERT: A  363 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8750 (tp-100)
REVERT: A  579 ILE cc_start: 0.9448 (pp) cc_final: 0.9079 (pt)
REVERT: A  580 LEU cc_start: 0.9093 (mt) cc_final: 0.8809 (mt)
REVERT: A  651 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9092 (tp)
REVERT: A  662 GLN cc_start: 0.8618 (mt0) cc_final: 0.8141 (mt0)
  outliers start: 19
  outliers final: 4
  residues processed: 168
  average time/residue: 0.0603
  time to fit residues: 13.2396
Evaluate side-chains
  109 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0970
   overall best weight:    0.6378
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 ASN
A 615 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.092049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.074810 restraints weight = 16989.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.076885 restraints weight = 11865.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.078379 restraints weight = 8881.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.079427 restraints weight = 7066.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.080250 restraints weight = 5925.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8694  Z= 0.173
  Angle     :  0.818   9.337  11948  Z= 0.430
  Chirality :  0.046   0.345   1482
  Planarity :  0.006   0.057   1484
  Dihedral  :  6.186  19.162   1248
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.58 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.77 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.85 (0.23), residues: 1182
  helix: -1.55 (0.17), residues: 778
  sheet: -2.38 (0.74), residues: 46
  loop : -2.20 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 345 
 TYR   0.037   0.002   TYR A 572 
 PHE   0.019   0.002   PHE A 664 
 TRP   0.020   0.002   TRP A  61 
 HIS   0.013   0.002   HIS B 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8694)
  covalent geometry    : angle       0.81755 (11948)
  hydrogen bonds       : bond        0.04989 (  536)
  hydrogen bonds       : angle       5.82154 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  158 TRP cc_start: 0.7706 (t-100) cc_final: 0.7370 (t-100)
REVERT: A  161 LEU cc_start: 0.9503 (mt) cc_final: 0.9272 (pp)
REVERT: A  178 ARG cc_start: 0.9348 (ttt90) cc_final: 0.9090 (ttt-90)
REVERT: A  180 GLN cc_start: 0.9263 (tp-100) cc_final: 0.8917 (tm-30)
REVERT: A  209 LYS cc_start: 0.9158 (tttt) cc_final: 0.8835 (tptt)
REVERT: A  315 PHE cc_start: 0.9270 (m-80) cc_final: 0.8501 (m-10)
REVERT: A  579 ILE cc_start: 0.9503 (pt) cc_final: 0.9251 (pt)
REVERT: A  594 LEU cc_start: 0.9510 (pp) cc_final: 0.9117 (mp)
  outliers start: 1
  outliers final: 1
  residues processed: 133
  average time/residue: 0.0537
  time to fit residues: 9.6785
Evaluate side-chains
  110 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 89 optimal weight:    0.2980
   chunk 73 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    2.2586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 615 HIS
A 618 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.089363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.072550 restraints weight = 17388.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.074593 restraints weight = 11936.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.076073 restraints weight = 8886.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.077154 restraints weight = 7020.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.077980 restraints weight = 5822.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8694  Z= 0.169
  Angle     :  0.733   8.639  11948  Z= 0.387
  Chirality :  0.043   0.153   1482
  Planarity :  0.006   0.059   1484
  Dihedral  :  5.552  18.775   1248
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.77 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  4.51 %
    Favored  : 94.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.25), residues: 1182
  helix: -0.63 (0.18), residues: 770
  sheet: -2.36 (0.78), residues: 46
  loop : -2.03 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 450 
 TYR   0.033   0.002   TYR B 586 
 PHE   0.026   0.002   PHE B 514 
 TRP   0.022   0.002   TRP B  61 
 HIS   0.002   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8694)
  covalent geometry    : angle       0.73301 (11948)
  hydrogen bonds       : bond        0.04474 (  536)
  hydrogen bonds       : angle       5.22783 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 128
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 TRP cc_start: 0.7802 (t-100) cc_final: 0.7505 (t-100)
REVERT: A  161 LEU cc_start: 0.9453 (mt) cc_final: 0.9247 (pp)
REVERT: A  178 ARG cc_start: 0.9321 (ttt90) cc_final: 0.9008 (ttt-90)
REVERT: A  180 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8730 (tm-30)
REVERT: A  209 LYS cc_start: 0.9168 (tttt) cc_final: 0.8792 (tppt)
REVERT: A  315 PHE cc_start: 0.9421 (m-80) cc_final: 0.8471 (m-10)
REVERT: A  594 LEU cc_start: 0.9532 (pp) cc_final: 0.9222 (mp)
REVERT: A  656 PHE cc_start: 0.8852 (t80) cc_final: 0.8433 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0504
  time to fit residues: 8.8759
Evaluate side-chains
  101 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 83 optimal weight:    7.9990
   chunk 64 optimal weight:   20.0000
   chunk 109 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0370
   overall best weight:    0.7460
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 308 GLN
A 351 ASN
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 618 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.091245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.074131 restraints weight = 17189.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.076119 restraints weight = 11954.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.077614 restraints weight = 8955.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.078674 restraints weight = 7114.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.079549 restraints weight = 5958.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.4559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8694  Z= 0.141
  Angle     :  0.702   8.881  11948  Z= 0.360
  Chirality :  0.041   0.148   1482
  Planarity :  0.005   0.061   1484
  Dihedral  :  5.210  17.286   1248
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.60 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  3.98 %
    Favored  : 95.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.25), residues: 1182
  helix:  0.10 (0.20), residues: 748
  sheet: -2.26 (1.00), residues: 34
  loop : -2.02 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 619 
 TYR   0.015   0.002   TYR B 586 
 PHE   0.019   0.001   PHE A 514 
 TRP   0.013   0.002   TRP B  61 
 HIS   0.007   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8694)
  covalent geometry    : angle       0.70236 (11948)
  hydrogen bonds       : bond        0.03845 (  536)
  hydrogen bonds       : angle       4.79786 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  158 TRP cc_start: 0.7724 (t-100) cc_final: 0.7479 (t-100)
REVERT: A  161 LEU cc_start: 0.9452 (mt) cc_final: 0.9190 (pp)
REVERT: A  178 ARG cc_start: 0.9306 (ttt90) cc_final: 0.8437 (ttt-90)
REVERT: A  180 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8900 (tm-30)
REVERT: A  315 PHE cc_start: 0.9341 (m-80) cc_final: 0.8475 (m-10)
REVERT: A  594 LEU cc_start: 0.9543 (pp) cc_final: 0.9162 (mp)
REVERT: A  668 PHE cc_start: 0.7283 (t80) cc_final: 0.6235 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0493
  time to fit residues: 8.6881
Evaluate side-chains
  99 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 6 optimal weight:    0.1980
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 45 optimal weight:   20.0000
   chunk 113 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.6186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 ASN
A 617 HIS
** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.088921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.072414 restraints weight = 17854.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.074272 restraints weight = 12594.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.075716 restraints weight = 9484.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.076681 restraints weight = 7555.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.077404 restraints weight = 6342.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.5024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8694  Z= 0.161
  Angle     :  0.722   8.976  11948  Z= 0.372
  Chirality :  0.042   0.143   1482
  Planarity :  0.005   0.065   1484
  Dihedral  :  5.084  23.536   1248
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.26), residues: 1182
  helix:  0.50 (0.20), residues: 756
  sheet: -2.37 (0.97), residues: 34
  loop : -1.87 (0.34), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 450 
 TYR   0.017   0.002   TYR B 164 
 PHE   0.018   0.002   PHE B 514 
 TRP   0.014   0.002   TRP B 613 
 HIS   0.005   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8694)
  covalent geometry    : angle       0.72168 (11948)
  hydrogen bonds       : bond        0.03986 (  536)
  hydrogen bonds       : angle       4.69775 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 TRP cc_start: 0.7805 (t-100) cc_final: 0.7544 (t-100)
REVERT: A  161 LEU cc_start: 0.9420 (mt) cc_final: 0.9182 (pp)
REVERT: A  178 ARG cc_start: 0.9319 (ttt90) cc_final: 0.8459 (ttt-90)
REVERT: A  180 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8704 (tm-30)
REVERT: A  315 PHE cc_start: 0.9418 (m-80) cc_final: 0.8872 (m-10)
REVERT: A  594 LEU cc_start: 0.9585 (pp) cc_final: 0.9182 (mp)
REVERT: A  668 PHE cc_start: 0.7213 (t80) cc_final: 0.6299 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0496
  time to fit residues: 8.4347
Evaluate side-chains
  95 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0870
   chunk 4 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 88 optimal weight:    8.9990
   overall best weight:    1.1360
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 ASN
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
A 618 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.090443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.073324 restraints weight = 17491.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.075222 restraints weight = 12389.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.076659 restraints weight = 9367.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.077699 restraints weight = 7496.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.078516 restraints weight = 6280.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.5453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8694  Z= 0.133
  Angle     :  0.682   8.170  11948  Z= 0.347
  Chirality :  0.041   0.151   1482
  Planarity :  0.005   0.064   1484
  Dihedral  :  4.929  25.559   1248
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  2.65 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.26), residues: 1182
  helix:  0.71 (0.20), residues: 756
  sheet: -2.41 (0.96), residues: 34
  loop : -1.95 (0.34), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 661 
 TYR   0.016   0.001   TYR A 164 
 PHE   0.023   0.001   PHE B 459 
 TRP   0.013   0.001   TRP A 613 
 HIS   0.004   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8694)
  covalent geometry    : angle       0.68201 (11948)
  hydrogen bonds       : bond        0.03632 (  536)
  hydrogen bonds       : angle       4.42632 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ILE cc_start: 0.8871 (tp) cc_final: 0.8627 (pt)
REVERT: A   57 ASN cc_start: 0.6474 (m-40) cc_final: 0.6191 (m-40)
REVERT: A  158 TRP cc_start: 0.7838 (t-100) cc_final: 0.7490 (t-100)
REVERT: A  161 LEU cc_start: 0.9426 (mt) cc_final: 0.9167 (pp)
REVERT: A  180 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8741 (tm-30)
REVERT: A  222 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8964 (mp0)
REVERT: A  315 PHE cc_start: 0.9391 (m-80) cc_final: 0.8349 (m-10)
REVERT: A  361 ILE cc_start: 0.9354 (mt) cc_final: 0.9138 (mm)
REVERT: A  374 ILE cc_start: 0.9488 (pt) cc_final: 0.9273 (pt)
REVERT: A  574 VAL cc_start: 0.8980 (p) cc_final: 0.8529 (p)
REVERT: A  594 LEU cc_start: 0.9536 (pp) cc_final: 0.9233 (mp)
REVERT: A  631 MET cc_start: 0.8562 (tpt) cc_final: 0.8362 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0460
  time to fit residues: 7.9251
Evaluate side-chains
  101 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 63 optimal weight:   30.0000
   chunk 20 optimal weight:    0.0030
   chunk 47 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 67 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0010
   overall best weight:    0.4998
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 ASN
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 618 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.092122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.074658 restraints weight = 17375.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.076682 restraints weight = 12217.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.078178 restraints weight = 9220.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.079221 restraints weight = 7340.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.079987 restraints weight = 6159.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.5787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8694  Z= 0.129
  Angle     :  0.681   7.502  11948  Z= 0.346
  Chirality :  0.041   0.150   1482
  Planarity :  0.005   0.063   1484
  Dihedral  :  4.822  25.216   1248
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  3.45 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.26), residues: 1182
  helix:  0.79 (0.20), residues: 762
  sheet: -2.81 (0.87), residues: 38
  loop : -1.98 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 345 
 TYR   0.017   0.002   TYR B 171 
 PHE   0.034   0.002   PHE B 514 
 TRP   0.011   0.001   TRP B  61 
 HIS   0.004   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8694)
  covalent geometry    : angle       0.68076 (11948)
  hydrogen bonds       : bond        0.03507 (  536)
  hydrogen bonds       : angle       4.34860 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ILE cc_start: 0.8830 (tp) cc_final: 0.8620 (pt)
REVERT: A   61 TRP cc_start: 0.8894 (p-90) cc_final: 0.8552 (p-90)
REVERT: A  158 TRP cc_start: 0.7706 (t-100) cc_final: 0.7384 (t-100)
REVERT: A  161 LEU cc_start: 0.9390 (mt) cc_final: 0.9140 (pp)
REVERT: A  180 GLN cc_start: 0.9212 (tp-100) cc_final: 0.8809 (tm-30)
REVERT: A  209 LYS cc_start: 0.9242 (tttt) cc_final: 0.8860 (tppt)
REVERT: A  222 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8975 (mp0)
REVERT: A  315 PHE cc_start: 0.9318 (m-80) cc_final: 0.8878 (m-10)
REVERT: A  361 ILE cc_start: 0.9415 (mt) cc_final: 0.9180 (mm)
REVERT: A  447 HIS cc_start: 0.9001 (t-90) cc_final: 0.8683 (t-90)
REVERT: A  465 PHE cc_start: 0.8711 (t80) cc_final: 0.8415 (t80)
REVERT: A  574 VAL cc_start: 0.8964 (p) cc_final: 0.8675 (p)
REVERT: A  594 LEU cc_start: 0.9486 (pp) cc_final: 0.9189 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0516
  time to fit residues: 9.1531
Evaluate side-chains
  100 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 115 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0970
   chunk 24 optimal weight:    7.9990
   chunk 113 optimal weight:    0.8980
   chunk 119 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.6778
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 299 GLN
A 351 ASN
** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.091698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.074503 restraints weight = 17105.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.076469 restraints weight = 12062.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.077952 restraints weight = 9096.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.079043 restraints weight = 7234.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.079819 restraints weight = 6027.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.6058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8694  Z= 0.129
  Angle     :  0.690   7.582  11948  Z= 0.347
  Chirality :  0.041   0.170   1482
  Planarity :  0.005   0.063   1484
  Dihedral  :  4.613  23.776   1248
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.39 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.26), residues: 1182
  helix:  0.90 (0.20), residues: 774
  sheet: -2.99 (0.85), residues: 38
  loop : -2.06 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 345 
 TYR   0.014   0.001   TYR A 164 
 PHE   0.028   0.002   PHE B 514 
 TRP   0.010   0.001   TRP B  61 
 HIS   0.003   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8694)
  covalent geometry    : angle       0.69037 (11948)
  hydrogen bonds       : bond        0.03425 (  536)
  hydrogen bonds       : angle       4.22949 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ASN cc_start: 0.6381 (m-40) cc_final: 0.6133 (m-40)
REVERT: A   61 TRP cc_start: 0.8805 (p-90) cc_final: 0.8569 (p-90)
REVERT: A  178 ARG cc_start: 0.9225 (ttt90) cc_final: 0.8717 (ttt-90)
REVERT: A  180 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8903 (tm-30)
REVERT: A  209 LYS cc_start: 0.9266 (tttt) cc_final: 0.8876 (tppt)
REVERT: A  222 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8947 (mp0)
REVERT: A  315 PHE cc_start: 0.9311 (m-80) cc_final: 0.8271 (m-10)
REVERT: A  447 HIS cc_start: 0.9075 (t-90) cc_final: 0.8705 (t-90)
REVERT: A  465 PHE cc_start: 0.8602 (t80) cc_final: 0.8340 (t80)
REVERT: A  594 LEU cc_start: 0.9533 (pp) cc_final: 0.9132 (mp)
REVERT: A  627 PHE cc_start: 0.9447 (t80) cc_final: 0.9114 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0482
  time to fit residues: 8.5973
Evaluate side-chains
  103 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0170
   chunk 45 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0670
   chunk 65 optimal weight:    0.0670
   chunk 103 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 119 optimal weight:    9.9990
   chunk 84 optimal weight:    0.0980
   chunk 50 optimal weight:    0.1980
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.0894
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
A 618 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.093413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.076378 restraints weight = 17385.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.078317 restraints weight = 12314.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.079731 restraints weight = 9360.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.080761 restraints weight = 7504.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.081581 restraints weight = 6327.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.6379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8694  Z= 0.135
  Angle     :  0.713   8.148  11948  Z= 0.361
  Chirality :  0.042   0.190   1482
  Planarity :  0.005   0.062   1484
  Dihedral  :  4.661  30.686   1248
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.53 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.26), residues: 1182
  helix:  0.84 (0.20), residues: 774
  sheet: -3.06 (0.86), residues: 38
  loop : -2.19 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 345 
 TYR   0.015   0.001   TYR A 171 
 PHE   0.037   0.002   PHE A 627 
 TRP   0.011   0.001   TRP B  61 
 HIS   0.002   0.001   HIS B 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8694)
  covalent geometry    : angle       0.71344 (11948)
  hydrogen bonds       : bond        0.03476 (  536)
  hydrogen bonds       : angle       4.18902 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ASN cc_start: 0.6631 (m-40) cc_final: 0.6403 (m110)
REVERT: A  178 ARG cc_start: 0.9276 (ttt90) cc_final: 0.8980 (ttt-90)
REVERT: A  180 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8920 (tm-30)
REVERT: A  209 LYS cc_start: 0.9256 (tttt) cc_final: 0.8845 (tppt)
REVERT: A  222 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8960 (mp0)
REVERT: A  315 PHE cc_start: 0.9180 (m-80) cc_final: 0.8848 (m-10)
REVERT: A  361 ILE cc_start: 0.9436 (mt) cc_final: 0.9205 (mm)
REVERT: A  447 HIS cc_start: 0.9082 (t-90) cc_final: 0.8608 (t70)
REVERT: A  465 PHE cc_start: 0.8482 (t80) cc_final: 0.8261 (t80)
REVERT: A  594 LEU cc_start: 0.9546 (pp) cc_final: 0.9149 (mp)
REVERT: A  606 TYR cc_start: 0.7531 (m-80) cc_final: 0.7309 (m-80)
REVERT: A  619 ARG cc_start: 0.8741 (mmt180) cc_final: 0.8430 (mmp80)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0446
  time to fit residues: 8.4453
Evaluate side-chains
  100 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 3 optimal weight:   30.0000
   chunk 79 optimal weight:    0.0980
   chunk 98 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.092742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.075456 restraints weight = 17201.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.077385 restraints weight = 12221.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.078807 restraints weight = 9328.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.079861 restraints weight = 7513.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.080675 restraints weight = 6329.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.6658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8694  Z= 0.135
  Angle     :  0.725  14.222  11948  Z= 0.362
  Chirality :  0.042   0.215   1482
  Planarity :  0.006   0.061   1484
  Dihedral  :  4.595  29.362   1248
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.26), residues: 1182
  helix:  0.82 (0.20), residues: 772
  sheet: -3.15 (0.85), residues: 38
  loop : -2.06 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 345 
 TYR   0.010   0.001   TYR A 572 
 PHE   0.027   0.002   PHE B 514 
 TRP   0.032   0.002   TRP B 613 
 HIS   0.002   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8694)
  covalent geometry    : angle       0.72491 (11948)
  hydrogen bonds       : bond        0.03735 (  536)
  hydrogen bonds       : angle       4.17516 ( 1590)

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 ARG cc_start: 0.9352 (ttt90) cc_final: 0.9082 (ttt-90)
REVERT: A  180 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8940 (tm-30)
REVERT: A  209 LYS cc_start: 0.9237 (tttt) cc_final: 0.8849 (tppt)
REVERT: A  222 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8952 (mp0)
REVERT: A  315 PHE cc_start: 0.9219 (m-80) cc_final: 0.8983 (m-10)
REVERT: A  361 ILE cc_start: 0.9438 (mt) cc_final: 0.9199 (mm)
REVERT: A  447 HIS cc_start: 0.9105 (t-90) cc_final: 0.8639 (t70)
REVERT: A  465 PHE cc_start: 0.8558 (t80) cc_final: 0.8352 (t80)
REVERT: A  594 LEU cc_start: 0.9556 (pp) cc_final: 0.9168 (mp)
REVERT: A  606 TYR cc_start: 0.7633 (m-80) cc_final: 0.7398 (m-80)
REVERT: A  618 GLN cc_start: 0.8834 (tt0) cc_final: 0.8620 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.0506
  time to fit residues: 9.2864
Evaluate side-chains
  99 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 102 optimal weight:    0.3980
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0370
   chunk 53 optimal weight:    0.0970
   chunk 76 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0770
   chunk 66 optimal weight:    0.4980
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.1814
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.094726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.077143 restraints weight = 17025.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.079114 restraints weight = 12104.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.080568 restraints weight = 9236.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.081693 restraints weight = 7431.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.082541 restraints weight = 6232.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.6846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8694  Z= 0.137
  Angle     :  0.736  12.370  11948  Z= 0.365
  Chirality :  0.043   0.213   1482
  Planarity :  0.005   0.057   1484
  Dihedral  :  4.679  32.899   1248
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  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 : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.26), residues: 1182
  helix:  0.80 (0.20), residues: 772
  sheet: -3.13 (0.85), residues: 38
  loop : -2.23 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 450 
 TYR   0.012   0.001   TYR A 171 
 PHE   0.026   0.001   PHE A 514 
 TRP   0.030   0.002   TRP B 613 
 HIS   0.002   0.001   HIS B 617 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8694)
  covalent geometry    : angle       0.73624 (11948)
  hydrogen bonds       : bond        0.03537 (  536)
  hydrogen bonds       : angle       4.15426 ( 1590)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1022.49 seconds
wall clock time: 18 minutes 28.80 seconds (1108.80 seconds total)