Starting phenix.real_space_refine
on Tue Mar  3 13:53:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dcr_30640/03_2026/7dcr_30640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dcr_30640/03_2026/7dcr_30640.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dcr_30640/03_2026/7dcr_30640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dcr_30640/03_2026/7dcr_30640.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dcr_30640/03_2026/7dcr_30640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dcr_30640/03_2026/7dcr_30640.map"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 55 atoms to isotropic.
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      35      5.16       5
     C    3613      2.51       5
     N     964      2.21       5
     O    1041      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5653
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "x"
      Number of atoms: 5197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 653, 5197
          Classifications: {'peptide': 653}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 619}
    Chain: "y"
      Number of atoms: 456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 456
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 1.39, per 1000 atoms: 0.25
  Number of scatterers: 5653
  At special positions: 0
  Unit cell: (86.7875, 88.1125, 80.825, 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      35     16.00
     O    1041      8.00
     N     964      7.00
     C    3613      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: 0.48
  Conformation dependent library (CDL) restraints added in 320.6 milliseconds
  

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      45.1% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'x' and resid 228 through 237
      removed outlier: 3.526A  pdb=" N   LEU x 232 " --> pdb=" O   TYR x 228 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU x 235 " --> pdb=" O   GLU x 231 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 255 through 264
      removed outlier: 3.514A  pdb=" N   VAL x 261 " --> pdb=" O   PRO x 257 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 279 through 295
      removed outlier: 3.686A  pdb=" N   THR x 284 " --> pdb=" O   ARG x 280 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL x 286 " --> pdb=" O   ALA x 282 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN x 295 " --> pdb=" O   ALA x 291 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 323 through 329
      removed outlier: 3.719A  pdb=" N   LEU x 327 " --> pdb=" O   THR x 323 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 330 through 332
      No H-bonds generated for 'chain 'x' and resid 330 through 332'
    Processing helix  chain 'x' and resid 347 through 351
    Processing helix  chain 'x' and resid 352 through 357
    Processing helix  chain 'x' and resid 357 through 365
      removed outlier: 3.505A  pdb=" N   ASP x 364 " --> pdb=" O   GLY x 360 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE x 365 " --> pdb=" O   LEU x 361 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 382 through 390
      removed outlier: 3.523A  pdb=" N   SER x 387 " --> pdb=" O   ALA x 383 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 418 through 431
      removed outlier: 3.547A  pdb=" N   ILE x 425 " --> pdb=" O   ALA x 421 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR x 431 " --> pdb=" O   GLN x 427 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 444 through 463
      removed outlier: 3.535A  pdb=" N   LYS x 454 " --> pdb=" O   ARG x 450 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   MET x 459 " --> pdb=" O   LEU x 455 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU x 462 " --> pdb=" O   ILE x 458 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 479 through 488
      removed outlier: 4.082A  pdb=" N   LYS x 485 " --> pdb=" O   GLU x 481 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE x 486 " --> pdb=" O   GLN x 482 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   PHE x 487 " --> pdb=" O   GLN x 483 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN x 488 " --> pdb=" O   LEU x 484 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 542 through 551
    Processing helix  chain 'x' and resid 566 through 573
    Processing helix  chain 'x' and resid 587 through 597
      removed outlier: 3.519A  pdb=" N   LEU x 592 " --> pdb=" O   SER x 588 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 612 through 626
      removed outlier: 3.572A  pdb=" N   LYS x 618 " --> pdb=" O   PRO x 614 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER x 619 " --> pdb=" O   THR x 615 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU x 623 " --> pdb=" O   SER x 619 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE x 625 " --> pdb=" O   GLU x 621 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 636 through 643
      removed outlier: 3.625A  pdb=" N   CYS x 643 " --> pdb=" O   GLY x 639 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 650 through 661
      removed outlier: 3.585A  pdb=" N   VAL x 654 " --> pdb=" O   GLU x 650 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA x 659 " --> pdb=" O   LEU x 655 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 667 through 679
      removed outlier: 3.915A  pdb=" N   THR x 673 " --> pdb=" O   GLU x 669 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE x 674 " --> pdb=" O   GLU x 670 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER x 676 " --> pdb=" O   LEU x 672 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 688 through 697
      removed outlier: 3.785A  pdb=" N   ALA x 692 " --> pdb=" O   GLN x 688 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ALA x 694 " --> pdb=" O   ARG x 690 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER x 695 " --> pdb=" O   ASP x 691 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL x 696 " --> pdb=" O   ALA x 692 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 702 through 717
      removed outlier: 3.584A  pdb=" N   TYR x 707 " --> pdb=" O   ASP x 703 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   PHE x 711 " --> pdb=" O   TYR x 707 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 720 through 727
      removed outlier: 3.795A  pdb=" N   CYS x 724 " --> pdb=" O   SER x 720 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN x 725 " --> pdb=" O   ARG x 721 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP x 726 " --> pdb=" O   SER x 722 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 730 through 752
      removed outlier: 3.608A  pdb=" N   MET x 734 " --> pdb=" O   GLN x 730 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG x 736 " --> pdb=" O   LYS x 732 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LYS x 750 " --> pdb=" O   ARG x 746 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 754 through 764
      removed outlier: 3.523A  pdb=" N   ALA x 760 " --> pdb=" O   LYS x 756 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE x 764 " --> pdb=" O   ALA x 760 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 767 through 781
      removed outlier: 3.520A  pdb=" N   ILE x 771 " --> pdb=" O   ILE x 767 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ASN x 772 " --> pdb=" O   ALA x 768 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   ALA x 773 " --> pdb=" O   GLY x 769 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   THR x 776 " --> pdb=" O   ASN x 772 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 813 through 821
      removed outlier: 3.866A  pdb=" N   VAL x 817 " --> pdb=" O   SER x 813 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   HIS x 819 " --> pdb=" O   LEU x 815 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS x 820 " --> pdb=" O   PHE x 816 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 852 through 857
    Processing helix  chain 'x' and resid 859 through 867
      removed outlier: 3.570A  pdb=" N   PHE x 863 " --> pdb=" O   VAL x 859 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ASP x 865 " --> pdb=" O   GLN x 861 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   LEU x 866 " --> pdb=" O   ILE x 862 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 95 through 100
    Processing helix  chain 'y' and resid 101 through 111
      removed outlier: 3.808A  pdb=" N   ASP y 107 " --> pdb=" O   GLU y 103 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU y 110 " --> pdb=" O   GLY y 106 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG y 111 " --> pdb=" O   ASP y 107 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'x' and resid 310 through 311
      removed outlier: 3.593A  pdb=" N   TYR x 304 " --> pdb=" O   LYS x 311 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLY x 303 " --> pdb=" O   TYR x 321 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ILE x 273 " --> pdb=" O   LYS x 320 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   MET x 322 " --> pdb=" O   ILE x 273 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   ILE x 275 " --> pdb=" O   MET x 322 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   GLN x 272 " --> pdb=" O   TYR x 340 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   CYS x 342 " --> pdb=" O   GLN x 272 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   SER x 341 " --> pdb=" O   LYS x 373 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   LEU x 375 " --> pdb=" O   SER x 341 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE x 343 " --> pdb=" O   LEU x 375 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   SER x 377 " --> pdb=" O   ILE x 343 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE x 345 " --> pdb=" O   SER x 377 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   PHE x 396 " --> pdb=" O   VAL x 241 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   ILE x 243 " --> pdb=" O   PHE x 396 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'x' and resid 406 through 409
      removed outlier: 7.074A  pdb=" N   ARG x 514 " --> pdb=" O   LYS x 560 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   PHE x 562 " --> pdb=" O   ARG x 514 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL x 516 " --> pdb=" O   PHE x 562 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ASP x 437 " --> pdb=" O   TYR x 515 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ILE x 517 " --> pdb=" O   ASP x 437 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU x 439 " --> pdb=" O   ILE x 517 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ILE x 438 " --> pdb=" O   VAL x 498 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   ALA x 500 " --> pdb=" O   ILE x 438 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL x 440 " --> pdb=" O   ALA x 500 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   GLN x 468 " --> pdb=" O   ARG x 495 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   VAL x 497 " --> pdb=" O   GLN x 468 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ILE x 470 " --> pdb=" O   VAL x 497 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   LEU x 499 " --> pdb=" O   ILE x 470 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   THR x 472 " --> pdb=" O   LEU x 499 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'x' and resid 521 through 527
      removed outlier: 5.421A  pdb=" N   LEU x 835 " --> pdb=" O   THR x 534 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   THR x 538 " --> pdb=" O   LEU x 837 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLN x 834 " --> pdb=" O   ARG x 844 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'x' and resid 795 through 797
      removed outlier: 3.744A  pdb=" N   TYR x 829 " --> pdb=" O   ILE x 849 " (cutoff:3.500A)

    175 hydrogen bonds defined for protein.
    516 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.88

  Time building geometry restraints manager: 0.62 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: 1795
        1.34 -     1.46: 767
        1.46 -     1.57: 3137
        1.57 -     1.69: 1
        1.69 -     1.81: 57
  Bond restraints: 5757
  Sorted by residual:
  bond pdb=" CA  ARG x 584 "
       pdb=" CB  ARG x 584 "
    ideal  model  delta    sigma   weight residual
    1.531  1.614 -0.083 3.12e-02 1.03e+03 7.09e+00
  bond pdb=" C   THR x 681 "
       pdb=" N   PRO x 682 "
    ideal  model  delta    sigma   weight residual
    1.337  1.352 -0.016 1.11e-02 8.12e+03 2.03e+00
  bond pdb=" C   ILE x 613 "
       pdb=" N   PRO x 614 "
    ideal  model  delta    sigma   weight residual
    1.336  1.352 -0.017 1.23e-02 6.61e+03 1.84e+00
  bond pdb=" CB  ARG x 584 "
       pdb=" CG  ARG x 584 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.82e+00
  bond pdb=" N   ASP y 144 "
       pdb=" CA  ASP y 144 "
    ideal  model  delta    sigma   weight residual
    1.458  1.480 -0.022 1.77e-02 3.19e+03 1.53e+00
  ... (remaining 5752 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 7407
        1.82 -     3.64: 305
        3.64 -     5.46: 43
        5.46 -     7.28: 15
        7.28 -     9.10: 9
  Bond angle restraints: 7779
  Sorted by residual:
  angle pdb=" C   HIS y 142 "
        pdb=" N   PRO y 143 "
        pdb=" CA  PRO y 143 "
      ideal   model   delta    sigma   weight residual
     119.84  125.33   -5.49 1.25e+00 6.40e-01 1.93e+01
  angle pdb=" C   VAL x 297 "
        pdb=" N   LEU x 298 "
        pdb=" CA  LEU x 298 "
      ideal   model   delta    sigma   weight residual
     121.54  129.70   -8.16 1.91e+00 2.74e-01 1.82e+01
  angle pdb=" CA  ARG x 584 "
        pdb=" CB  ARG x 584 "
        pdb=" CG  ARG x 584 "
      ideal   model   delta    sigma   weight residual
     114.10  122.05   -7.95 2.00e+00 2.50e-01 1.58e+01
  angle pdb=" N   LEU x 298 "
        pdb=" CA  LEU x 298 "
        pdb=" C   LEU x 298 "
      ideal   model   delta    sigma   weight residual
     110.80  103.10    7.70 2.13e+00 2.20e-01 1.31e+01
  angle pdb=" C   LEU x 434 "
        pdb=" N   PRO x 435 "
        pdb=" CD  PRO x 435 "
      ideal   model   delta    sigma   weight residual
     120.60  112.96    7.64 2.20e+00 2.07e-01 1.21e+01
  ... (remaining 7774 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.93: 3343
       14.93 -    29.85: 137
       29.85 -    44.77: 52
       44.77 -    59.70: 6
       59.70 -    74.62: 6
  Dihedral angle restraints: 3544
    sinusoidal: 1477
      harmonic: 2067
  Sorted by residual:
  dihedral pdb=" CA  PHE x 605 "
           pdb=" C   PHE x 605 "
           pdb=" N   PRO x 606 "
           pdb=" CA  PRO x 606 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.99  -23.01     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  VAL x 297 "
           pdb=" C   VAL x 297 "
           pdb=" N   LEU x 298 "
           pdb=" CA  LEU x 298 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.89   22.11     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  LEU x 607 "
           pdb=" C   LEU x 607 "
           pdb=" N   MET x 608 "
           pdb=" CA  MET x 608 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.66  -21.34     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 3541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 781
       0.078 -    0.155: 110
       0.155 -    0.233: 7
       0.233 -    0.310: 2
       0.310 -    0.388: 1
  Chirality restraints: 901
  Sorted by residual:
  chirality pdb=" CA  ASP y 144 "
            pdb=" N   ASP y 144 "
            pdb=" C   ASP y 144 "
            pdb=" CB  ASP y 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.76e+00
  chirality pdb=" CB  ILE x 635 "
            pdb=" CA  ILE x 635 "
            pdb=" CG1 ILE x 635 "
            pdb=" CG2 ILE x 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CB  THR x 585 "
            pdb=" CA  THR x 585 "
            pdb=" OG1 THR x 585 "
            pdb=" CG2 THR x 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 898 not shown)

  Planarity restraints: 986
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN x 757 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.02e+00
        pdb=" CG  ASN x 757 "   -0.039 2.00e-02 2.50e+03
        pdb=" OD1 ASN x 757 "    0.015 2.00e-02 2.50e+03
        pdb=" ND2 ASN x 757 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS x 810 "   -0.035 5.00e-02 4.00e+02   5.32e-02 4.52e+00
        pdb=" N   PRO x 811 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO x 811 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO x 811 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR x 313 "   -0.034 5.00e-02 4.00e+02   5.21e-02 4.34e+00
        pdb=" N   PRO x 314 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO x 314 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO x 314 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 983 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1294
        2.79 -     3.32: 4845
        3.32 -     3.84: 8983
        3.84 -     4.37: 10831
        4.37 -     4.90: 18170
  Nonbonded interactions: 44123
  Sorted by model distance:
  nonbonded pdb=" OG1 THR x 636 "
            pdb=" O   VAL y  89 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   SER x 683 "
            pdb=" OG1 THR x 733 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   SER x 717 "
            pdb=" OG  SER x 720 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   GLN x 427 "
            pdb=" OG1 THR x 431 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" NZ  LYS x 689 "
            pdb=" OD1 ASP x 703 "
     model   vdw
     2.354 3.120
  ... (remaining 44118 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.530
  Find NCS groups from input model:        0.020
  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:             0.010
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
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      :  0.005   0.083   5757  Z= 0.208
  Angle     :  0.894   9.099   7779  Z= 0.464
  Chirality :  0.055   0.388    901
  Planarity :  0.007   0.053    986
  Dihedral  : 10.492  74.622   2204
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.00 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  3.93 %
    Favored  : 95.44 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -4.71 (0.24), residues: 701
  helix: -4.37 (0.12), residues: 296
  sheet: -0.85 (0.49), residues: 107
  loop : -2.44 (0.31), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG x 777 
 TYR   0.023   0.003   TYR x 321 
 PHE   0.013   0.002   PHE x 565 
 TRP   0.031   0.004   TRP x 723 
 HIS   0.012   0.002   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 5757)
  covalent geometry    : angle       0.89372 ( 7779)
  hydrogen bonds       : bond        0.32859 (  175)
  hydrogen bonds       : angle       9.67804 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: x  584 ARG cc_start: 0.6619 (pmt-80) cc_final: 0.5582 (ppt170)
REVERT: x  854 TRP cc_start: 0.7522 (m-10) cc_final: 0.7105 (m-10)
  outliers start: 4
  outliers final: 1
  residues processed: 157
  average time/residue: 0.0988
  time to fit residues: 19.1651
Evaluate side-chains
  91 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain y residue  144 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0570
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0020
   overall best weight:    0.3644

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

Flipped N/Q/H residues before XYZ refinement:
x 255 GLN
x 258 GLN
x 315 ASN
x 408 HIS
x 727 HIS
x 796 GLN
y  98 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.153616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.124334 restraints weight = 6569.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.21
r_work: 0.3378 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5757  Z= 0.104
  Angle     :  0.550   5.074   7779  Z= 0.288
  Chirality :  0.044   0.169    901
  Planarity :  0.005   0.042    986
  Dihedral  :  5.178  49.406    765
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  7.08 %
    Favored  : 90.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -2.93 (0.28), residues: 701
  helix: -2.45 (0.23), residues: 306
  sheet: -0.36 (0.51), residues: 106
  loop : -1.78 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG x 280 
 TYR   0.011   0.001   TYR x 259 
 PHE   0.009   0.001   PHE x 731 
 TRP   0.011   0.001   TRP x 568 
 HIS   0.004   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5757)
  covalent geometry    : angle       0.55030 ( 7779)
  hydrogen bonds       : bond        0.03758 (  175)
  hydrogen bonds       : angle       4.91582 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: x  326 MET cc_start: 0.8497 (mmm) cc_final: 0.8229 (mmm)
REVERT: x  447 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7668 (mt-10)
REVERT: x  584 ARG cc_start: 0.6587 (pmt-80) cc_final: 0.6058 (pmt-80)
REVERT: x  847 LEU cc_start: 0.8163 (tm) cc_final: 0.7937 (tp)
  outliers start: 15
  outliers final: 4
  residues processed: 106
  average time/residue: 0.0933
  time to fit residues: 12.2121
Evaluate side-chains
  78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain x residue  815 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.147475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.118495 restraints weight = 6649.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.10
r_work: 0.3304 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5757  Z= 0.156
  Angle     :  0.588   6.355   7779  Z= 0.299
  Chirality :  0.046   0.231    901
  Planarity :  0.005   0.039    986
  Dihedral  :  4.563  18.541    763
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.22 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -1.95 (0.30), residues: 701
  helix: -1.28 (0.27), residues: 309
  sheet: -0.50 (0.52), residues: 105
  loop : -1.44 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG x 777 
 TYR   0.021   0.002   TYR x 832 
 PHE   0.013   0.002   PHE x 719 
 TRP   0.012   0.002   TRP x 568 
 HIS   0.003   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 5757)
  covalent geometry    : angle       0.58771 ( 7779)
  hydrogen bonds       : bond        0.03701 (  175)
  hydrogen bonds       : angle       4.31399 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: x  279 ARG cc_start: 0.8515 (tpp80) cc_final: 0.7664 (mtm110)
REVERT: x  347 GLU cc_start: 0.8412 (mp0) cc_final: 0.8198 (mm-30)
REVERT: x  575 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8102 (mm-30)
REVERT: x  584 ARG cc_start: 0.6822 (pmt-80) cc_final: 0.6061 (pmt-80)
REVERT: x  847 LEU cc_start: 0.8404 (tm) cc_final: 0.8132 (tp)
REVERT: x  854 TRP cc_start: 0.7967 (m-10) cc_final: 0.7249 (m-10)
  outliers start: 12
  outliers final: 7
  residues processed: 86
  average time/residue: 0.1022
  time to fit residues: 11.0206
Evaluate side-chains
  76 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  513 ILE
Chi-restraints excluded: chain x residue  522 VAL
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  619 SER
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain x residue  812 THR
Chi-restraints excluded: chain x residue  815 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0770
   chunk 68 optimal weight:    6.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
x 258 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.150343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.120718 restraints weight = 6590.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.17
r_work: 0.3342 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5757  Z= 0.104
  Angle     :  0.523   5.300   7779  Z= 0.265
  Chirality :  0.044   0.225    901
  Planarity :  0.004   0.038    986
  Dihedral  :  4.300  16.570    763
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.79 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.32), residues: 701
  helix: -0.54 (0.29), residues: 306
  sheet: -0.29 (0.53), residues: 105
  loop : -1.23 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG x 280 
 TYR   0.013   0.001   TYR x 527 
 PHE   0.008   0.001   PHE x 779 
 TRP   0.009   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5757)
  covalent geometry    : angle       0.52330 ( 7779)
  hydrogen bonds       : bond        0.02910 (  175)
  hydrogen bonds       : angle       3.94753 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: x  279 ARG cc_start: 0.8444 (tpp80) cc_final: 0.7529 (mtm110)
REVERT: x  575 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8146 (mm-30)
REVERT: x  584 ARG cc_start: 0.6684 (pmt-80) cc_final: 0.5641 (ppt170)
REVERT: x  854 TRP cc_start: 0.8009 (m-10) cc_final: 0.7239 (m-10)
  outliers start: 12
  outliers final: 8
  residues processed: 85
  average time/residue: 0.1001
  time to fit residues: 10.7431
Evaluate side-chains
  75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  513 ILE
Chi-restraints excluded: chain x residue  522 VAL
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  619 SER
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain x residue  815 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 69 optimal weight:    9.9990
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.152336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.122547 restraints weight = 6712.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.20
r_work: 0.3361 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5757  Z= 0.096
  Angle     :  0.506   5.720   7779  Z= 0.259
  Chirality :  0.043   0.218    901
  Planarity :  0.004   0.036    986
  Dihedral  :  4.132  15.919    763
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.79 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.73 (0.32), residues: 701
  helix:  0.05 (0.30), residues: 306
  sheet: -0.13 (0.54), residues: 105
  loop : -1.08 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG x 450 
 TYR   0.012   0.001   TYR x 527 
 PHE   0.007   0.001   PHE x 779 
 TRP   0.007   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 5757)
  covalent geometry    : angle       0.50580 ( 7779)
  hydrogen bonds       : bond        0.02630 (  175)
  hydrogen bonds       : angle       3.72914 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: x  294 MET cc_start: 0.7539 (mtp) cc_final: 0.7279 (ttm)
REVERT: x  575 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: x  584 ARG cc_start: 0.6561 (pmt-80) cc_final: 0.5421 (ppt170)
REVERT: x  854 TRP cc_start: 0.7974 (m-10) cc_final: 0.7208 (m-10)
REVERT: y   71 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5780 (mt)
  outliers start: 13
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0959
  time to fit residues: 10.6832
Evaluate side-chains
  78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  522 VAL
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  619 SER
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain y residue   71 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 23 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
x 239 ASN
x 502 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.150520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.120774 restraints weight = 6651.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.19
r_work: 0.3334 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5757  Z= 0.112
  Angle     :  0.525   6.316   7779  Z= 0.267
  Chirality :  0.044   0.220    901
  Planarity :  0.004   0.035    986
  Dihedral  :  4.113  16.069    763
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.74 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.46 (0.33), residues: 701
  helix:  0.36 (0.31), residues: 306
  sheet: -0.02 (0.53), residues: 109
  loop : -1.06 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG x 450 
 TYR   0.016   0.001   TYR x 832 
 PHE   0.010   0.001   PHE x 779 
 TRP   0.008   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5757)
  covalent geometry    : angle       0.52522 ( 7779)
  hydrogen bonds       : bond        0.02756 (  175)
  hydrogen bonds       : angle       3.70139 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: x  294 MET cc_start: 0.7544 (mtp) cc_final: 0.7301 (ttm)
REVERT: x  584 ARG cc_start: 0.6544 (pmt-80) cc_final: 0.4441 (mmp-170)
REVERT: x  854 TRP cc_start: 0.8009 (m-10) cc_final: 0.7168 (m-10)
REVERT: y   71 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5769 (mt)
  outliers start: 13
  outliers final: 8
  residues processed: 83
  average time/residue: 0.0898
  time to fit residues: 9.6100
Evaluate side-chains
  77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  513 ILE
Chi-restraints excluded: chain x residue  522 VAL
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  619 SER
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain x residue  812 THR
Chi-restraints excluded: chain y residue   71 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 18 optimal weight:    0.1980
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0980
   chunk 64 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   chunk 25 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.2980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.153650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.124238 restraints weight = 6655.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.19
r_work: 0.3373 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5757  Z= 0.090
  Angle     :  0.502   5.400   7779  Z= 0.255
  Chirality :  0.043   0.161    901
  Planarity :  0.004   0.035    986
  Dihedral  :  3.975  15.451    763
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.84 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.06 (0.33), residues: 701
  helix:  0.84 (0.31), residues: 301
  sheet: -0.12 (0.51), residues: 119
  loop : -0.89 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG x 450 
 TYR   0.011   0.001   TYR x 527 
 PHE   0.006   0.001   PHE x 779 
 TRP   0.006   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 5757)
  covalent geometry    : angle       0.50228 ( 7779)
  hydrogen bonds       : bond        0.02381 (  175)
  hydrogen bonds       : angle       3.55517 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: x  584 ARG cc_start: 0.6537 (pmt-80) cc_final: 0.4505 (mmp-170)
REVERT: x  854 TRP cc_start: 0.7946 (m-10) cc_final: 0.7174 (m-10)
REVERT: y   71 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.5743 (mt)
  outliers start: 9
  outliers final: 4
  residues processed: 83
  average time/residue: 0.0931
  time to fit residues: 9.9390
Evaluate side-chains
  74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  619 SER
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain y residue   71 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   chunk 46 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9990
   chunk 64 optimal weight:    0.3980
   chunk 20 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0670
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.3318

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

Flipped N/Q/H residues before XYZ refinement:
x 502 ASN
x 572 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.154392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.125052 restraints weight = 6574.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.19
r_work: 0.3386 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5757  Z= 0.089
  Angle     :  0.496   5.811   7779  Z= 0.253
  Chirality :  0.043   0.146    901
  Planarity :  0.004   0.037    986
  Dihedral  :  3.875  15.440    763
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.99 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.18 (0.33), residues: 701
  helix:  1.13 (0.31), residues: 301
  sheet:  0.00 (0.51), residues: 119
  loop : -0.88 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG x 450 
 TYR   0.010   0.001   TYR x 527 
 PHE   0.009   0.001   PHE x 396 
 TRP   0.006   0.001   TRP x 568 
 HIS   0.005   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 5757)
  covalent geometry    : angle       0.49606 ( 7779)
  hydrogen bonds       : bond        0.02328 (  175)
  hydrogen bonds       : angle       3.46551 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: x  372 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8317 (tp)
REVERT: x  584 ARG cc_start: 0.6493 (pmt-80) cc_final: 0.4598 (mmp-170)
REVERT: x  854 TRP cc_start: 0.7953 (m-10) cc_final: 0.7198 (m-10)
REVERT: y   71 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5703 (mt)
  outliers start: 12
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0932
  time to fit residues: 9.5666
Evaluate side-chains
  75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  372 LEU
Chi-restraints excluded: chain x residue  522 VAL
Chi-restraints excluded: chain x residue  576 LEU
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  619 SER
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain y residue   71 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    0.0470
   chunk 52 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 65 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.152668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.123126 restraints weight = 6604.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.18
r_work: 0.3362 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5757  Z= 0.103
  Angle     :  0.518   5.781   7779  Z= 0.263
  Chirality :  0.044   0.170    901
  Planarity :  0.004   0.039    986
  Dihedral  :  3.953  16.424    763
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.78 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.29 (0.33), residues: 701
  helix:  1.23 (0.31), residues: 301
  sheet:  0.09 (0.51), residues: 115
  loop : -0.84 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG x 450 
 TYR   0.014   0.001   TYR x 832 
 PHE   0.010   0.001   PHE x 779 
 TRP   0.007   0.001   TRP x 568 
 HIS   0.005   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5757)
  covalent geometry    : angle       0.51761 ( 7779)
  hydrogen bonds       : bond        0.02560 (  175)
  hydrogen bonds       : angle       3.48956 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: x  372 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8314 (tp)
REVERT: x  450 ARG cc_start: 0.6701 (mtm110) cc_final: 0.6461 (mtm110)
REVERT: x  584 ARG cc_start: 0.6581 (pmt-80) cc_final: 0.4563 (mmp-170)
REVERT: x  854 TRP cc_start: 0.7965 (m-10) cc_final: 0.7191 (m-10)
REVERT: y   71 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5719 (mt)
  outliers start: 10
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0843
  time to fit residues: 8.5608
Evaluate side-chains
  77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  372 LEU
Chi-restraints excluded: chain x residue  443 THR
Chi-restraints excluded: chain x residue  522 VAL
Chi-restraints excluded: chain x residue  576 LEU
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  619 SER
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain y residue   71 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 64 optimal weight:    0.2980
   chunk 68 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    0.1980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 57 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
x 502 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.154326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.125108 restraints weight = 6627.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.13
r_work: 0.3392 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5757  Z= 0.093
  Angle     :  0.500   5.492   7779  Z= 0.255
  Chirality :  0.043   0.150    901
  Planarity :  0.004   0.040    986
  Dihedral  :  3.852  15.081    763
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.94 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.51 (0.33), residues: 701
  helix:  1.54 (0.31), residues: 300
  sheet:  0.13 (0.52), residues: 119
  loop : -0.86 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG x 450 
 TYR   0.010   0.001   TYR x 527 
 PHE   0.009   0.001   PHE x 396 
 TRP   0.006   0.001   TRP x 568 
 HIS   0.005   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 5757)
  covalent geometry    : angle       0.50012 ( 7779)
  hydrogen bonds       : bond        0.02352 (  175)
  hydrogen bonds       : angle       3.43138 (  516)

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

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

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1402 Ramachandran restraints generated.
    701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: x  372 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8304 (tp)
REVERT: x  584 ARG cc_start: 0.6543 (pmt-80) cc_final: 0.4622 (mmp-170)
REVERT: x  854 TRP cc_start: 0.7909 (m-10) cc_final: 0.7125 (m-10)
REVERT: y   71 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5709 (mt)
  outliers start: 9
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0874
  time to fit residues: 8.7151
Evaluate side-chains
  74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  372 LEU
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  576 LEU
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain x residue  812 THR
Chi-restraints excluded: chain y residue   71 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
x 502 ASN
x 525 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.154139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.124648 restraints weight = 6545.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.18
r_work: 0.3386 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   5757  Z= 0.162
  Angle     :  1.002  59.190   7779  Z= 0.590
  Chirality :  0.058   1.122    901
  Planarity :  0.005   0.098    986
  Dihedral  :  4.023  31.538    763
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.25 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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:  0.54 (0.33), residues: 701
  helix:  1.54 (0.31), residues: 300
  sheet:  0.14 (0.52), residues: 119
  loop : -0.81 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG x 450 
 TYR   0.010   0.001   TYR x 832 
 PHE   0.014   0.001   PHE x 605 
 TRP   0.005   0.001   TRP x 568 
 HIS   0.004   0.001   HIS x 810 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5757)
  covalent geometry    : angle       1.00232 ( 7779)
  hydrogen bonds       : bond        0.02395 (  175)
  hydrogen bonds       : angle       3.43305 (  516)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1863.85 seconds
wall clock time: 32 minutes 29.11 seconds (1949.11 seconds total)