Starting phenix.real_space_refine
on Thu Mar  6 09:05:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dcr_30640/03_2025/7dcr_30640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dcr_30640/03_2025/7dcr_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dcr_30640/03_2025/7dcr_30640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dcr_30640/03_2025/7dcr_30640.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dcr_30640/03_2025/7dcr_30640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dcr_30640/03_2025/7dcr_30640.cif"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.20, per 1000 atoms: 0.74
  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: 1.29
  Conformation dependent library (CDL) restraints added in 634.5 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: 0.72
  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: 1.79

  Time building geometry restraints manager: 1.50 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:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.460
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.440
-------------------------------------------------------------------------------
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= 0.327
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.031   0.004   TRP x 723 
 HIS   0.012   0.002   HIS x 810 
 PHE   0.013   0.002   PHE x 565 
 TYR   0.023   0.003   TYR x 321 
 ARG   0.005   0.001   ARG x 777 

*********************** 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  : 0.631 
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: 0.2210
  time to fit residues: 42.7240
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  : 0.579 
-------------------------------------------------------------------------------
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 59 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0050
   chunk 35 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.152465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.123476 restraints weight = 6479.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.17
r_work: 0.3369 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5757  Z= 0.169
  Angle     :  0.561   5.148   7779  Z= 0.293
  Chirality :  0.044   0.169    901
  Planarity :  0.005   0.041    986
  Dihedral  :  5.209  49.665    765
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  7.08 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.28), residues: 701
  helix: -2.46 (0.23), residues: 306
  sheet: -0.46 (0.51), residues: 107
  loop : -1.77 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP x 568 
 HIS   0.004   0.001   HIS x 810 
 PHE   0.009   0.001   PHE x 731 
 TYR   0.012   0.001   TYR x 832 
 ARG   0.006   0.000   ARG x 280 

*********************** 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
  108 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: x  447 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7634 (mt-10)
REVERT: x  575 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7949 (mm-30)
REVERT: x  584 ARG cc_start: 0.6625 (pmt-80) cc_final: 0.5894 (pmt-80)
REVERT: x  847 LEU cc_start: 0.8216 (tm) cc_final: 0.7996 (tp)
  outliers start: 16
  outliers final: 6
  residues processed: 104
  average time/residue: 0.2356
  time to fit residues: 30.6607
Evaluate side-chains
  80 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
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  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 57 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   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 = 0.147555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.118632 restraints weight = 6632.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.14
r_work: 0.3286 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5757  Z= 0.245
  Angle     :  0.590   5.877   7779  Z= 0.301
  Chirality :  0.046   0.237    901
  Planarity :  0.005   0.040    986
  Dihedral  :  4.578  18.530    763
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  :  9.43 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.30), residues: 701
  helix: -1.26 (0.28), residues: 309
  sheet: -0.57 (0.51), residues: 105
  loop : -1.46 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP x 568 
 HIS   0.004   0.001   HIS x 810 
 PHE   0.014   0.002   PHE x 719 
 TYR   0.021   0.002   TYR x 832 
 ARG   0.007   0.001   ARG x 777 

*********************** 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
  90 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: x  279 ARG cc_start: 0.8521 (tpp80) cc_final: 0.7578 (mtm110)
REVERT: x  347 GLU cc_start: 0.8438 (mp0) cc_final: 0.8169 (mm-30)
REVERT: x  575 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8110 (mm-30)
REVERT: x  584 ARG cc_start: 0.6718 (pmt-80) cc_final: 0.5959 (pmt-80)
REVERT: x  847 LEU cc_start: 0.8375 (tm) cc_final: 0.8114 (tp)
REVERT: x  854 TRP cc_start: 0.8051 (m-10) cc_final: 0.7304 (m-10)
  outliers start: 14
  outliers final: 8
  residues processed: 88
  average time/residue: 0.2244
  time to fit residues: 25.0166
Evaluate side-chains
  78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
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 26 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.150557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.121206 restraints weight = 6717.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.16
r_work: 0.3319 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5757  Z= 0.169
  Angle     :  0.528   5.122   7779  Z= 0.268
  Chirality :  0.044   0.236    901
  Planarity :  0.004   0.038    986
  Dihedral  :  4.300  16.567    763
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.48 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.32), residues: 701
  helix: -0.50 (0.29), residues: 306
  sheet: -0.41 (0.52), residues: 105
  loop : -1.23 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 810 
 PHE   0.008   0.001   PHE x 779 
 TYR   0.013   0.001   TYR x 832 
 ARG   0.004   0.000   ARG x 777 

*********************** 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
  91 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
REVERT: x  347 GLU cc_start: 0.8376 (mp0) cc_final: 0.8099 (mm-30)
REVERT: x  575 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8137 (mm-30)
REVERT: x  584 ARG cc_start: 0.6540 (pmt-80) cc_final: 0.5538 (ppt170)
REVERT: x  854 TRP cc_start: 0.8002 (m-10) cc_final: 0.7209 (m-10)
  outliers start: 12
  outliers final: 9
  residues processed: 87
  average time/residue: 0.2179
  time to fit residues: 24.0952
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  : 0.651 
-------------------------------------------------------------------------------
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 x residue  815 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0170
   chunk 1 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0370
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.4696

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.150590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.121210 restraints weight = 6591.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.15
r_work: 0.3352 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3338

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= 0.146
  Angle     :  0.502   5.507   7779  Z= 0.257
  Chirality :  0.043   0.220    901
  Planarity :  0.004   0.036    986
  Dihedral  :  4.154  15.967    763
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.95 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.32), residues: 701
  helix:  0.05 (0.30), residues: 306
  sheet: -0.22 (0.53), residues: 105
  loop : -1.10 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 810 
 PHE   0.006   0.001   PHE x 779 
 TYR   0.012   0.001   TYR x 832 
 ARG   0.005   0.000   ARG x 450 

*********************** 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
  85 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: x  294 MET cc_start: 0.7309 (ttt) cc_final: 0.7005 (ttm)
REVERT: x  575 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8163 (mm-30)
REVERT: x  584 ARG cc_start: 0.6506 (pmt-80) cc_final: 0.5742 (pmt-80)
REVERT: x  854 TRP cc_start: 0.7980 (m-10) cc_final: 0.7216 (m-10)
REVERT: y   71 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5780 (mt)
  outliers start: 13
  outliers final: 6
  residues processed: 81
  average time/residue: 0.1826
  time to fit residues: 19.5814
Evaluate side-chains
  74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
Chi-restraints excluded: chain x residue  254 THR
Chi-restraints excluded: chain x residue  502 ASN
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 40 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.150655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.121089 restraints weight = 6625.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.17
r_work: 0.3327 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5757  Z= 0.172
  Angle     :  0.521   5.927   7779  Z= 0.264
  Chirality :  0.044   0.216    901
  Planarity :  0.004   0.036    986
  Dihedral  :  4.128  16.054    763
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.89 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.33), residues: 701
  helix:  0.30 (0.30), residues: 306
  sheet: -0.27 (0.50), residues: 119
  loop : -1.01 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 810 
 PHE   0.010   0.001   PHE x 779 
 TYR   0.015   0.001   TYR x 832 
 ARG   0.005   0.000   ARG x 450 

*********************** 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
  87 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: x  294 MET cc_start: 0.7318 (ttt) cc_final: 0.7057 (ttm)
REVERT: x  575 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8149 (mm-30)
REVERT: x  584 ARG cc_start: 0.6524 (pmt-80) cc_final: 0.5727 (pmt-80)
REVERT: x  854 TRP cc_start: 0.8009 (m-10) cc_final: 0.7192 (m-10)
REVERT: y   71 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5780 (mt)
  outliers start: 15
  outliers final: 7
  residues processed: 83
  average time/residue: 0.1963
  time to fit residues: 21.1174
Evaluate side-chains
  77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  225 VAL
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 15 optimal weight:    0.0970
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:    0.4980
   chunk 59 optimal weight:    0.1980
   chunk 26 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.153256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.123979 restraints weight = 6610.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.18
r_work: 0.3368 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3579

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= 0.147
  Angle     :  0.511   5.698   7779  Z= 0.259
  Chirality :  0.043   0.169    901
  Planarity :  0.004   0.036    986
  Dihedral  :  3.994  15.619    763
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.52 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.33), residues: 701
  helix:  0.64 (0.31), residues: 306
  sheet: -0.18 (0.50), residues: 119
  loop : -0.90 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 810 
 PHE   0.007   0.001   PHE x 779 
 TYR   0.011   0.001   TYR x 832 
 ARG   0.006   0.000   ARG x 450 

*********************** 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: 13
    poor density    : 72
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
REVERT: x  294 MET cc_start: 0.7311 (ttt) cc_final: 0.7049 (ttm)
REVERT: x  372 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8279 (tp)
REVERT: x  584 ARG cc_start: 0.6532 (pmt-80) cc_final: 0.5951 (pmt-80)
REVERT: x  854 TRP cc_start: 0.7978 (m-10) cc_final: 0.7202 (m-10)
REVERT: y   71 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5749 (mt)
  outliers start: 13
  outliers final: 7
  residues processed: 82
  average time/residue: 0.1904
  time to fit residues: 20.7116
Evaluate side-chains
  75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
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  585 THR
Chi-restraints excluded: chain x residue  608 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0170
   chunk 67 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.6420

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.152191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.122669 restraints weight = 6593.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.18
r_work: 0.3350 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5757  Z= 0.165
  Angle     :  0.515   5.281   7779  Z= 0.263
  Chirality :  0.044   0.163    901
  Planarity :  0.004   0.038    986
  Dihedral  :  4.017  15.926    763
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.99 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.33), residues: 701
  helix:  0.93 (0.31), residues: 301
  sheet: -0.07 (0.50), residues: 119
  loop : -0.86 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP x 568 
 HIS   0.005   0.001   HIS x 810 
 PHE   0.009   0.001   PHE x 779 
 TYR   0.015   0.001   TYR x 832 
 ARG   0.007   0.000   ARG x 450 

*********************** 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
  80 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: x  294 MET cc_start: 0.7305 (ttt) cc_final: 0.7096 (ttm)
REVERT: x  372 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8307 (tp)
REVERT: x  584 ARG cc_start: 0.6541 (pmt-80) cc_final: 0.5987 (pmt-80)
REVERT: x  854 TRP cc_start: 0.7964 (m-10) cc_final: 0.7143 (m-10)
REVERT: y   71 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5711 (mt)
  outliers start: 14
  outliers final: 9
  residues processed: 76
  average time/residue: 0.2126
  time to fit residues: 21.3135
Evaluate side-chains
  73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
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  608 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2855 > 50:
  distance: 29 - 31:  34.884
  distance: 31 - 32:  50.463
  distance: 32 - 33:  28.110
  distance: 32 - 35:  27.133
  distance: 33 - 34:  50.201
  distance: 33 - 43:  28.708
  distance: 34 - 99:  53.354
  distance: 35 - 36:  68.238
  distance: 36 - 37:  39.687
  distance: 36 - 38:  56.569
  distance: 37 - 39:  56.875
  distance: 38 - 40:  27.559
  distance: 39 - 41:  40.842
  distance: 40 - 41:  42.847
  distance: 43 - 44:  56.668
  distance: 44 - 45:  38.480
  distance: 45 - 46:  24.430
  distance: 45 - 52:  40.423
  distance: 47 - 48:  69.764
  distance: 48 - 49:  38.820
  distance: 49 - 50:  38.934
  distance: 49 - 51:  57.404
  distance: 52 - 53:  40.580
  distance: 53 - 54:  56.408
  distance: 54 - 55:   4.995
  distance: 54 - 60:  39.500
  distance: 56 - 57:  63.236
  distance: 56 - 58:  57.643
  distance: 57 - 59:  47.960
  distance: 61 - 62:  42.777
  distance: 61 - 64:  56.053
  distance: 62 - 63:  29.365
  distance: 62 - 71:  40.209
  distance: 64 - 65:  39.268
  distance: 65 - 66:  42.711
  distance: 66 - 67:  40.887
  distance: 67 - 68:  29.011
  distance: 68 - 69:  11.628
  distance: 68 - 70:  42.254
  distance: 71 - 72:  40.798
  distance: 72 - 73:  41.240
  distance: 72 - 75:  48.700
  distance: 73 - 74:  16.371
  distance: 73 - 82:  11.029
  distance: 75 - 76:  19.684
  distance: 76 - 77:  17.225
  distance: 76 - 78:  48.079
  distance: 77 - 79:  19.212
  distance: 80 - 81:  37.672
  distance: 82 - 83:  26.597
  distance: 83 - 84:  17.501
  distance: 83 - 86:  33.968
  distance: 84 - 91:  54.222
  distance: 86 - 87:  50.527
  distance: 87 - 88:  38.964
  distance: 88 - 89:  28.422
  distance: 88 - 90:  28.085
  distance: 91 - 92:  38.470
  distance: 92 - 95:  39.707
  distance: 93 - 94:   9.558
  distance: 93 - 99:  56.113
  distance: 95 - 96:  39.839
  distance: 96 - 97:  40.967
  distance: 99 - 100:  30.944
  distance: 100 - 101:  10.913
  distance: 100 - 103:  57.805
  distance: 101 - 108:  40.059
  distance: 103 - 104:  55.322
  distance: 104 - 105:  39.964
  distance: 105 - 106:  39.936
  distance: 106 - 107:  39.414
  distance: 108 - 109:  57.734
  distance: 109 - 110:  39.192
  distance: 109 - 112:  40.960
  distance: 110 - 115:  40.222
  distance: 112 - 113:  56.057
  distance: 112 - 114:  41.286
  distance: 116 - 117:  63.870
  distance: 116 - 119:  40.908
  distance: 117 - 118:  34.781
  distance: 117 - 122:  29.235