Starting phenix.real_space_refine (version: dev)
on Mon Apr  4 13:37:22 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/04_2022/7dd3_30643.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/04_2022/7dd3_30643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/04_2022/7dd3_30643.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/04_2022/7dd3_30643.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/04_2022/7dd3_30643.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd3_30643/04_2022/7dd3_30643.pdb"
  }
  resolution = 3.2
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 5929
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "x"
      Number of atoms: 5193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 653, 5193
          Classifications: {'peptide': 653}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 619, 'PCIS': 1}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "y"
      Number of atoms: 572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 572
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "G"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 164
          Classifications: {'RNA': 9}
          Modifications used: {'rna3p_pyr': 5, 'rna2p_pyr': 3}
          Link IDs: {'rna3p': 5, 'rna2p': 3}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'  U:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 4.02, per 1000 atoms: 0.68
  Number of scatterers: 5929
  At special positions: 0
  Unit cell: (145.22, 115.54, 86.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       9     15.00
     O    1130      8.00
     N    1000      7.00
     C    3756      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.01
  Conformation dependent library (CDL) restraints added in 880.6 milliseconds
  

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 5 sheets defined
      47.0% alpha, 11.0% beta
      0 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'x' and resid 215 through 221
      removed outlier: 3.988A  pdb=" N   LYS x 221 " --> pdb=" O   GLN x 217 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 223 through 227
      removed outlier: 3.533A  pdb=" N   GLN x 227 " --> pdb=" O   PRO x 224 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 228 through 239
      removed outlier: 4.254A  pdb=" N   GLN x 234 " --> pdb=" O   ASP x 230 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 254 through 264
      removed outlier: 4.218A  pdb=" N   GLN x 258 " --> pdb=" O   THR x 254 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU x 260 " --> pdb=" O   LEU x 256 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL x 261 " --> pdb=" O   PRO x 257 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 279 through 294
      removed outlier: 3.552A  pdb=" N   THR x 284 " --> pdb=" O   ARG x 280 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG x 289 " --> pdb=" O   SER x 285 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 323 through 334
      removed outlier: 3.654A  pdb=" N   LEU x 327 " --> pdb=" O   THR x 323 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU x 328 " --> pdb=" O   ASP x 324 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ARG x 329 " --> pdb=" O   GLY x 325 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE x 331 " --> pdb=" O   LEU x 327 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU x 332 " --> pdb=" O   LEU x 328 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR x 333 " --> pdb=" O   ARG x 329 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 352 through 369
      removed outlier: 4.135A  pdb=" N   ASP x 364 " --> pdb=" O   GLY x 360 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU x 366 " --> pdb=" O   LEU x 362 " (cutoff:3.500A)
      Proline residue:  x 367  - end of helix
    Processing helix  chain 'x' and resid 382 through 390
      removed outlier: 3.799A  pdb=" N   PHE x 386 " --> pdb=" O   ASN x 382 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER x 387 " --> pdb=" O   ALA x 383 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU x 388 " --> pdb=" O   LYS x 384 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   PHE x 389 " --> pdb=" O   LYS x 385 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 416 through 432
      removed outlier: 3.534A  pdb=" N   ALA x 420 " --> pdb=" O   ASN x 416 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE x 426 " --> pdb=" O   ILE x 422 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   THR x 431 " --> pdb=" O   GLN x 427 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 445 through 462
      removed outlier: 3.806A  pdb=" N   THR x 451 " --> pdb=" O   GLU x 447 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE x 458 " --> pdb=" O   LYS x 454 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER x 460 " --> pdb=" O   GLU x 456 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 479 through 484
    Processing helix  chain 'x' and resid 542 through 551
    Processing helix  chain 'x' and resid 566 through 573
    Processing helix  chain 'x' and resid 580 through 585
      removed outlier: 3.565A  pdb=" N   ARG x 584 " --> pdb=" O   PRO x 580 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 589 through 597
    Processing helix  chain 'x' and resid 612 through 626
      removed outlier: 3.654A  pdb=" N   SER x 619 " --> pdb=" O   THR x 615 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU x 620 " --> pdb=" O   LEU x 616 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU x 626 " --> pdb=" O   ASN x 622 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 636 through 645
      removed outlier: 3.694A  pdb=" N   MET x 641 " --> pdb=" O   ARG x 637 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS x 643 " --> pdb=" O   GLY x 639 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLU x 644 " --> pdb=" O   LYS x 640 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 650 through 658
      removed outlier: 3.604A  pdb=" N   VAL x 654 " --> pdb=" O   GLU x 650 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TYR x 656 " --> pdb=" O   ALA x 652 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 667 through 679
      removed outlier: 4.164A  pdb=" N   THR x 673 " --> pdb=" O   GLU x 669 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   HIS x 679 " --> pdb=" O   VAL x 675 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 688 through 697
      removed outlier: 3.725A  pdb=" N   ALA x 692 " --> pdb=" O   GLN x 688 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   SER x 695 " --> pdb=" O   ASP x 691 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL x 696 " --> pdb=" O   ALA x 692 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 704 through 716
    Processing helix  chain 'x' and resid 721 through 727
      removed outlier: 3.710A  pdb=" N   GLN x 725 " --> pdb=" O   ARG x 721 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 730 through 751
    Processing helix  chain 'x' and resid 752 through 763
      removed outlier: 3.782A  pdb=" N   LYS x 756 " --> pdb=" O   GLY x 752 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN x 759 " --> pdb=" O   GLU x 755 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ALA x 760 " --> pdb=" O   LYS x 756 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG x 761 " --> pdb=" O   ASN x 757 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 770 through 783
      removed outlier: 3.889A  pdb=" N   THR x 776 " --> pdb=" O   ASN x 772 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ARG x 777 " --> pdb=" O   ALA x 773 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER x 781 " --> pdb=" O   ARG x 777 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 813 through 821
      removed outlier: 3.563A  pdb=" N   HIS x 819 " --> pdb=" O   LEU x 815 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 852 through 859
      removed outlier: 4.129A  pdb=" N   ILE x 856 " --> pdb=" O   GLU x 852 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 859 through 867
      removed outlier: 6.378A  pdb=" N   ASP x 865 " --> pdb=" O   GLN x 861 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU x 866 " --> pdb=" O   ILE x 862 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE x 867 " --> pdb=" O   PHE x 863 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 9 through 14
    Processing helix  chain 'y' and resid 93 through 100
      removed outlier: 3.865A  pdb=" N   TYR y  97 " --> pdb=" O   THR y  93 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN y  98 " --> pdb=" O   GLU y  94 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 101 through 112
      removed outlier: 4.142A  pdb=" N   GLY y 106 " --> pdb=" O   VAL y 102 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ASP y 107 " --> pdb=" O   GLU y 103 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU y 110 " --> pdb=" O   GLY y 106 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'x' and resid 310 through 311
      removed outlier: 7.443A  pdb=" N   GLN x 272 " --> pdb=" O   CYS x 342 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   MET x 344 " --> pdb=" O   GLN x 272 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ALA x 274 " --> pdb=" O   MET x 344 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   SER x 341 " --> pdb=" O   LYS x 373 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   LEU x 375 " --> pdb=" O   SER x 341 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE x 343 " --> pdb=" O   LEU x 375 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   SER x 377 " --> pdb=" O   ILE x 343 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ILE x 345 " --> pdb=" O   SER x 377 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   PHE x 396 " --> pdb=" O   VAL x 241 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE x 243 " --> pdb=" O   PHE x 396 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   VAL x 398 " --> pdb=" O   ILE x 243 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   MET x 245 " --> pdb=" O   VAL x 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'x' and resid 406 through 409
      removed outlier: 6.267A  pdb=" N   ASP x 437 " --> pdb=" O   TYR x 515 " (cutoff:3.500A)
      removed outlier: 7.700A  pdb=" N   ILE x 517 " --> pdb=" O   ASP x 437 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU x 439 " --> pdb=" O   ILE x 517 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   ILE x 438 " --> pdb=" O   VAL x 498 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   ALA x 500 " --> pdb=" O   ILE x 438 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   VAL x 440 " --> pdb=" O   ALA x 500 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   GLN x 468 " --> pdb=" O   ARG x 495 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   VAL x 497 " --> pdb=" O   GLN x 468 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   ILE x 470 " --> pdb=" O   VAL x 497 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   LEU x 499 " --> pdb=" O   ILE x 470 " (cutoff:3.500A)
      removed outlier: 6.275A  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 528
    Processing sheet with id=AA4, first strand: chain 'x' and resid 795 through 797
      removed outlier: 3.690A  pdb=" N   VAL x 830 " --> pdb=" O   VAL x 788 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   TYR x 829 " --> pdb=" O   ILE x 849 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'x' and resid 808 through 809
      removed outlier: 6.803A  pdb=" N   SER x 808 " --> pdb=" O   ILE x 843 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    190 hydrogen bonds defined for protein.
    558 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      4 stacking parallelities
  Total time for adding SS restraints: 1.95

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1616
        1.33 -     1.45: 928
        1.45 -     1.57: 3429
        1.57 -     1.69: 18
        1.69 -     1.80: 55
  Bond restraints: 6046
  Sorted by residual:
  bond pdb=" N   THR y  93 "
       pdb=" CA  THR y  93 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.75e+00
  bond pdb=" CA  THR y  93 "
       pdb=" CB  THR y  93 "
    ideal  model  delta    sigma   weight residual
    1.530  1.573 -0.043 1.69e-02 3.50e+03 6.48e+00
  bond pdb=" CG  LEU x 835 "
       pdb=" CD1 LEU x 835 "
    ideal  model  delta    sigma   weight residual
    1.521  1.443  0.078 3.30e-02 9.18e+02 5.60e+00
  bond pdb=" CB  VAL x 788 "
       pdb=" CG2 VAL x 788 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.48e+00
  bond pdb=" CG  LEU x 831 "
       pdb=" CD2 LEU x 831 "
    ideal  model  delta    sigma   weight residual
    1.521  1.446  0.075 3.30e-02 9.18e+02 5.18e+00
  ... (remaining 6041 not shown)

  Histogram of bond angle deviations from ideal:
       96.36 -   103.90: 121
      103.90 -   111.43: 2624
      111.43 -   118.96: 2335
      118.96 -   126.50: 3041
      126.50 -   134.03: 74
  Bond angle restraints: 8195
  Sorted by residual:
  angle pdb=" C   LYS x 300 "
        pdb=" N   GLU x 301 "
        pdb=" CA  GLU x 301 "
      ideal   model   delta    sigma   weight residual
     121.54  130.17   -8.63 1.91e+00 2.74e-01 2.04e+01
  angle pdb=" N   THR x 681 "
        pdb=" CA  THR x 681 "
        pdb=" C   THR x 681 "
      ideal   model   delta    sigma   weight residual
     109.81  118.85   -9.04 2.21e+00 2.05e-01 1.67e+01
  angle pdb=" N   ILE x 273 "
        pdb=" CA  ILE x 273 "
        pdb=" C   ILE x 273 "
      ideal   model   delta    sigma   weight residual
     109.21  114.59   -5.38 1.36e+00 5.41e-01 1.56e+01
  angle pdb=" CB  MET x 322 "
        pdb=" CG  MET x 322 "
        pdb=" SD  MET x 322 "
      ideal   model   delta    sigma   weight residual
     112.70  102.61   10.09 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" N   THR y  93 "
        pdb=" CA  THR y  93 "
        pdb=" CB  THR y  93 "
      ideal   model   delta    sigma   weight residual
     110.49  116.11   -5.62 1.69e+00 3.50e-01 1.11e+01
  ... (remaining 8190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 3478
       16.59 -    33.19: 161
       33.19 -    49.78: 59
       49.78 -    66.37: 11
       66.37 -    82.96: 3
  Dihedral angle restraints: 3712
    sinusoidal: 1603
      harmonic: 2109
  Sorted by residual:
  dihedral pdb=" C   THR y  93 "
           pdb=" N   THR y  93 "
           pdb=" CA  THR y  93 "
           pdb=" CB  THR y  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.68   12.68     0      2.50e+00 1.60e-01 2.57e+01
  dihedral pdb=" N   THR y  93 "
           pdb=" C   THR y  93 "
           pdb=" CA  THR y  93 "
           pdb=" CB  THR y  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.17  -11.77     0      2.50e+00 1.60e-01 2.22e+01
  dihedral pdb=" CA  ARG x 584 "
           pdb=" C   ARG x 584 "
           pdb=" N   THR x 585 "
           pdb=" CA  THR x 585 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.47  -21.53     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 3709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 742
       0.074 -    0.148: 200
       0.148 -    0.222: 16
       0.222 -    0.296: 1
       0.296 -    0.370: 2
  Chirality restraints: 961
  Sorted by residual:
  chirality pdb=" CA  THR y  93 "
            pdb=" N   THR y  93 "
            pdb=" C   THR y  93 "
            pdb=" CB  THR y  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.16    0.37 2.00e-01 2.50e+01 3.43e+00
  chirality pdb=" CB  ILE x 843 "
            pdb=" CA  ILE x 843 "
            pdb=" CG1 ILE x 843 "
            pdb=" CG2 ILE x 843 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.23e+00
  chirality pdb=" CA  THR x 681 "
            pdb=" N   THR x 681 "
            pdb=" C   THR x 681 "
            pdb=" CB  THR x 681 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.30    0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 958 not shown)

  Planarity restraints: 1008
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE x 783 "   -0.008 2.00e-02 2.50e+03   2.02e-02 7.17e+00
        pdb=" CG  PHE x 783 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE x 783 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 PHE x 783 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE x 783 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE x 783 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE x 783 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU x 223 "    0.036 5.00e-02 4.00e+02   5.46e-02 4.76e+00
        pdb=" N   PRO x 224 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO x 224 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO x 224 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS x 810 "   -0.036 5.00e-02 4.00e+02   5.41e-02 4.68e+00
        pdb=" N   PRO x 811 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO x 811 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO x 811 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1005 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1995
        2.87 -     3.37: 5326
        3.37 -     3.88: 9135
        3.88 -     4.39: 10580
        4.39 -     4.90: 17919
  Nonbonded interactions: 44955
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN x 305 "
            pdb=" NZ  LYS x 320 "
     model   vdw
     2.357 2.520
  nonbonded pdb=" O   LEU x 337 "
            pdb=" NH1 ARG x 369 "
     model   vdw
     2.362 2.520
  nonbonded pdb=" O   LEU x 508 "
            pdb=" NH2 ARG x 552 "
     model   vdw
     2.363 2.520
  nonbonded pdb=" O   ALA x 420 "
            pdb=" OG1 THR x 424 "
     model   vdw
     2.399 2.440
  nonbonded pdb=" NZ  LYS x 363 "
            pdb=" O   PHE x 389 "
     model   vdw
     2.411 2.520
  ... (remaining 44950 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      34      5.16       5
     C    3756      2.51       5
     N    1000      2.21       5
     O    1130      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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:             0.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.170
  Check model and map are aligned:         0.090
  Convert atoms to be neutral:             0.050
  Process input model:                     20.690
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
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      :  0.012   0.080   6046  Z= 0.769
  Angle     :  1.056  10.087   8195  Z= 0.562
  Chirality :  0.064   0.370    961
  Planarity :  0.008   0.055   1008
  Dihedral  : 11.804  82.961   2344
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.32 %
    Favored  : 94.54 %
  Rotamer Outliers :  2.31 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -3.77 (0.26), residues: 714
  helix: -3.83 (0.15), residues: 269
  sheet: -1.38 (0.46), residues: 122
  loop : -1.52 (0.31), residues: 323

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 4
  residues processed: 173
  average time/residue: 0.2116
  time to fit residues: 46.1256
Evaluate side-chains
  97 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.620 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0657
  time to fit residues: 1.3312
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 65 optimal weight:   30.0000
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
x 239 ASN
x 382 ASN
x 412 GLN
x 419 HIS
x 427 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6046  Z= 0.236
  Angle     :  0.649  10.140   8195  Z= 0.337
  Chirality :  0.045   0.243    961
  Planarity :  0.005   0.042   1008
  Dihedral  :  7.968  63.129    872
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.36 %
    Favored  : 96.50 %
  Rotamer Outliers :  3.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -2.18 (0.29), residues: 714
  helix: -1.57 (0.25), residues: 308
  sheet: -0.40 (0.54), residues: 96
  loop : -1.50 (0.34), residues: 310

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1746
  time to fit residues: 27.2347
Evaluate side-chains
  95 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.702 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0839
  time to fit residues: 2.2850
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 65 optimal weight:   50.0000
   chunk 70 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
x 382 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6046  Z= 0.202
  Angle     :  0.579   9.188   8195  Z= 0.292
  Chirality :  0.044   0.148    961
  Planarity :  0.004   0.038   1008
  Dihedral  :  7.602  60.392    872
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer Outliers :  2.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -1.17 (0.31), residues: 714
  helix: -0.51 (0.28), residues: 305
  sheet: -0.01 (0.56), residues: 96
  loop : -1.17 (0.35), residues: 313

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 4
  residues processed: 114
  average time/residue: 0.1720
  time to fit residues: 26.1712
Evaluate side-chains
  88 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.728 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0762
  time to fit residues: 1.5066
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 33 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 31 optimal weight:    0.1980
   chunk 43 optimal weight:    0.2980
   chunk 65 optimal weight:   30.0000
   chunk 69 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.5780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6046  Z= 0.156
  Angle     :  0.538   9.717   8195  Z= 0.270
  Chirality :  0.042   0.143    961
  Planarity :  0.004   0.071   1008
  Dihedral  :  7.368  62.855    872
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer Outliers :  2.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.66 (0.32), residues: 714
  helix:  0.02 (0.30), residues: 308
  sheet:  0.01 (0.55), residues: 100
  loop : -0.96 (0.37), residues: 306

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 6
  residues processed: 101
  average time/residue: 0.1734
  time to fit residues: 23.4438
Evaluate side-chains
  90 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.634 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0641
  time to fit residues: 1.5863
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 48 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6046  Z= 0.158
  Angle     :  0.523   8.877   8195  Z= 0.262
  Chirality :  0.042   0.147    961
  Planarity :  0.004   0.052   1008
  Dihedral  :  7.174  64.051    872
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer Outliers :  1.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.35 (0.32), residues: 714
  helix:  0.42 (0.30), residues: 311
  sheet:  0.21 (0.54), residues: 105
  loop : -1.02 (0.36), residues: 298

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.709 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 101
  average time/residue: 0.1736
  time to fit residues: 23.7171
Evaluate side-chains
  90 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.731 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0646
  time to fit residues: 1.4729
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 62 optimal weight:    0.2980
   chunk 13 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0030
   chunk 36 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.8394

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

Flipped N/Q/H residues before XYZ refinement:
x 382 ASN
x 429 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6046  Z= 0.177
  Angle     :  0.535   8.682   8195  Z= 0.271
  Chirality :  0.043   0.170    961
  Planarity :  0.004   0.045   1008
  Dihedral  :  7.106  62.973    872
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.48 %
    Favored  : 95.38 %
  Rotamer Outliers :  1.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.27 (0.32), residues: 714
  helix:  0.55 (0.30), residues: 311
  sheet:  0.27 (0.55), residues: 105
  loop : -1.07 (0.36), residues: 298

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.716 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 95
  average time/residue: 0.1572
  time to fit residues: 20.6380
Evaluate side-chains
  86 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.622 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0546
  time to fit residues: 1.3465
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
x 429 HIS
x 725 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6046  Z= 0.177
  Angle     :  0.541   9.895   8195  Z= 0.271
  Chirality :  0.043   0.174    961
  Planarity :  0.004   0.044   1008
  Dihedral  :  7.056  62.120    872
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.34 %
    Favored  : 95.52 %
  Rotamer Outliers :  1.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.15 (0.32), residues: 714
  helix:  0.67 (0.31), residues: 308
  sheet:  0.28 (0.55), residues: 105
  loop : -0.99 (0.36), residues: 301

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.701 
Fit side-chains
  outliers start: 7
  outliers final: 2
  residues processed: 93
  average time/residue: 0.1633
  time to fit residues: 20.8138
Evaluate side-chains
  85 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.727 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0850
  time to fit residues: 1.4230
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0870
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 34 optimal weight:    9.9990
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
x 429 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6046  Z= 0.146
  Angle     :  0.526   8.425   8195  Z= 0.265
  Chirality :  0.042   0.183    961
  Planarity :  0.004   0.042   1008
  Dihedral  :  6.989  63.338    872
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.62 %
    Favored  : 95.24 %
  Rotamer Outliers :  0.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.04 (0.33), residues: 714
  helix:  0.71 (0.31), residues: 312
  sheet:  0.18 (0.55), residues: 108
  loop : -0.83 (0.37), residues: 294

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.624 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 91
  average time/residue: 0.1690
  time to fit residues: 20.8841
Evaluate side-chains
  86 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.712 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0581
  time to fit residues: 1.1042
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0570
   overall best weight:    0.8500

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

Flipped N/Q/H residues before XYZ refinement:
x 382 ASN
x 429 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6046  Z= 0.177
  Angle     :  0.539   9.433   8195  Z= 0.270
  Chirality :  0.042   0.183    961
  Planarity :  0.004   0.045   1008
  Dihedral  :  6.939  62.317    872
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.62 %
    Favored  : 95.24 %
  Rotamer Outliers :  0.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.00 (0.33), residues: 714
  helix:  0.82 (0.31), residues: 308
  sheet: -0.05 (0.56), residues: 103
  loop : -0.76 (0.37), residues: 303

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.721 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1684
  time to fit residues: 21.6502
Evaluate side-chains
  85 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.722 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0416
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
x 382 ASN
x 429 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6046  Z= 0.215
  Angle     :  0.559  10.432   8195  Z= 0.279
  Chirality :  0.043   0.180    961
  Planarity :  0.005   0.091   1008
  Dihedral  :  6.913  60.036    872
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.32 %
    Favored  : 94.54 %
  Rotamer Outliers :  0.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.33), residues: 714
  helix:  0.83 (0.31), residues: 307
  sheet: -0.07 (0.56), residues: 103
  loop : -0.79 (0.37), residues: 304

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.647 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 90
  average time/residue: 0.1559
  time to fit residues: 19.6647
Evaluate side-chains
  82 residues out of total 651 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.706 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0584
  time to fit residues: 1.0994
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0970
   chunk 57 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 3 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0370
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
x 382 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.163582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.117537 restraints weight = 7433.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.79
r_work: 0.3498 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work: 0.3468 rms_B_bonded: 2.56 restraints_weight: 0.1250
r_work: 0.3452 rms_B_bonded: 2.64 restraints_weight: 0.0625
r_work: 0.3436 rms_B_bonded: 2.76 restraints_weight: 0.0312
r_work: 0.3419 rms_B_bonded: 2.92 restraints_weight: 0.0156
r_work: 0.3401 rms_B_bonded: 3.11 restraints_weight: 0.0078
r_work: 0.3382 rms_B_bonded: 3.35 restraints_weight: 0.0039
r_work: 0.3361 rms_B_bonded: 3.63 restraints_weight: 0.0020
r_work: 0.3338 rms_B_bonded: 3.96 restraints_weight: 0.0010
r_work: 0.3313 rms_B_bonded: 4.36 restraints_weight: 0.0005
r_work: 0.3286 rms_B_bonded: 4.82 restraints_weight: 0.0002
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.047   6046  Z= 0.156
  Angle     :  0.553   9.387   8195  Z= 0.272
  Chirality :  0.042   0.174    961
  Planarity :  0.004   0.080   1008
  Dihedral  :  6.862  61.577    872
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.62 %
    Favored  : 95.24 %
  Rotamer Outliers :  0.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.10 (0.33), residues: 714
  helix:  0.94 (0.31), residues: 307
  sheet:  0.05 (0.57), residues: 103
  loop : -0.76 (0.37), residues: 304

===============================================================================
Job complete
usr+sys time: 1491.32 seconds
wall clock time: 27 minutes 48.87 seconds (1668.87 seconds total)