Starting phenix.real_space_refine (version: dev)
on Sun Dec 11 15:21:13 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2022/7kpw_22990.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2022/7kpw_22990.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2022/7kpw_22990.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2022/7kpw_22990.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2022/7kpw_22990.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2022/7kpw_22990.pdb"
  }
  resolution = 4.9
  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=   0.001
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: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib"
  Total number of atoms: 4313
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 4313
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 865, 4313
          Classifications: {'peptide': 865}
          Incomplete info: {'truncation_to_alanine': 830}
          Link IDs: {'PTRANS': 22, 'TRANS': 842}
          Chain breaks: 1
          Unresolved chain link angles: 22
          Unresolved non-hydrogen bonds: 2975
          Unresolved non-hydrogen angles: 3799
          Unresolved non-hydrogen dihedrals: 2479
          Unresolved non-hydrogen chiralities: 290
          Planarities with less than four sites: {'GLN:plan1': 43, 'HIS:plan': 17, 'TYR:plan': 32, 'ASN:plan1': 64, 'TRP:plan': 8, 'ASP:plan': 45, 'PHE:plan': 60, 'GLU:plan': 50, 'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 1540
  Time building chain proxies: 3.12, per 1000 atoms: 0.72
  Number of scatterers: 4313
  At special positions: 0
  Unit cell: (86.67, 86.67, 119.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     865      8.00
     N     865      7.00
     C    2583      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: 1.97
  Conformation dependent library (CDL) restraints added in 935.2 milliseconds
  

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 0 sheets defined
      82.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'C' and resid 421 through 428
      removed outlier: 3.587A  pdb=" N   SER C 425 " --> pdb=" O   LYS C 421 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE C 426 " --> pdb=" O   ASN C 422 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ARG C 427 " --> pdb=" O   ASN C 423 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN C 428 " --> pdb=" O   SER C 424 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 421 through 428'
    Processing helix  chain 'C' and resid 438 through 444
      removed outlier: 3.524A  pdb=" N   ILE C 443 " --> pdb=" O   PHE C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 456 through 466
      removed outlier: 3.587A  pdb=" N   PHE C 464 " --> pdb=" O   ILE C 460 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR C 465 " --> pdb=" O   ASP C 461 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 470 through 476
      removed outlier: 4.112A  pdb=" N   GLU C 474 " --> pdb=" O   ASP C 470 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP C 476 " --> pdb=" O   PRO C 472 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 483 through 496
      removed outlier: 3.537A  pdb=" N   LYS C 490 " --> pdb=" O   LEU C 486 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE C 495 " --> pdb=" O   ILE C 491 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   LEU C 496 " --> pdb=" O   ILE C 492 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 502 through 517
    Processing helix  chain 'C' and resid 524 through 543
      removed outlier: 4.218A  pdb=" N   ASP C 528 " --> pdb=" O   SER C 524 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU C 529 " --> pdb=" O   THR C 525 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TRP C 539 " --> pdb=" O   GLU C 535 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL C 542 " --> pdb=" O   ILE C 538 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   PHE C 543 " --> pdb=" O   TRP C 539 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 546 through 572
      removed outlier: 3.521A  pdb=" N   GLN C 552 " --> pdb=" O   ASN C 548 " (cutoff:3.500A)
      Proline residue:  C 561  - end of helix
      removed outlier: 3.547A  pdb=" N   LEU C 570 " --> pdb=" O   LEU C 566 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   THR C 572 " --> pdb=" O   ASN C 568 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 573 through 588
      Proline residue:  C 579  - end of helix
      removed outlier: 3.782A  pdb=" N   ILE C 586 " --> pdb=" O   ILE C 582 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER C 587 " --> pdb=" O   ARG C 583 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   SER C 588 " --> pdb=" O   LYS C 584 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 592 through 605
      removed outlier: 3.636A  pdb=" N   SER C 596 " --> pdb=" O   TYR C 592 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ASN C 597 " --> pdb=" O   LEU C 593 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LEU C 605 " --> pdb=" O   VAL C 601 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 610 through 624
      removed outlier: 4.648A  pdb=" N   MET C 615 " --> pdb=" O   ILE C 611 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LYS C 616 " --> pdb=" O   SER C 612 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 633 through 651
      removed outlier: 3.951A  pdb=" N   MET C 651 " --> pdb=" O   GLU C 647 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 653 through 664
    Processing helix  chain 'C' and resid 667 through 685
      removed outlier: 4.275A  pdb=" N   LYS C 671 " --> pdb=" O   PRO C 667 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU C 676 " --> pdb=" O   ILE C 672 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TRP C 677 " --> pdb=" O   MET C 673 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 691 through 704
      removed outlier: 3.603A  pdb=" N   LEU C 695 " --> pdb=" O   ASN C 691 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE C 704 " --> pdb=" O   LYS C 700 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 707 through 721
      removed outlier: 3.538A  pdb=" N   HIS C 711 " --> pdb=" O   GLU C 707 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE C 712 " --> pdb=" O   VAL C 708 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 725 through 740
      removed outlier: 3.637A  pdb=" N   LEU C 734 " --> pdb=" O   SER C 730 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   MET C 735 " --> pdb=" O   LEU C 731 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASP C 736 " --> pdb=" O   GLU C 732 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   CYS C 740 " --> pdb=" O   ASP C 736 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 742 through 747
      removed outlier: 4.064A  pdb=" N   SER C 746 " --> pdb=" O   GLN C 742 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLN C 747 " --> pdb=" O   LYS C 743 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 742 through 747'
    Processing helix  chain 'C' and resid 748 through 763
    Processing helix  chain 'C' and resid 773 through 788
      Proline residue:  C 782  - end of helix
    Processing helix  chain 'C' and resid 791 through 813
      removed outlier: 3.501A  pdb=" N   LYS C 796 " --> pdb=" O   PRO C 792 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE C 803 " --> pdb=" O   ASN C 799 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU C 804 " --> pdb=" O   ASP C 800 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU C 805 " --> pdb=" O   LEU C 801 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LYS C 813 " --> pdb=" O   TYR C 809 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 814 through 827
      removed outlier: 4.024A  pdb=" N   LYS C 818 " --> pdb=" O   LEU C 814 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU C 825 " --> pdb=" O   ASN C 821 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 836 through 854
      removed outlier: 4.641A  pdb=" N   THR C 843 " --> pdb=" O   ALA C 839 " (cutoff:3.500A)
      Proline residue:  C 847  - end of helix
      removed outlier: 3.762A  pdb=" N   VAL C 852 " --> pdb=" O   GLU C 848 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ILE C 854 " --> pdb=" O   PHE C 850 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 860 through 878
      removed outlier: 4.686A  pdb=" N   ILE C 864 " --> pdb=" O   ASN C 860 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASP C 865 " --> pdb=" O   SER C 861 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 878 through 893
    Processing helix  chain 'C' and resid 896 through 907
      removed outlier: 3.621A  pdb=" N   LYS C 906 " --> pdb=" O   ASP C 902 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 909 through 916
    Processing helix  chain 'C' and resid 918 through 927
      removed outlier: 3.585A  pdb=" N   GLN C 923 " --> pdb=" O   PHE C 919 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY C 927 " --> pdb=" O   GLN C 923 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 937 through 948
      removed outlier: 3.815A  pdb=" N   ASN C 941 " --> pdb=" O   ILE C 937 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU C 948 " --> pdb=" O   GLY C 944 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 949 through 963
      removed outlier: 3.781A  pdb=" N   PHE C 962 " --> pdb=" O   ILE C 958 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLU C 963 " --> pdb=" O   LYS C 959 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 967 through 983
    Processing helix  chain 'C' and resid 986 through 1004
      removed outlier: 3.502A  pdb=" N   LYS C 991 " --> pdb=" O   GLU C 987 " (cutoff:3.500A)
      Proline residue:  C1000  - end of helix
    Processing helix  chain 'C' and resid 1006 through 1023
      removed outlier: 3.793A  pdb=" N   LEU C1014 " --> pdb=" O   ILE C1010 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASN C1015 " --> pdb=" O   MET C1011 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASP C1016 " --> pdb=" O   LEU C1012 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1072 through 1083
      removed outlier: 4.261A  pdb=" N   GLU C1076 " --> pdb=" O   ILE C1072 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   PHE C1083 " --> pdb=" O   VAL C1079 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1087 through 1103
    Processing helix  chain 'C' and resid 1106 through 1126
      removed outlier: 3.749A  pdb=" N   GLU C1111 " --> pdb=" O   ALA C1107 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE C1116 " --> pdb=" O   ASP C1112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1128 through 1146
    Processing helix  chain 'C' and resid 1146 through 1172
      removed outlier: 3.998A  pdb=" N   ASN C1169 " --> pdb=" O   LYS C1165 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   TYR C1170 " --> pdb=" O   ILE C1166 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL C1172 " --> pdb=" O   ASP C1168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1174 through 1196
      removed outlier: 3.547A  pdb=" N   LEU C1181 " --> pdb=" O   ILE C1177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1204 through 1218
      removed outlier: 3.614A  pdb=" N   ARG C1208 " --> pdb=" O   ILE C1204 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU C1218 " --> pdb=" O   ASN C1214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1218 through 1224
    Processing helix  chain 'C' and resid 1225 through 1239
      removed outlier: 4.166A  pdb=" N   ILE C1239 " --> pdb=" O   HIS C1235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1239 through 1251
      removed outlier: 4.433A  pdb=" N   ILE C1243 " --> pdb=" O   ILE C1239 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA C1245 " --> pdb=" O   GLN C1241 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP C1250 " --> pdb=" O   ASP C1246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1259 through 1272
    Processing helix  chain 'C' and resid 1276 through 1296
    Processing helix  chain 'C' and resid 1307 through 1314
    Processing helix  chain 'C' and resid 1319 through 1326
      removed outlier: 3.673A  pdb=" N   VAL C1323 " --> pdb=" O   VAL C1319 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR C1326 " --> pdb=" O   PHE C1322 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1278 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: 1.32

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        1.20 -     1.27: 858
        1.27 -     1.35: 870
        1.35 -     1.42: 0
        1.42 -     1.49: 862
        1.49 -     1.56: 1721
  Bond restraints: 4311
  Sorted by residual:
  bond pdb=" C   LEU C 661 "
       pdb=" O   LEU C 661 "
    ideal  model  delta    sigma   weight residual
    1.237  1.296 -0.059 1.17e-02 7.31e+03 2.56e+01
  bond pdb=" C   ARG C 802 "
       pdb=" O   ARG C 802 "
    ideal  model  delta    sigma   weight residual
    1.237  1.293 -0.056 1.17e-02 7.31e+03 2.30e+01
  bond pdb=" C   GLY C 944 "
       pdb=" O   GLY C 944 "
    ideal  model  delta    sigma   weight residual
    1.234  1.290 -0.056 1.20e-02 6.94e+03 2.20e+01
  bond pdb=" C   VAL C 808 "
       pdb=" O   VAL C 808 "
    ideal  model  delta    sigma   weight residual
    1.237  1.288 -0.050 1.17e-02 7.31e+03 1.85e+01
  bond pdb=" C   ILE C 912 "
       pdb=" O   ILE C 912 "
    ideal  model  delta    sigma   weight residual
    1.237  1.283 -0.046 1.17e-02 7.31e+03 1.56e+01
  ... (remaining 4306 not shown)

  Histogram of bond angle deviations from ideal:
       97.77 -   104.44: 2
      104.44 -   111.10: 2057
      111.10 -   117.76: 1321
      117.76 -   124.42: 2583
      124.42 -   131.09: 62
  Bond angle restraints: 6025
  Sorted by residual:
  angle pdb=" N   LEU C 494 "
        pdb=" CA  LEU C 494 "
        pdb=" C   LEU C 494 "
      ideal   model   delta    sigma   weight residual
     111.14  127.60  -16.46 1.08e+00 8.57e-01 2.32e+02
  angle pdb=" N   ILE C 495 "
        pdb=" CA  ILE C 495 "
        pdb=" C   ILE C 495 "
      ideal   model   delta    sigma   weight residual
     113.20  124.91  -11.71 9.60e-01 1.09e+00 1.49e+02
  angle pdb=" N   ASP C1073 "
        pdb=" CA  ASP C1073 "
        pdb=" C   ASP C1073 "
      ideal   model   delta    sigma   weight residual
     111.28  123.07  -11.79 1.09e+00 8.42e-01 1.17e+02
  angle pdb=" N   ILE C1171 "
        pdb=" CA  ILE C1171 "
        pdb=" C   ILE C1171 "
      ideal   model   delta    sigma   weight residual
     110.53  119.35   -8.82 9.40e-01 1.13e+00 8.81e+01
  angle pdb=" N   LEU C 939 "
        pdb=" CA  LEU C 939 "
        pdb=" C   LEU C 939 "
      ideal   model   delta    sigma   weight residual
     111.36  121.37  -10.01 1.09e+00 8.42e-01 8.44e+01
  ... (remaining 6020 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     3.23: 2373
        3.23 -     6.46: 145
        6.46 -     9.70: 38
        9.70 -    12.93: 10
       12.93 -    16.16: 3
  Dihedral angle restraints: 2569
    sinusoidal: 0
      harmonic: 2569
  Sorted by residual:
  dihedral pdb=" N   PRO C 613 "
           pdb=" C   PRO C 613 "
           pdb=" CA  PRO C 613 "
           pdb=" CB  PRO C 613 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  129.00  -13.90     0      2.50e+00 1.60e-01 3.09e+01
  dihedral pdb=" N   PRO C1255 "
           pdb=" C   PRO C1255 "
           pdb=" CA  PRO C1255 "
           pdb=" CB  PRO C1255 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  127.95  -12.85     0      2.50e+00 1.60e-01 2.64e+01
  dihedral pdb=" N   PRO C 472 "
           pdb=" C   PRO C 472 "
           pdb=" CA  PRO C 472 "
           pdb=" CB  PRO C 472 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  127.10  -12.00     0      2.50e+00 1.60e-01 2.30e+01
  ... (remaining 2566 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 704
       0.122 -    0.245: 116
       0.245 -    0.367: 24
       0.367 -    0.490: 7
       0.490 -    0.612: 2
  Chirality restraints: 853
  Sorted by residual:
  chirality pdb=" CA  LEU C 494 "
            pdb=" N   LEU C 494 "
            pdb=" C   LEU C 494 "
            pdb=" CB  LEU C 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.90    0.61 2.00e-01 2.50e+01 9.37e+00
  chirality pdb=" CA  PRO C 613 "
            pdb=" N   PRO C 613 "
            pdb=" C   PRO C 613 "
            pdb=" CB  PRO C 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.18    0.54 2.00e-01 2.50e+01 7.21e+00
  chirality pdb=" CA  PRO C1255 "
            pdb=" N   PRO C1255 "
            pdb=" C   PRO C1255 "
            pdb=" CB  PRO C1255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.24    0.48 2.00e-01 2.50e+01 5.75e+00
  ... (remaining 850 not shown)

  Planarity restraints: 863
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C1082 "    0.018 2.00e-02 2.50e+03   3.53e-02 1.25e+01
        pdb=" C   ASP C1082 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ASP C1082 "    0.023 2.00e-02 2.50e+03
        pdb=" N   PHE C1083 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C 667 "    0.017 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   PRO C 667 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   PRO C 667 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU C 668 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 945 "    0.016 2.00e-02 2.50e+03   3.28e-02 1.07e+01
        pdb=" C   SER C 945 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   SER C 945 "    0.021 2.00e-02 2.50e+03
        pdb=" N   TYR C 946 "    0.019 2.00e-02 2.50e+03
  ... (remaining 860 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1604
        2.84 -     3.36: 4890
        3.36 -     3.87: 6576
        3.87 -     4.39: 6002
        4.39 -     4.90: 9978
  Nonbonded interactions: 29050
  Sorted by model distance:
  nonbonded pdb=" O   ASP C 526 "
            pdb=" N   LEU C 529 "
     model   vdw
     2.327 2.520
  nonbonded pdb=" O   LEU C1013 "
            pdb=" N   ASP C1016 "
     model   vdw
     2.501 2.520
  nonbonded pdb=" O   ASP C 526 "
            pdb=" C   GLU C 527 "
     model   vdw
     2.528 3.270
  nonbonded pdb=" O   ALA C 733 "
            pdb=" N   ASP C 736 "
     model   vdw
     2.528 2.520
  nonbonded pdb=" O   ILE C1009 "
            pdb=" N   LEU C1012 "
     model   vdw
     2.553 2.520
  ... (remaining 29045 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: 3
    Type Number    sf(0)   Gaussians
     C    2583      2.51       5
     N     865      2.21       5
     O     865      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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          11.610
  Check model and map are aligned:         0.060
  Convert atoms to be neutral:             0.040
  Process input model:                     16.760
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
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      :  0.009   0.059   4311  Z= 0.639
  Angle     :  1.535  16.459   6025  Z= 1.270
  Chirality :  0.105   0.612    853
  Planarity :  0.007   0.035    863
  Dihedral  :  1.886  16.161    863
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  1.16 %
    Allowed  :  3.95 %
    Favored  : 94.89 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.47 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.09 (0.30), residues: 861
  helix:  4.33 (0.19), residues: 602
  sheet:  None (None), residues: 0
  loop : -1.61 (0.37), residues: 259

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.550 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0456
  time to fit residues: 2.9385
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.529 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6735
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 40 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4311  Z= 0.145
  Angle     :  0.448   8.724   6025  Z= 0.299
  Chirality :  0.038   0.139    853
  Planarity :  0.003   0.017    863
  Dihedral  :  4.864  31.481    863
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 0.82
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  4.18 %
    Favored  : 95.35 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    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:  2.42 (0.30), residues: 861
  helix:  2.78 (0.20), residues: 627
  sheet:  None (None), residues: 0
  loop : -1.92 (0.43), residues: 234

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.524 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0433
  time to fit residues: 2.8750
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.528 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6413
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    3.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.8750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.008   0.070   4311  Z= 0.557
  Angle     :  0.918   7.991   6025  Z= 0.666
  Chirality :  0.045   0.153    853
  Planarity :  0.007   0.025    863
  Dihedral  :  8.774  35.814    863
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  1.16 %
    Allowed  : 12.54 %
    Favored  : 86.30 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.48 %

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: -2.74 (0.26), residues: 861
  helix: -0.96 (0.19), residues: 594
  sheet:  None (None), residues: 0
  loop : -3.68 (0.35), residues: 267

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.470 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0422
  time to fit residues: 2.8470
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.534 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7397
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0060
   chunk 74 optimal weight:    0.2980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.7800

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.8045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4311  Z= 0.144
  Angle     :  0.444   5.742   6025  Z= 0.303
  Chirality :  0.037   0.133    853
  Planarity :  0.003   0.013    863
  Dihedral  :  5.596  34.661    863
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 1.31
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.48 %
    Favored  : 91.06 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.24 (0.29), residues: 861
  helix:  0.98 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.50 (0.39), residues: 229

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.555 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0429
  time to fit residues: 2.8182
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.568 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6881
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 42 optimal weight:    0.5980
   chunk 74 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.8553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4311  Z= 0.155
  Angle     :  0.426   5.427   6025  Z= 0.291
  Chirality :  0.037   0.129    853
  Planarity :  0.002   0.010    863
  Dihedral  :  5.137  29.652    863
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 10.57 %
    Favored  : 88.97 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.30), residues: 861
  helix:  1.77 (0.21), residues: 631
  sheet:  None (None), residues: 0
  loop : -3.35 (0.39), residues: 230

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.525 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0425
  time to fit residues: 2.8858
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.517 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6878
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 6 optimal weight:    0.0070
   chunk 43 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    1.5202

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.9524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4311  Z= 0.221
  Angle     :  0.489   5.869   6025  Z= 0.341
  Chirality :  0.038   0.140    853
  Planarity :  0.003   0.015    863
  Dihedral  :  5.908  34.525    863
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 11.03 %
    Favored  : 88.50 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.08 (0.30), residues: 861
  helix:  1.15 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -3.57 (0.38), residues: 233

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.567 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0427
  time to fit residues: 2.8117
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.489 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6525
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0970
   chunk 60 optimal weight:    8.9990
   chunk 70 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0980
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.1980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.9741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4311  Z= 0.174
  Angle     :  0.433   5.379   6025  Z= 0.299
  Chirality :  0.037   0.145    853
  Planarity :  0.003   0.014    863
  Dihedral  :  5.255  32.222    863
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 10.45 %
    Favored  : 89.08 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.31), residues: 861
  helix:  1.56 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -3.74 (0.39), residues: 219

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.550 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0416
  time to fit residues: 2.7741
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.481 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6736
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0770
   chunk 52 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 75 optimal weight:    0.5980
   chunk 79 optimal weight:    7.9990
   chunk 72 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.5538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.9685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.001   0.014   4311  Z= 0.098
  Angle     :  0.367   5.046   6025  Z= 0.246
  Chirality :  0.036   0.132    853
  Planarity :  0.002   0.011    863
  Dihedral  :  4.478  29.444    863
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.83 %
    Favored  : 90.71 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.32), residues: 861
  helix:  2.31 (0.22), residues: 645
  sheet:  None (None), residues: 0
  loop : -3.45 (0.40), residues: 216

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.570 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0424
  time to fit residues: 2.8462
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.536 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7058
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    0.0370
   chunk 46 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 60 optimal weight:    0.2980
   chunk 23 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 50 optimal weight:    0.2980
   chunk 81 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.5262

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          1.0263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4311  Z= 0.220
  Angle     :  0.465   5.308   6025  Z= 0.327
  Chirality :  0.037   0.143    853
  Planarity :  0.003   0.014    863
  Dihedral  :  5.418  31.286    863
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 12.31 %
    Favored  : 87.22 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  0.44 (0.31), residues: 861
  helix:  1.58 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -3.69 (0.39), residues: 225

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.551 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0435
  time to fit residues: 2.8805
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.507 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7024
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0020
   chunk 85 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0870
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   chunk 72 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.8768

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          1.0265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4311  Z= 0.134
  Angle     :  0.395   5.209   6025  Z= 0.270
  Chirality :  0.037   0.140    853
  Planarity :  0.002   0.013    863
  Dihedral  :  4.804  30.376    863
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  9.52 %
    Favored  : 89.90 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.06 (0.31), residues: 861
  helix:  2.03 (0.22), residues: 640
  sheet:  None (None), residues: 0
  loop : -3.58 (0.39), residues: 221

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

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

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1722 Ramachandran restraints generated.
    861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.559 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0477
  time to fit residues: 3.0480
Evaluate side-chains
  26 residues out of total 830 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.534 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6846
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 18 optimal weight:    0.5980
   chunk 68 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    2.7188

-------------------------------------------------------------------------------
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 = 0.3079 r_free = 0.3079 target = 0.067208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.056078 restraints weight = 29162.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.056241 restraints weight = 28593.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.056228 restraints weight = 27115.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          1.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.059   4311  Z= 0.363
  Angle     :  0.637   5.600   6025  Z= 0.455
  Chirality :  0.040   0.158    853
  Planarity :  0.005   0.020    863
  Dihedral  :  6.907  34.805    863
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 14.63 %
    Favored  : 84.79 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -1.66 (0.29), residues: 861
  helix: -0.02 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -4.25 (0.37), residues: 225

===============================================================================
Job complete
usr+sys time: 936.30 seconds
wall clock time: 17 minutes 23.65 seconds (1043.65 seconds total)