Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 16:00:33 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/04_2023/6lly_0915_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/04_2023/6lly_0915.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/04_2023/6lly_0915.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/04_2023/6lly_0915.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/04_2023/6lly_0915_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/04_2023/6lly_0915_updated.pdb"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      58      5.16       5
     Be      1      3.05       5
     C    4958      2.51       5
     N    1299      2.21       5
     O    1454      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   20": "OE1" <-> "OE2"
    Residue "A GLU   45": "OE1" <-> "OE2"
    Residue "A GLU   58": "OE1" <-> "OE2"
    Residue "A GLU   90": "OE1" <-> "OE2"
    Residue "A GLU  113": "OE1" <-> "OE2"
    Residue "A ASP  133": "OD1" <-> "OD2"
    Residue "A ASP  176": "OD1" <-> "OD2"
    Residue "A ASP  203": "OD1" <-> "OD2"
    Residue "A GLU  255": "OE1" <-> "OE2"
    Residue "A PHE  382": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  394": "OE1" <-> "OE2"
    Residue "A ASP  399": "OD1" <-> "OD2"
    Residue "A ASP  426": "OD1" <-> "OD2"
    Residue "A TYR  427": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  489": "NH1" <-> "NH2"
    Residue "A TYR  497": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  550": "OE1" <-> "OE2"
    Residue "A ASP  556": "OD1" <-> "OD2"
    Residue "A ASP  567": "OD1" <-> "OD2"
    Residue "A GLU  574": "OE1" <-> "OE2"
    Residue "A ASP  667": "OD1" <-> "OD2"
    Residue "A PHE  808": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  836": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  842": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  882": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  981": "OE1" <-> "OE2"
    Residue "A PHE  985": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 7774
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1008, 7774
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'peptide': 1006, 'undetermined': 2}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 960, None: 2}
            Not linked:
              pdbres="SER A1042 "
              pdbres="BEF A2001 "
            Not linked:
              pdbres="BEF A2001 "
              pdbres=" MG A2002 "
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" BE  BEF A2001 " occ=0.00
      ... (2 atoms not shown)
      pdb=" F3  BEF A2001 " occ=0.00
  Time building chain proxies: 4.32, per 1000 atoms: 0.56
  Number of scatterers: 7774
  At special positions: 0
  Unit cell: (88.395, 97.11, 145.665, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      58     16.00
     Mg      1     11.99
     F       3      9.00
     O    1454      8.00
     N    1299      7.00
     C    4958      6.00
     Be      1      4.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.01
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      43 helices and 9 sheets defined
      48.6% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 6
      No H-bonds generated for 'chain 'A' and resid 4 through 6'
    Processing helix  chain 'A' and resid 9 through 15
    Processing helix  chain 'A' and resid 26 through 35
      removed outlier: 3.518A  pdb=" N   ARG A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 57
      removed outlier: 3.720A  pdb=" N   ILE A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A  55 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 77
    Processing helix  chain 'A' and resid 86 through 116
      removed outlier: 4.110A  pdb=" N   GLU A  90 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      Proline residue:  A  91  - end of helix
      removed outlier: 3.586A  pdb=" N   ILE A  94 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A 100 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASN A 101 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE A 103 " --> pdb=" O   ALA A 100 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN A 108 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ARG A 110 " --> pdb=" O   TRP A 107 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA A 112 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU A 113 " --> pdb=" O   ARG A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 227 through 229
      No H-bonds generated for 'chain 'A' and resid 227 through 229'
    Processing helix  chain 'A' and resid 231 through 241
    Processing helix  chain 'A' and resid 248 through 274
    Processing helix  chain 'A' and resid 288 through 306
      removed outlier: 4.103A  pdb=" N   ILE A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   TYR A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 328
    Processing helix  chain 'A' and resid 337 through 339
      No H-bonds generated for 'chain 'A' and resid 337 through 339'
    Processing helix  chain 'A' and resid 341 through 344
    Processing helix  chain 'A' and resid 404 through 406
      No H-bonds generated for 'chain 'A' and resid 404 through 406'
    Processing helix  chain 'A' and resid 408 through 420
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.687A  pdb=" N   LEU A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 467
      No H-bonds generated for 'chain 'A' and resid 464 through 467'
    Processing helix  chain 'A' and resid 470 through 478
    Processing helix  chain 'A' and resid 517 through 523
      removed outlier: 3.928A  pdb=" N   ARG A 523 " --> pdb=" O   GLY A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 553
    Processing helix  chain 'A' and resid 572 through 574
      No H-bonds generated for 'chain 'A' and resid 572 through 574'
    Processing helix  chain 'A' and resid 580 through 586
      removed outlier: 4.117A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 615
      removed outlier: 3.693A  pdb=" N   LYS A 611 " --> pdb=" O   ALA A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 638
    Processing helix  chain 'A' and resid 654 through 658
    Processing helix  chain 'A' and resid 662 through 671
      removed outlier: 3.767A  pdb=" N   ASP A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 692
      removed outlier: 3.947A  pdb=" N   SER A 684 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 712
      Proline residue:  A 708  - end of helix
      removed outlier: 3.520A  pdb=" N   LYS A 711 " --> pdb=" O   PRO A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 729
      removed outlier: 3.500A  pdb=" N   ALA A 729 " --> pdb=" O   VAL A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 780
      removed outlier: 3.514A  pdb=" N   GLU A 747 " --> pdb=" O   ALA A 744 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ARG A 750 " --> pdb=" O   GLU A 747 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ILE A 752 " --> pdb=" O   GLY A 749 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR A 753 " --> pdb=" O   ARG A 750 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE A 759 " --> pdb=" O   MET A 756 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE A 760 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG A 761 " --> pdb=" O   GLN A 758 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   TYR A 762 " --> pdb=" O   PHE A 759 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A 764 " --> pdb=" O   ARG A 761 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER A 765 " --> pdb=" O   TYR A 762 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASN A 767 " --> pdb=" O   ILE A 764 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL A 768 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 766 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL A 772 " --> pdb=" O   GLY A 769 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   CYS A 773 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE A 775 " --> pdb=" O   VAL A 772 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 776 " --> pdb=" O   CYS A 773 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   LEU A 780 " --> pdb=" O   THR A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 796
      removed outlier: 3.698A  pdb=" N   TRP A 793 " --> pdb=" O   VAL A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 808
      removed outlier: 3.707A  pdb=" N   GLY A 807 " --> pdb=" O   ALA A 803 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   PHE A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 856
      removed outlier: 3.503A  pdb=" N   ILE A 839 " --> pdb=" O   ARG A 835 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 870
      No H-bonds generated for 'chain 'A' and resid 867 through 870'
    Processing helix  chain 'A' and resid 872 through 874
      No H-bonds generated for 'chain 'A' and resid 872 through 874'
    Processing helix  chain 'A' and resid 888 through 891
    Processing helix  chain 'A' and resid 894 through 912
    Processing helix  chain 'A' and resid 926 through 928
      No H-bonds generated for 'chain 'A' and resid 926 through 928'
    Processing helix  chain 'A' and resid 930 through 948
      removed outlier: 3.543A  pdb=" N   LEU A 947 " --> pdb=" O   HIS A 943 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR A 948 " --> pdb=" O   PHE A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 955
      No H-bonds generated for 'chain 'A' and resid 952 through 955'
    Processing helix  chain 'A' and resid 963 through 989
      Proline residue:  A 975  - end of helix
      removed outlier: 3.881A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1030
      Proline residue:  A1024  - end of helix
    Processing sheet with id=  A, first strand: chain 'A' and resid 126 through 129
    Processing sheet with id=  B, first strand: chain 'A' and resid 150 through 153
      removed outlier: 6.914A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 173 through 175
      removed outlier: 4.630A  pdb=" N   LEU A 173 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 331 through 333
      removed outlier: 3.543A  pdb=" N   ILE A 715 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ARG A 619 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   SER A 350 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   ILE A 621 " --> pdb=" O   SER A 350 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 395 through 397
      removed outlier: 5.202A  pdb=" N   ASN A 380 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LEU A 369 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   PHE A 382 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   PHE A 367 " --> pdb=" O   PHE A 382 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ILE A 384 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   ARG A 365 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   GLY A 597 " --> pdb=" O   CYS A 364 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   MET A 366 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   CYS A 595 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 4.997A  pdb=" N   ILE A 368 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.874A  pdb=" N   VAL A 593 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 13.050A  pdb=" N   ASP A 370 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.588A  pdb=" N   THR A 591 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'A' and resid 425 through 428
    Processing sheet with id=  G, first strand: chain 'A' and resid 479 through 481
    Processing sheet with id=  H, first strand: chain 'A' and resid 532 through 535
      removed outlier: 6.893A  pdb=" N   LEU A 590 " --> pdb=" O   THR A 525 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   ILE A 527 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   PHE A 592 " --> pdb=" O   ILE A 527 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   VAL A 529 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'A' and resid 651 through 653
      removed outlier: 6.359A  pdb=" N   CYS A 674 " --> pdb=" O   PHE A 652 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  I

    319 hydrogen bonds defined for protein.
    810 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: 2.65

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2534
        1.34 -     1.46: 1323
        1.46 -     1.57: 3971
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 7918
  Sorted by residual:
  bond pdb=" BE  BEF A2001 "
       pdb=" F2  BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.559 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" BE  BEF A2001 "
       pdb=" F3  BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.544 -0.068 2.00e-02 2.50e+03 1.17e+01
  bond pdb=" BE  BEF A2001 "
       pdb=" F1  BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.532 -0.056 2.00e-02 2.50e+03 7.95e+00
  bond pdb=" CA  ASP A 556 "
       pdb=" CB  ASP A 556 "
    ideal  model  delta    sigma   weight residual
    1.522  1.538 -0.016 1.32e-02 5.74e+03 1.45e+00
  bond pdb=" CA  LYS A 400 "
       pdb=" CB  LYS A 400 "
    ideal  model  delta    sigma   weight residual
    1.534  1.550 -0.016 1.57e-02 4.06e+03 1.06e+00
  ... (remaining 7913 not shown)

  Histogram of bond angle deviations from ideal:
      100.18 -   106.93: 239
      106.93 -   113.69: 4539
      113.69 -   120.45: 2915
      120.45 -   127.21: 2968
      127.21 -   133.97: 84
  Bond angle restraints: 10745
  Sorted by residual:
  angle pdb=" F2  BEF A2001 "
        pdb=" BE  BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.96  106.79   13.17 3.00e+00 1.11e-01 1.93e+01
  angle pdb=" F1  BEF A2001 "
        pdb=" BE  BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     120.12  109.35   10.77 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" C   PHE A1040 "
        pdb=" N   TRP A1041 "
        pdb=" CA  TRP A1041 "
      ideal   model   delta    sigma   weight residual
     120.82  126.14   -5.32 1.50e+00 4.44e-01 1.26e+01
  angle pdb=" N   LYS A 876 "
        pdb=" CA  LYS A 876 "
        pdb=" C   LYS A 876 "
      ideal   model   delta    sigma   weight residual
     113.20  109.26    3.94 1.21e+00 6.83e-01 1.06e+01
  angle pdb=" N   ASP A 881 "
        pdb=" CA  ASP A 881 "
        pdb=" C   ASP A 881 "
      ideal   model   delta    sigma   weight residual
     114.09  109.45    4.64 1.55e+00 4.16e-01 8.95e+00
  ... (remaining 10740 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 4463
       17.70 -    35.40: 274
       35.40 -    53.10: 44
       53.10 -    70.79: 6
       70.79 -    88.49: 6
  Dihedral angle restraints: 4793
    sinusoidal: 1886
      harmonic: 2907
  Sorted by residual:
  dihedral pdb=" CB  GLU A 113 "
           pdb=" CG  GLU A 113 "
           pdb=" CD  GLU A 113 "
           pdb=" OE1 GLU A 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.49  -88.49     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  LYS A 876 "
           pdb=" C   LYS A 876 "
           pdb=" N   GLU A 877 "
           pdb=" CA  GLU A 877 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.30   15.70     0      5.00e+00 4.00e-02 9.86e+00
  dihedral pdb=" CA  ALA A 216 "
           pdb=" C   ALA A 216 "
           pdb=" N   GLY A 217 "
           pdb=" CA  GLY A 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.83  -15.17     0      5.00e+00 4.00e-02 9.21e+00
  ... (remaining 4790 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 721
       0.027 -    0.054: 336
       0.054 -    0.081: 121
       0.081 -    0.107: 62
       0.107 -    0.134: 24
  Chirality restraints: 1264
  Sorted by residual:
  chirality pdb=" CA  VAL A 283 "
            pdb=" N   VAL A 283 "
            pdb=" C   VAL A 283 "
            pdb=" CB  VAL A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.51e-01
  chirality pdb=" CA  ILE A 392 "
            pdb=" N   ILE A 392 "
            pdb=" C   ILE A 392 "
            pdb=" CB  ILE A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  VAL A 534 "
            pdb=" N   VAL A 534 "
            pdb=" C   VAL A 534 "
            pdb=" CB  VAL A 534 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1261 not shown)

  Planarity restraints: 1366
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 952 "    0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO A 953 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 953 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 953 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 974 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 975 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 975 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 975 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 801 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.30e+00
        pdb=" N   PRO A 802 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 802 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 802 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1363 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 73
        2.61 -     3.19: 6939
        3.19 -     3.76: 11985
        3.76 -     4.33: 17811
        4.33 -     4.90: 28271
  Nonbonded interactions: 65079
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.043 2.170
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.075 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.078 2.170
  nonbonded pdb=" OD2 ASP A 351 "
            pdb=" F1  BEF A2001 "
     model   vdw
     2.129 2.390
  nonbonded pdb=" O   VAL A 969 "
            pdb=" OG  SER A 973 "
     model   vdw
     2.226 2.440
  ... (remaining 65074 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
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.220
  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:          1.670
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     23.280
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
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      :  0.003   0.083   7918  Z= 0.195
  Angle     :  0.603  13.174  10745  Z= 0.355
  Chirality :  0.040   0.134   1264
  Planarity :  0.004   0.043   1366
  Dihedral  : 12.235  88.493   2907
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer Outliers :  0.12 %
  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: -4.03 (0.21), residues: 998
  helix: -3.45 (0.15), residues: 481
  sheet: -1.54 (0.50), residues: 106
  loop : -1.70 (0.26), residues: 411

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.840 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 1.3314
  time to fit residues: 213.1401
Evaluate side-chains
  110 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.927 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3050
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 177 GLN
A 275 ASN
A 278 HIS
A 469 ASN
A 472 ASN
A 477 GLN
A 615 GLN
A 671 ASN
A 682 HIS
A 767 ASN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 822 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7918  Z= 0.178
  Angle     :  0.533   6.320  10745  Z= 0.281
  Chirality :  0.041   0.133   1264
  Planarity :  0.005   0.042   1366
  Dihedral  :  4.392  15.350   1063
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer Outliers :  2.56 %
  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: -2.14 (0.23), residues: 998
  helix: -1.33 (0.21), residues: 486
  sheet: -1.37 (0.51), residues: 87
  loop : -1.35 (0.27), residues: 425

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.909 
Fit side-chains
  outliers start: 22
  outliers final: 6
  residues processed: 123
  average time/residue: 1.2642
  time to fit residues: 164.5986
Evaluate side-chains
  112 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.921 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 1
  residues processed: 5
  average time/residue: 0.3049
  time to fit residues: 3.1741
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0570
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   overall best weight:    0.9304

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 275 ASN
A 469 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7918  Z= 0.179
  Angle     :  0.517   6.262  10745  Z= 0.267
  Chirality :  0.041   0.131   1264
  Planarity :  0.004   0.043   1366
  Dihedral  :  4.324  15.105   1063
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer Outliers :  2.68 %
  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: -1.19 (0.25), residues: 998
  helix: -0.34 (0.23), residues: 484
  sheet: -1.46 (0.48), residues: 90
  loop : -1.02 (0.28), residues: 424

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.830 
Fit side-chains
  outliers start: 23
  outliers final: 9
  residues processed: 121
  average time/residue: 1.2172
  time to fit residues: 156.4996
Evaluate side-chains
  112 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 1.044 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 4
  residues processed: 6
  average time/residue: 0.3557
  time to fit residues: 3.8556
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 47 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7918  Z= 0.250
  Angle     :  0.557   6.239  10745  Z= 0.288
  Chirality :  0.043   0.133   1264
  Planarity :  0.004   0.044   1366
  Dihedral  :  4.486  15.878   1063
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer Outliers :  3.49 %
  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: -0.99 (0.25), residues: 998
  helix: -0.13 (0.24), residues: 483
  sheet: -1.48 (0.47), residues: 91
  loop : -0.93 (0.28), residues: 424

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.919 
Fit side-chains
  outliers start: 30
  outliers final: 11
  residues processed: 121
  average time/residue: 1.2494
  time to fit residues: 160.3095
Evaluate side-chains
  114 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.847 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 3
  residues processed: 9
  average time/residue: 0.2757
  time to fit residues: 4.2584
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 86 optimal weight:    0.0000
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7918  Z= 0.152
  Angle     :  0.504   5.805  10745  Z= 0.258
  Chirality :  0.040   0.128   1264
  Planarity :  0.004   0.043   1366
  Dihedral  :  4.229  15.311   1063
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer Outliers :  2.10 %
  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: -0.55 (0.26), residues: 998
  helix:  0.30 (0.24), residues: 484
  sheet: -1.42 (0.47), residues: 90
  loop : -0.78 (0.28), residues: 424

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.937 
Fit side-chains
  outliers start: 18
  outliers final: 8
  residues processed: 121
  average time/residue: 1.1868
  time to fit residues: 153.0372
Evaluate side-chains
  113 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.924 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 6
  residues processed: 3
  average time/residue: 0.1047
  time to fit residues: 1.7921
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0970
   chunk 44 optimal weight:    5.9990
   chunk 8 optimal weight:    0.4980
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 93 optimal weight:    0.0370
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3856

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7918  Z= 0.133
  Angle     :  0.484   5.416  10745  Z= 0.247
  Chirality :  0.039   0.125   1264
  Planarity :  0.003   0.041   1366
  Dihedral  :  4.024  14.376   1063
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer Outliers :  2.10 %
  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: -0.21 (0.26), residues: 998
  helix:  0.60 (0.25), residues: 482
  sheet: -1.24 (0.48), residues: 90
  loop : -0.64 (0.28), residues: 426

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.691 
Fit side-chains
  outliers start: 18
  outliers final: 6
  residues processed: 123
  average time/residue: 1.1290
  time to fit residues: 147.9217
Evaluate side-chains
  112 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.893 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 5
  residues processed: 2
  average time/residue: 0.1144
  time to fit residues: 1.6009
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 81 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0870
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7918  Z= 0.153
  Angle     :  0.499   5.573  10745  Z= 0.255
  Chirality :  0.040   0.128   1264
  Planarity :  0.004   0.040   1366
  Dihedral  :  4.064  15.236   1063
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer Outliers :  2.10 %
  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: -0.16 (0.26), residues: 998
  helix:  0.63 (0.25), residues: 484
  sheet: -1.13 (0.48), residues: 90
  loop : -0.61 (0.29), residues: 424

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.919 
Fit side-chains
  outliers start: 18
  outliers final: 12
  residues processed: 119
  average time/residue: 1.1353
  time to fit residues: 144.6039
Evaluate side-chains
  114 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.894 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 8
  residues processed: 5
  average time/residue: 0.1036
  time to fit residues: 2.1308
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0040
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7918  Z= 0.153
  Angle     :  0.501   5.731  10745  Z= 0.255
  Chirality :  0.040   0.133   1264
  Planarity :  0.004   0.040   1366
  Dihedral  :  4.029  15.518   1063
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer Outliers :  1.75 %
  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: -0.12 (0.26), residues: 998
  helix:  0.63 (0.25), residues: 489
  sheet: -1.04 (0.48), residues: 90
  loop : -0.58 (0.29), residues: 419

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.828 
Fit side-chains
  outliers start: 15
  outliers final: 9
  residues processed: 117
  average time/residue: 1.1124
  time to fit residues: 139.0303
Evaluate side-chains
  115 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.818 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 8
  residues processed: 2
  average time/residue: 0.0915
  time to fit residues: 1.4628
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7918  Z= 0.233
  Angle     :  0.563   5.910  10745  Z= 0.286
  Chirality :  0.043   0.150   1264
  Planarity :  0.004   0.040   1366
  Dihedral  :  4.329  16.281   1063
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer Outliers :  2.10 %
  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: -0.34 (0.26), residues: 998
  helix:  0.42 (0.24), residues: 487
  sheet: -1.11 (0.48), residues: 90
  loop : -0.66 (0.29), residues: 421

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.941 
Fit side-chains
  outliers start: 18
  outliers final: 10
  residues processed: 120
  average time/residue: 1.1130
  time to fit residues: 142.6341
Evaluate side-chains
  118 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.832 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 7
  residues processed: 3
  average time/residue: 0.0896
  time to fit residues: 1.6638
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0980
   chunk 79 optimal weight:    0.1980
   chunk 8 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.4582

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7918  Z= 0.146
  Angle     :  0.512   7.061  10745  Z= 0.260
  Chirality :  0.040   0.129   1264
  Planarity :  0.004   0.040   1366
  Dihedral  :  4.046  16.016   1063
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer Outliers :  1.05 %
  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: -0.06 (0.26), residues: 998
  helix:  0.67 (0.25), residues: 487
  sheet: -0.99 (0.49), residues: 90
  loop : -0.55 (0.29), residues: 421

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.985 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 121
  average time/residue: 1.1425
  time to fit residues: 147.7581
Evaluate side-chains
  113 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.925 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 8
  residues processed: 0
  time to fit residues: 1.3678
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0570
   chunk 33 optimal weight:    0.0980
   chunk 81 optimal weight:    0.0470
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.3396

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.190559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.150986 restraints weight = 7737.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 1.63
r_work: 0.3462 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7918  Z= 0.136
  Angle     :  0.504   7.358  10745  Z= 0.253
  Chirality :  0.039   0.126   1264
  Planarity :  0.004   0.043   1366
  Dihedral  :  3.895  14.610   1063
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer Outliers :  1.63 %
  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:  0.10 (0.27), residues: 998
  helix:  0.80 (0.25), residues: 489
  sheet: -0.90 (0.49), residues: 90
  loop : -0.47 (0.29), residues: 419

===============================================================================
Job complete
usr+sys time: 3142.93 seconds
wall clock time: 56 minutes 33.73 seconds (3393.73 seconds total)