Starting phenix.real_space_refine
on Mon Mar 11 08:53:24 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/03_2024/6lly_0915_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/03_2024/6lly_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_0915/03_2024/6lly_0915.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/03_2024/6lly_0915.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/03_2024/6lly_0915_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lly_0915/03_2024/6lly_0915_updated.pdb"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.66, per 1000 atoms: 0.60
  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: 3.22
  Conformation dependent library (CDL) restraints added in 1.5 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: 2.18
  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: 2.73

  Time building geometry restraints manager: 3.42 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:             0.210
  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:          1.460
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     25.710
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:12.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.260
-------------------------------------------------------------------------------
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 %
    Allowed  :  3.38 %
    Favored  : 96.51 %
  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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1041 
 HIS   0.003   0.001   HIS A 682 
 PHE   0.016   0.001   PHE A 759 
 TYR   0.015   0.001   TYR A 836 
 ARG   0.003   0.000   ARG A 821 

*********************** 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  : 0.905 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.7725 (t60) cc_final: 0.7489 (t60)
REVERT: A  126 MET cc_start: 0.7771 (mmt) cc_final: 0.7310 (mmt)
REVERT: A  133 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6459 (m-30)
REVERT: A  176 ASP cc_start: 0.7391 (t70) cc_final: 0.7010 (t70)
REVERT: A  207 MET cc_start: 0.8345 (mmt) cc_final: 0.8102 (tpp)
REVERT: A  441 THR cc_start: 0.8745 (p) cc_final: 0.8494 (p)
REVERT: A  467 ARG cc_start: 0.7357 (ttt-90) cc_final: 0.6989 (mmm160)
REVERT: A  550 GLU cc_start: 0.7149 (tt0) cc_final: 0.6929 (mt-10)
REVERT: A  575 MET cc_start: 0.3524 (mmt) cc_final: 0.2153 (mmt)
REVERT: A  600 ASP cc_start: 0.8156 (t0) cc_final: 0.7481 (t70)
REVERT: A  756 MET cc_start: 0.8282 (ttm) cc_final: 0.8008 (ttm)
REVERT: A  968 MET cc_start: 0.8232 (tpp) cc_final: 0.7889 (tpp)
REVERT: A  978 LEU cc_start: 0.8441 (tp) cc_final: 0.8178 (tm)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 1.4132
  time to fit residues: 225.8026
Evaluate side-chains
  111 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.9990
   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:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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: 0.7580
moved from start:          0.1573

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= 0.181
  Angle     :  0.529   6.375  10745  Z= 0.278
  Chirality :  0.041   0.130   1264
  Planarity :  0.005   0.042   1366
  Dihedral  :  4.534  35.785   1065
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 10.71 %
    Favored  : 86.85 %
  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: -1.34 (0.21), residues: 486
  sheet: -1.43 (0.50), residues: 88
  loop : -1.32 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 682 
 PHE   0.016   0.001   PHE A 759 
 TYR   0.014   0.001   TYR A 867 
 ARG   0.006   0.000   ARG A 139 

*********************** 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
  136 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A   41 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7676 (mm)
REVERT: A   58 GLU cc_start: 0.6957 (tt0) cc_final: 0.6459 (tp30)
REVERT: A  126 MET cc_start: 0.7834 (mmt) cc_final: 0.7410 (mmt)
REVERT: A  412 GLU cc_start: 0.7883 (tt0) cc_final: 0.7609 (tt0)
REVERT: A  439 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6204 (tm-30)
REVERT: A  441 THR cc_start: 0.8542 (p) cc_final: 0.7206 (p)
REVERT: A  536 MET cc_start: 0.7223 (ttp) cc_final: 0.6898 (ttp)
REVERT: A  575 MET cc_start: 0.3524 (mmt) cc_final: 0.2226 (mmt)
REVERT: A  600 ASP cc_start: 0.8182 (t0) cc_final: 0.7576 (t70)
REVERT: A  836 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6002 (p90)
REVERT: A  968 MET cc_start: 0.8198 (tpp) cc_final: 0.7894 (tpp)
REVERT: A  978 LEU cc_start: 0.8343 (tp) cc_final: 0.7995 (tm)
  outliers start: 21
  outliers final: 7
  residues processed: 124
  average time/residue: 1.2610
  time to fit residues: 165.8529
Evaluate side-chains
  115 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  111 ASN
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  836 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0370
   chunk 25 optimal weight:    0.8980
   chunk 90 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.5216

-------------------------------------------------------------------------------
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: 0.7550
moved from start:          0.1868

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= 0.137
  Angle     :  0.484   5.911  10745  Z= 0.251
  Chirality :  0.040   0.132   1264
  Planarity :  0.004   0.042   1366
  Dihedral  :  4.145  13.622   1063
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.04 %
    Favored  : 84.63 %
  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: -1.10 (0.25), residues: 998
  helix: -0.25 (0.23), residues: 483
  sheet: -1.28 (0.48), residues: 87
  loop : -1.04 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.014   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 130 
 ARG   0.003   0.000   ARG A 139 

*********************** 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
  131 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.933 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7573 (pt0)
REVERT: A   58 GLU cc_start: 0.6842 (tt0) cc_final: 0.6360 (tp30)
REVERT: A  126 MET cc_start: 0.7802 (mmt) cc_final: 0.7335 (mmt)
REVERT: A  220 MET cc_start: 0.7840 (mtp) cc_final: 0.7566 (mtt)
REVERT: A  412 GLU cc_start: 0.7696 (tt0) cc_final: 0.7286 (tt0)
REVERT: A  441 THR cc_start: 0.8462 (p) cc_final: 0.8044 (p)
REVERT: A  479 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6755 (tpp)
REVERT: A  549 ARG cc_start: 0.7294 (mpp80) cc_final: 0.6952 (mpp80)
REVERT: A  575 MET cc_start: 0.3491 (mmt) cc_final: 0.2273 (mmt)
REVERT: A  756 MET cc_start: 0.7821 (ttm) cc_final: 0.7091 (mmt)
REVERT: A  836 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6145 (p90)
REVERT: A  896 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8098 (tpp)
REVERT: A  908 MET cc_start: 0.8411 (mmp) cc_final: 0.8163 (mmp)
REVERT: A  942 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7599 (mt)
REVERT: A  968 MET cc_start: 0.8215 (tpp) cc_final: 0.7871 (tpp)
REVERT: A  978 LEU cc_start: 0.8248 (tp) cc_final: 0.7903 (tm)
  outliers start: 20
  outliers final: 7
  residues processed: 120
  average time/residue: 1.2343
  time to fit residues: 158.1148
Evaluate side-chains
  116 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue  954 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0670
   chunk 26 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.4124

-------------------------------------------------------------------------------
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: 0.7607
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7918  Z= 0.235
  Angle     :  0.544   6.152  10745  Z= 0.281
  Chirality :  0.042   0.141   1264
  Planarity :  0.004   0.042   1366
  Dihedral  :  4.388  14.191   1063
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 12.81 %
    Favored  : 83.35 %
  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: -0.88 (0.25), residues: 998
  helix: -0.04 (0.24), residues: 483
  sheet: -1.42 (0.47), residues: 91
  loop : -0.88 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 793 
 HIS   0.002   0.001   HIS A   5 
 PHE   0.016   0.001   PHE A 759 
 TYR   0.011   0.002   TYR A 295 
 ARG   0.004   0.000   ARG A 134 

*********************** 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
  142 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A   58 GLU cc_start: 0.6908 (tt0) cc_final: 0.6447 (tp30)
REVERT: A  126 MET cc_start: 0.7818 (mmt) cc_final: 0.7401 (mmt)
REVERT: A  134 ARG cc_start: 0.7754 (pmm-80) cc_final: 0.7472 (pmm-80)
REVERT: A  220 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7626 (mtt)
REVERT: A  381 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7641 (mt-10)
REVERT: A  412 GLU cc_start: 0.7710 (tt0) cc_final: 0.7390 (tt0)
REVERT: A  439 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6251 (tm-30)
REVERT: A  441 THR cc_start: 0.8435 (p) cc_final: 0.7388 (p)
REVERT: A  479 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6746 (tpp)
REVERT: A  482 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6276 (mt-10)
REVERT: A  548 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7582 (mp)
REVERT: A  549 ARG cc_start: 0.7256 (mpp80) cc_final: 0.6742 (mpp80)
REVERT: A  575 MET cc_start: 0.3421 (mmt) cc_final: 0.2183 (mmt)
REVERT: A  599 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8297 (pt)
REVERT: A  600 ASP cc_start: 0.8245 (t0) cc_final: 0.7641 (t70)
REVERT: A  836 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6117 (p90)
REVERT: A  896 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8096 (tpp)
REVERT: A  923 ARG cc_start: 0.7440 (mtp-110) cc_final: 0.6913 (mmt180)
REVERT: A  968 MET cc_start: 0.8194 (tpp) cc_final: 0.7991 (tpp)
REVERT: A  978 LEU cc_start: 0.8302 (tp) cc_final: 0.7975 (tm)
  outliers start: 33
  outliers final: 9
  residues processed: 125
  average time/residue: 1.2098
  time to fit residues: 160.2603
Evaluate side-chains
  126 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  381 GLU
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 0 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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: 0.7580
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7918  Z= 0.173
  Angle     :  0.507   5.895  10745  Z= 0.259
  Chirality :  0.041   0.127   1264
  Planarity :  0.004   0.042   1366
  Dihedral  :  4.211  13.501   1063
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.09 %
    Favored  : 82.77 %
  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: -0.57 (0.26), residues: 998
  helix:  0.26 (0.24), residues: 483
  sheet: -1.39 (0.48), residues: 90
  loop : -0.75 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.014   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 130 
 ARG   0.004   0.000   ARG A 134 

*********************** 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
  139 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A   58 GLU cc_start: 0.6872 (tt0) cc_final: 0.6375 (tp30)
REVERT: A  126 MET cc_start: 0.7704 (mmt) cc_final: 0.7314 (mmt)
REVERT: A  220 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7622 (mtt)
REVERT: A  245 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.5758 (pt0)
REVERT: A  381 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7679 (mt-10)
REVERT: A  439 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6312 (tm-30)
REVERT: A  441 THR cc_start: 0.8384 (p) cc_final: 0.7409 (p)
REVERT: A  479 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6662 (tpp)
REVERT: A  482 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6193 (mt-10)
REVERT: A  494 MET cc_start: 0.8301 (tmt) cc_final: 0.7785 (tmt)
REVERT: A  549 ARG cc_start: 0.7366 (mpp80) cc_final: 0.6868 (mpp80)
REVERT: A  575 MET cc_start: 0.3514 (mmt) cc_final: 0.2313 (mmt)
REVERT: A  756 MET cc_start: 0.7812 (ttm) cc_final: 0.7072 (mmt)
REVERT: A  836 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6090 (p90)
REVERT: A  896 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8098 (tpp)
REVERT: A  968 MET cc_start: 0.8204 (tpp) cc_final: 0.7925 (tpp)
REVERT: A  978 LEU cc_start: 0.8239 (tp) cc_final: 0.7895 (tm)
  outliers start: 27
  outliers final: 13
  residues processed: 125
  average time/residue: 1.1727
  time to fit residues: 155.8286
Evaluate side-chains
  126 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ASN
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  381 GLU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  942 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.0970
   chunk 56 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0070
   chunk 93 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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: 0.7537
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7918  Z= 0.134
  Angle     :  0.479   5.505  10745  Z= 0.245
  Chirality :  0.039   0.125   1264
  Planarity :  0.004   0.040   1366
  Dihedral  :  3.987  14.017   1063
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.67 %
    Favored  : 82.65 %
  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:  0.61 (0.25), residues: 483
  sheet: -1.27 (0.48), residues: 90
  loop : -0.64 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A   5 
 PHE   0.013   0.001   PHE A 759 
 TYR   0.017   0.001   TYR A 990 
 ARG   0.004   0.000   ARG A 467 

*********************** 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
  138 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7679 (mmt) cc_final: 0.7278 (mmt)
REVERT: A  220 MET cc_start: 0.7808 (mtp) cc_final: 0.7538 (mtp)
REVERT: A  245 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5880 (pt0)
REVERT: A  328 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7144 (ttmm)
REVERT: A  441 THR cc_start: 0.8323 (p) cc_final: 0.7952 (p)
REVERT: A  482 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6275 (mt-10)
REVERT: A  494 MET cc_start: 0.8275 (tmt) cc_final: 0.7928 (tmt)
REVERT: A  575 MET cc_start: 0.3496 (mmt) cc_final: 0.2363 (mmt)
REVERT: A  756 MET cc_start: 0.7783 (ttm) cc_final: 0.7103 (mmt)
REVERT: A  836 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.6043 (p90)
REVERT: A  896 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8094 (tpp)
REVERT: A  924 MET cc_start: 0.7972 (ttp) cc_final: 0.7329 (ttm)
REVERT: A  968 MET cc_start: 0.8164 (tpp) cc_final: 0.7742 (tpp)
  outliers start: 23
  outliers final: 6
  residues processed: 125
  average time/residue: 1.1915
  time to fit residues: 158.8156
Evaluate side-chains
  120 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:   20.0000
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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: 0.7569
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7918  Z= 0.180
  Angle     :  0.511   5.676  10745  Z= 0.261
  Chirality :  0.041   0.136   1264
  Planarity :  0.004   0.040   1366
  Dihedral  :  4.103  13.872   1063
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.65 %
    Favored  : 80.68 %
  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: -0.21 (0.26), residues: 998
  helix:  0.59 (0.25), residues: 483
  sheet: -1.27 (0.47), residues: 90
  loop : -0.61 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.014   0.001   PHE A 759 
 TYR   0.019   0.002   TYR A 867 
 ARG   0.002   0.000   ARG A 821 

*********************** 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
  133 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7783 (mmt) cc_final: 0.7372 (mmt)
REVERT: A  149 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7999 (t0)
REVERT: A  328 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7182 (ttmm)
REVERT: A  441 THR cc_start: 0.8376 (p) cc_final: 0.8124 (p)
REVERT: A  494 MET cc_start: 0.8334 (tmt) cc_final: 0.7867 (tmt)
REVERT: A  575 MET cc_start: 0.3535 (mmt) cc_final: 0.2378 (mmt)
REVERT: A  599 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8073 (pt)
REVERT: A  756 MET cc_start: 0.7796 (ttm) cc_final: 0.7086 (mmt)
REVERT: A  836 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.5997 (p90)
REVERT: A  896 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8115 (tpp)
REVERT: A  924 MET cc_start: 0.7912 (ttp) cc_final: 0.7463 (ttm)
REVERT: A  968 MET cc_start: 0.8181 (tpp) cc_final: 0.7949 (tpp)
  outliers start: 23
  outliers final: 12
  residues processed: 121
  average time/residue: 1.1772
  time to fit residues: 151.3028
Evaluate side-chains
  124 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  945 LEU
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:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 92 optimal weight:    0.6980
   chunk 84 optimal weight:    0.1980
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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: 0.7551
moved from start:          0.2486

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= 0.150
  Angle     :  0.497   5.759  10745  Z= 0.253
  Chirality :  0.040   0.127   1264
  Planarity :  0.004   0.040   1366
  Dihedral  :  4.007  13.906   1063
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.30 %
    Favored  : 80.91 %
  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: -0.08 (0.26), residues: 998
  helix:  0.74 (0.25), residues: 482
  sheet: -1.25 (0.47), residues: 90
  loop : -0.59 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A   5 
 PHE   0.013   0.001   PHE A 759 
 TYR   0.015   0.001   TYR A 294 
 ARG   0.007   0.000   ARG A 467 

*********************** 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
  139 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7664 (mmt) cc_final: 0.7280 (mmt)
REVERT: A  149 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8076 (t0)
REVERT: A  207 MET cc_start: 0.8129 (tpp) cc_final: 0.7561 (mmm)
REVERT: A  220 MET cc_start: 0.7626 (mtp) cc_final: 0.7376 (mtt)
REVERT: A  328 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7150 (ttmm)
REVERT: A  441 THR cc_start: 0.8350 (p) cc_final: 0.8131 (p)
REVERT: A  494 MET cc_start: 0.8338 (tmt) cc_final: 0.7847 (tmt)
REVERT: A  559 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8242 (ptp-170)
REVERT: A  575 MET cc_start: 0.3525 (mmt) cc_final: 0.2389 (mmt)
REVERT: A  599 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8326 (pt)
REVERT: A  756 MET cc_start: 0.7786 (ttm) cc_final: 0.7084 (mmt)
REVERT: A  836 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.5977 (p90)
REVERT: A  896 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8120 (tpp)
REVERT: A  924 MET cc_start: 0.7800 (ttp) cc_final: 0.7595 (ttm)
REVERT: A  968 MET cc_start: 0.8176 (tpp) cc_final: 0.7909 (tpp)
  outliers start: 24
  outliers final: 10
  residues processed: 126
  average time/residue: 1.1737
  time to fit residues: 157.6981
Evaluate side-chains
  126 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  847 THR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 57 optimal weight:    9.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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: 0.7628
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7918  Z= 0.308
  Angle     :  0.606   6.243  10745  Z= 0.309
  Chirality :  0.045   0.159   1264
  Planarity :  0.004   0.041   1366
  Dihedral  :  4.531  15.925   1063
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.30 %
    Favored  : 80.56 %
  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: -0.56 (0.26), residues: 998
  helix:  0.25 (0.24), residues: 482
  sheet: -1.25 (0.48), residues: 90
  loop : -0.76 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 793 
 HIS   0.003   0.001   HIS A  15 
 PHE   0.017   0.002   PHE A 759 
 TYR   0.019   0.002   TYR A 867 
 ARG   0.004   0.000   ARG A 821 

*********************** 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
  142 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7773 (mmt) cc_final: 0.7335 (mmt)
REVERT: A  220 MET cc_start: 0.7695 (mtp) cc_final: 0.7448 (mtt)
REVERT: A  328 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7256 (ttmm)
REVERT: A  439 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6058 (tm-30)
REVERT: A  441 THR cc_start: 0.8401 (p) cc_final: 0.7342 (p)
REVERT: A  548 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7558 (mp)
REVERT: A  549 ARG cc_start: 0.7221 (mpp80) cc_final: 0.6941 (mpp80)
REVERT: A  559 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8265 (ptp-170)
REVERT: A  575 MET cc_start: 0.3359 (mmt) cc_final: 0.2145 (mmt)
REVERT: A  599 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8278 (pt)
REVERT: A  600 ASP cc_start: 0.8277 (t0) cc_final: 0.7824 (t70)
REVERT: A  836 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6039 (p90)
REVERT: A  896 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8128 (tpp)
REVERT: A  978 LEU cc_start: 0.8221 (tp) cc_final: 0.7875 (tm)
  outliers start: 27
  outliers final: 14
  residues processed: 127
  average time/residue: 1.1678
  time to fit residues: 157.9593
Evaluate side-chains
  132 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  847 THR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.0870
   chunk 66 optimal weight:    0.5980
   chunk 99 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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: 0.7564
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7918  Z= 0.159
  Angle     :  0.520   6.766  10745  Z= 0.264
  Chirality :  0.040   0.129   1264
  Planarity :  0.004   0.041   1366
  Dihedral  :  4.149  13.971   1063
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.11 %
    Favored  : 80.44 %
  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: -0.20 (0.26), residues: 998
  helix:  0.63 (0.25), residues: 481
  sheet: -1.20 (0.47), residues: 90
  loop : -0.66 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 278 
 PHE   0.013   0.001   PHE A 759 
 TYR   0.015   0.001   TYR A 294 
 ARG   0.006   0.000   ARG A 467 

********************** 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
  133 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7660 (mmt) cc_final: 0.7282 (mmt)
REVERT: A  220 MET cc_start: 0.7639 (mtp) cc_final: 0.7422 (mtp)
REVERT: A  245 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6032 (pt0)
REVERT: A  328 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7131 (ttmm)
REVERT: A  441 THR cc_start: 0.8390 (p) cc_final: 0.8148 (p)
REVERT: A  548 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7565 (mp)
REVERT: A  549 ARG cc_start: 0.7288 (mpp80) cc_final: 0.6956 (mpp80)
REVERT: A  575 MET cc_start: 0.3277 (mmt) cc_final: 0.2117 (mmt)
REVERT: A  599 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8306 (pt)
REVERT: A  756 MET cc_start: 0.7837 (ttm) cc_final: 0.7139 (mmt)
REVERT: A  836 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.5867 (p90)
REVERT: A  896 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8135 (tpp)
  outliers start: 21
  outliers final: 13
  residues processed: 123
  average time/residue: 1.0773
  time to fit residues: 141.5706
Evaluate side-chains
  130 residues out of total 861 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  847 THR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 33 optimal weight:    0.2980
   chunk 81 optimal weight:    0.0470
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.189444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.150083 restraints weight = 7746.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 1.65
r_work: 0.3446 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2653

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     :  0.510   6.212  10745  Z= 0.260
  Chirality :  0.040   0.131   1264
  Planarity :  0.004   0.041   1366
  Dihedral  :  4.051  13.830   1063
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.58 %
    Favored  : 80.33 %
  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:  0.71 (0.25), residues: 489
  sheet: -1.20 (0.45), residues: 93
  loop : -0.55 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A   5 
 PHE   0.013   0.001   PHE A 759 
 TYR   0.020   0.001   TYR A 867 
 ARG   0.007   0.000   ARG A 467 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3275.98 seconds
wall clock time: 58 minutes 42.84 seconds (3522.84 seconds total)