Starting phenix.real_space_refine
on Sun Dec 10 19:03:51 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/12_2023/7w84_32351.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/12_2023/7w84_32351.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/12_2023/7w84_32351.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/12_2023/7w84_32351.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/12_2023/7w84_32351.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/12_2023/7w84_32351.pdb"
  }
  resolution = 3.4
  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=   0.184 sd=   0.712
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7474 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4993      2.51       5
     N    1376      2.21       5
     O    1461      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  109": "NH1" <-> "NH2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A ARG  124": "NH1" <-> "NH2"
    Residue "A GLU  125": "OE1" <-> "OE2"
    Residue "A ARG  136": "NH1" <-> "NH2"
    Residue "A ARG  142": "NH1" <-> "NH2"
    Residue "A TYR  157": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  160": "OE1" <-> "OE2"
    Residue "A PHE  163": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  221": "NH1" <-> "NH2"
    Residue "A PHE  225": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  233": "OE1" <-> "OE2"
    Residue "A TYR  249": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  287": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  321": "OD1" <-> "OD2"
    Residue "A GLU  332": "OE1" <-> "OE2"
    Residue "A GLU  343": "OE1" <-> "OE2"
    Residue "A PHE  347": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  358": "NH1" <-> "NH2"
    Residue "A TYR  375": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  391": "OE1" <-> "OE2"
    Residue "A TYR  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  407": "OD1" <-> "OD2"
    Residue "A PHE  408": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  413": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  455": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  462": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  463": "OE1" <-> "OE2"
    Residue "A PHE  467": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  480": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  498": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  502": "NH1" <-> "NH2"
    Residue "A PHE  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  519": "NH1" <-> "NH2"
    Residue "A PHE  522": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  523": "OE1" <-> "OE2"
    Residue "A TYR  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  530": "OE1" <-> "OE2"
    Residue "A ASP  534": "OD1" <-> "OD2"
    Residue "A ASP  540": "OD1" <-> "OD2"
    Residue "A PHE  546": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  548": "OD1" <-> "OD2"
    Residue "A TYR  583": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  594": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  629": "OE1" <-> "OE2"
    Residue "A ASP  651": "OD1" <-> "OD2"
    Residue "A ASP  656": "OD1" <-> "OD2"
    Residue "A GLU  663": "OE1" <-> "OE2"
    Residue "A ASP  676": "OD1" <-> "OD2"
    Residue "A TYR  688": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  693": "OE1" <-> "OE2"
    Residue "A TYR  741": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  750": "OE1" <-> "OE2"
    Residue "A ASP  762": "OD1" <-> "OD2"
    Residue "A ASP  785": "OD1" <-> "OD2"
    Residue "A TYR  793": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  798": "OD1" <-> "OD2"
    Residue "A ARG  811": "NH1" <-> "NH2"
    Residue "A ASP  828": "OD1" <-> "OD2"
    Residue "A TYR  849": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  864": "OE1" <-> "OE2"
    Residue "A PHE  870": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  873": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  877": "OD1" <-> "OD2"
    Residue "A ARG  892": "NH1" <-> "NH2"
    Residue "A ASP  914": "OD1" <-> "OD2"
    Residue "A PHE  933": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  938": "OE1" <-> "OE2"
    Residue "A TYR  945": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  960": "NH1" <-> "NH2"
    Residue "A PHE  987": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  995": "OE1" <-> "OE2"
    Residue "A GLU  996": "OE1" <-> "OE2"
    Residue "A GLU 1003": "OE1" <-> "OE2"
    Residue "A TYR 1011": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1019": "OE1" <-> "OE2"
    Residue "A ASP 1035": "OD1" <-> "OD2"
    Residue "A ARG 1038": "NH1" <-> "NH2"
    Residue "A PHE 1040": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 1044": "OD1" <-> "OD2"
    Residue "A TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 1086": "NH1" <-> "NH2"
    Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 1117": "OD1" <-> "OD2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7879
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 995, 7879
          Classifications: {'peptide': 995}
          Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 949}
          Chain breaks: 1
  Time building chain proxies: 4.79, per 1000 atoms: 0.61
  Number of scatterers: 7879
  At special positions: 0
  Unit cell: (81.18, 104.28, 101.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1461      8.00
     N    1376      7.00
     C    4993      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 728 " - pdb=" SG  CYS A 805 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.12
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1874

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 8 sheets defined
      40.1% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 141 through 143
      No H-bonds generated for 'chain 'A' and resid 141 through 143'
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 4.249A  pdb=" N   GLU A 233 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 303
    Processing helix  chain 'A' and resid 312 through 322
      removed outlier: 3.726A  pdb=" N   LEU A 322 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 335
      removed outlier: 3.534A  pdb=" N   LEU A 327 " --> pdb=" O   SER A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 359
      removed outlier: 3.502A  pdb=" N   ASN A 356 " --> pdb=" O   ALA A 352 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   MET A 357 " --> pdb=" O   HIS A 353 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   LYS A 359 " --> pdb=" O   MET A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 401
      removed outlier: 3.690A  pdb=" N   LYS A 399 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
      removed outlier: 3.717A  pdb=" N   LEU A 426 " --> pdb=" O   PRO A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 434
    Processing helix  chain 'A' and resid 441 through 453
      removed outlier: 3.901A  pdb=" N   HIS A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 474
    Processing helix  chain 'A' and resid 487 through 496
      removed outlier: 3.570A  pdb=" N   GLY A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 513
    Processing helix  chain 'A' and resid 554 through 564
    Processing helix  chain 'A' and resid 627 through 636
    Processing helix  chain 'A' and resid 640 through 658
      removed outlier: 4.323A  pdb=" N   PHE A 644 " --> pdb=" O   LYS A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 671
      removed outlier: 3.965A  pdb=" N   LYS A 671 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 686
    Processing helix  chain 'A' and resid 693 through 715
    Processing helix  chain 'A' and resid 747 through 751
    Processing helix  chain 'A' and resid 794 through 800
    Processing helix  chain 'A' and resid 816 through 820
    Processing helix  chain 'A' and resid 862 through 877
      removed outlier: 3.613A  pdb=" N   ILE A 866 " --> pdb=" O   THR A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 892
    Processing helix  chain 'A' and resid 899 through 913
    Processing helix  chain 'A' and resid 914 through 916
      No H-bonds generated for 'chain 'A' and resid 914 through 916'
    Processing helix  chain 'A' and resid 934 through 938
      removed outlier: 4.131A  pdb=" N   MET A 937 " --> pdb=" O   PRO A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 966
    Processing helix  chain 'A' and resid 991 through 1012
      removed outlier: 3.944A  pdb=" N   GLU A 996 " --> pdb=" O   ASP A 992 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   ARG A 997 " --> pdb=" O   ALA A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1023
      removed outlier: 3.800A  pdb=" N   ILE A1020 " --> pdb=" O   ARG A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1034
      removed outlier: 4.341A  pdb=" N   ARG A1034 " --> pdb=" O   VAL A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1064
      removed outlier: 3.614A  pdb=" N   CYS A1064 " --> pdb=" O   TRP A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1067
      No H-bonds generated for 'chain 'A' and resid 1065 through 1067'
    Processing helix  chain 'A' and resid 1068 through 1082
      removed outlier: 3.554A  pdb=" N   HIS A1082 " --> pdb=" O   HIS A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1097
    Processing helix  chain 'A' and resid 1098 through 1103
    Processing helix  chain 'A' and resid 1103 through 1110
      removed outlier: 3.636A  pdb=" N   ALA A1107 " --> pdb=" O   LEU A1103 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183
      removed outlier: 6.699A  pdb=" N   ALA A 111 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL A 135 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   ALA A 113 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ASP A 133 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   LEU A 115 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   SER A 131 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU A 117 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   GLY A 134 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   LYS A 151 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 374
    Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 386
      removed outlier: 6.446A  pdb=" N   ILE A 377 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   TRP A 478 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 536 through 538
    Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 553
      removed outlier: 6.196A  pdb=" N   GLY A 551 " --> pdb=" O   THR A 588 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 625 through 626
      removed outlier: 3.609A  pdb=" N   VAL A 626 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ILE A 717 " --> pdb=" O   VAL A 626 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 739 through 740
      removed outlier: 8.531A  pdb=" N   VAL A 806 " --> pdb=" O   VAL A 724 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   ILE A 726 " --> pdb=" O   VAL A 806 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   PHE A 808 " --> pdb=" O   ILE A 726 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   CYS A 728 " --> pdb=" O   PHE A 808 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 744 through 745
      removed outlier: 6.814A  pdb=" N   THR A 766 " --> pdb=" O   ASP A 762 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ASP A 762 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL A 768 " --> pdb=" O   CYS A 760 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    855 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: 2.96

  Time building geometry restraints manager: 3.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2539
        1.34 -     1.46: 1164
        1.46 -     1.57: 4274
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 8052
  Sorted by residual:
  bond pdb=" CA  GLU A 252 "
       pdb=" C   GLU A 252 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.036 1.22e-02 6.72e+03 8.48e+00
  bond pdb=" N   ASN A1024 "
       pdb=" CA  ASN A1024 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.21e-02 6.83e+03 7.56e+00
  bond pdb=" N   ASP A 964 "
       pdb=" CA  ASP A 964 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.51e+00
  bond pdb=" CA  LEU A 362 "
       pdb=" C   LEU A 362 "
    ideal  model  delta    sigma   weight residual
    1.526  1.496  0.030 1.18e-02 7.18e+03 6.27e+00
  bond pdb=" N   SER A 602 "
       pdb=" CA  SER A 602 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.034 1.37e-02 5.33e+03 6.01e+00
  ... (remaining 8047 not shown)

  Histogram of bond angle deviations from ideal:
      100.15 -   106.96: 261
      106.96 -   113.78: 4442
      113.78 -   120.60: 3293
      120.60 -   127.42: 2801
      127.42 -   134.24: 86
  Bond angle restraints: 10883
  Sorted by residual:
  angle pdb=" N   ARG A 358 "
        pdb=" CA  ARG A 358 "
        pdb=" C   ARG A 358 "
      ideal   model   delta    sigma   weight residual
     111.07  100.65   10.42 1.07e+00 8.73e-01 9.48e+01
  angle pdb=" N   LEU A 251 "
        pdb=" CA  LEU A 251 "
        pdb=" C   LEU A 251 "
      ideal   model   delta    sigma   weight residual
     112.92  102.73   10.19 1.23e+00 6.61e-01 6.86e+01
  angle pdb=" N   ILE A 250 "
        pdb=" CA  ILE A 250 "
        pdb=" C   ILE A 250 "
      ideal   model   delta    sigma   weight residual
     106.21  113.52   -7.31 1.07e+00 8.73e-01 4.67e+01
  angle pdb=" CA  ILE A 250 "
        pdb=" C   ILE A 250 "
        pdb=" O   ILE A 250 "
      ideal   model   delta    sigma   weight residual
     122.63  118.63    4.00 8.70e-01 1.32e+00 2.12e+01
  angle pdb=" C   TYR A 249 "
        pdb=" N   ILE A 250 "
        pdb=" CA  ILE A 250 "
      ideal   model   delta    sigma   weight residual
     121.65  125.47   -3.82 9.40e-01 1.13e+00 1.65e+01
  ... (remaining 10878 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 4239
       17.80 -    35.60: 484
       35.60 -    53.40: 137
       53.40 -    71.20: 20
       71.20 -    89.00: 11
  Dihedral angle restraints: 4891
    sinusoidal: 1986
      harmonic: 2905
  Sorted by residual:
  dihedral pdb=" CB  CYS A 728 "
           pdb=" SG  CYS A 728 "
           pdb=" SG  CYS A 805 "
           pdb=" CB  CYS A 805 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.73   41.27     1      1.00e+01 1.00e-02 2.38e+01
  dihedral pdb=" CA  ALA A 851 "
           pdb=" C   ALA A 851 "
           pdb=" N   THR A 852 "
           pdb=" CA  THR A 852 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASN A 596 "
           pdb=" C   ASN A 596 "
           pdb=" N   LEU A 597 "
           pdb=" CA  LEU A 597 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.69   20.31     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 4888 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1065
       0.074 -    0.148: 119
       0.148 -    0.222: 3
       0.222 -    0.296: 3
       0.296 -    0.370: 3
  Chirality restraints: 1193
  Sorted by residual:
  chirality pdb=" CA  SER A 253 "
            pdb=" N   SER A 253 "
            pdb=" C   SER A 253 "
            pdb=" CB  SER A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.42e+00
  chirality pdb=" CA  LEU A 251 "
            pdb=" N   LEU A 251 "
            pdb=" C   LEU A 251 "
            pdb=" CB  LEU A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CA  MET A 357 "
            pdb=" N   MET A 357 "
            pdb=" C   MET A 357 "
            pdb=" CB  MET A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  ... (remaining 1190 not shown)

  Planarity restraints: 1405
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 249 "   -0.014 2.00e-02 2.50e+03   2.99e-02 8.93e+00
        pdb=" C   TYR A 249 "    0.052 2.00e-02 2.50e+03
        pdb=" O   TYR A 249 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ILE A 250 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 356 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.58e+00
        pdb=" C   ASN A 356 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ASN A 356 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A 357 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 973 "   -0.033 5.00e-02 4.00e+02   4.96e-02 3.93e+00
        pdb=" N   PRO A 974 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 974 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 974 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1402 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 115
        2.57 -     3.15: 6711
        3.15 -     3.73: 12535
        3.73 -     4.32: 16181
        4.32 -     4.90: 26669
  Nonbonded interactions: 62211
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 219 "
            pdb=" CG2 VAL A 220 "
     model   vdw
     1.982 3.460
  nonbonded pdb=" O   ARG A1085 "
            pdb=" NZ  LYS A1089 "
     model   vdw
     2.218 2.520
  nonbonded pdb=" NH2 ARG A 519 "
            pdb=" O   ILE A 565 "
     model   vdw
     2.221 2.520
  nonbonded pdb=" OD2 ASP A 590 "
            pdb=" OG1 THR A 592 "
     model   vdw
     2.234 2.440
  nonbonded pdb=" OG  SER A 754 "
            pdb=" OE2 GLU A 755 "
     model   vdw
     2.247 2.440
  ... (remaining 62206 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.080
  Process input model:                     25.850
  Find NCS groups from input model:        0.220
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
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      :  0.004   0.039   8052  Z= 0.266
  Angle     :  0.737  10.419  10883  Z= 0.456
  Chirality :  0.049   0.370   1193
  Planarity :  0.004   0.050   1405
  Dihedral  : 16.684  89.002   3014
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 18.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.92 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  7.85 %
    Allowed  : 20.52 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.60 (0.24), residues: 991
  helix: -0.59 (0.25), residues: 347
  sheet: -3.80 (0.38), residues: 101
  loop : -3.49 (0.23), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A1092 
   HIS   0.002   0.001   HIS A 445 
   PHE   0.011   0.001   PHE A 576 
   TYR   0.013   0.001   TYR A 998 
   ARG   0.003   0.000   ARG A 124 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 261
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 67
  outliers final: 45
  residues processed: 306
  average time/residue: 0.2440
  time to fit residues: 95.4688
Evaluate side-chains
  271 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 226
  time to evaluate  : 0.967 
Switching outliers to nearest non-outliers
  outliers start: 45
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1097
  time to fit residues: 9.1468
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 191 HIS
A 285 ASN
A 346 GLN
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 424 ASN
A 471 GLN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
A 739 GLN
A 747 ASN
A 889 HIS
A 909 HIS
A1024 ASN
A1078 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8052  Z= 0.210
  Angle     :  0.676  12.090  10883  Z= 0.343
  Chirality :  0.045   0.190   1193
  Planarity :  0.004   0.053   1405
  Dihedral  :  5.215  25.308   1101
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.30 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 28.84 %
    Favored  : 67.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -2.55 (0.26), residues: 991
  helix:  0.53 (0.27), residues: 355
  sheet: -3.24 (0.40), residues: 106
  loop : -3.09 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP A1076 
   HIS   0.010   0.001   HIS A 889 
   PHE   0.020   0.002   PHE A 435 
   TYR   0.023   0.002   TYR A 291 
   ARG   0.008   0.001   ARG A 358 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 240
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 18
  residues processed: 259
  average time/residue: 0.2247
  time to fit residues: 76.8021
Evaluate side-chains
  243 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 225
  time to evaluate  : 0.992 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0793
  time to fit residues: 3.9657
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0870
   chunk 74 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 90 optimal weight:    0.0050
   chunk 97 optimal weight:    0.0170
   chunk 80 optimal weight:    0.0010
   chunk 89 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 471 GLN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
A 617 ASN
A1082 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8052  Z= 0.170
  Angle     :  0.649  13.663  10883  Z= 0.323
  Chirality :  0.044   0.201   1193
  Planarity :  0.004   0.054   1405
  Dihedral  :  4.990  26.845   1101
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 28.84 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -2.09 (0.26), residues: 991
  helix:  0.98 (0.28), residues: 355
  sheet: -3.00 (0.43), residues: 100
  loop : -2.87 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.001   TRP A1076 
   HIS   0.003   0.001   HIS A 886 
   PHE   0.022   0.002   PHE A 870 
   TYR   0.019   0.002   TYR A 873 
   ARG   0.006   0.000   ARG A 358 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 246
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 37
  outliers final: 21
  residues processed: 269
  average time/residue: 0.2295
  time to fit residues: 80.6735
Evaluate side-chains
  247 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 226
  time to evaluate  : 0.882 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0757
  time to fit residues: 4.1148
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0970
   chunk 46 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 90 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 GLN
A 614 ASN
A 889 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8052  Z= 0.255
  Angle     :  0.710  11.826  10883  Z= 0.356
  Chirality :  0.046   0.190   1193
  Planarity :  0.005   0.053   1405
  Dihedral  :  5.261  26.480   1101
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 17.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.21 %
    Favored  : 87.79 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 31.18 %
    Favored  : 64.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -2.09 (0.26), residues: 991
  helix:  0.85 (0.27), residues: 359
  sheet: -2.96 (0.44), residues: 102
  loop : -2.80 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.030   0.002   TRP A1076 
   HIS   0.008   0.001   HIS A 889 
   PHE   0.024   0.002   PHE A 163 
   TYR   0.024   0.002   TYR A 873 
   ARG   0.006   0.001   ARG A 493 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 239
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 34
  outliers final: 21
  residues processed: 258
  average time/residue: 0.2182
  time to fit residues: 74.3782
Evaluate side-chains
  250 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 229
  time to evaluate  : 0.955 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0748
  time to fit residues: 4.1702
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 48 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8052  Z= 0.194
  Angle     :  0.689  12.624  10883  Z= 0.345
  Chirality :  0.045   0.189   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  5.131  25.438   1101
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 32.59 %
    Favored  : 64.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.95 (0.26), residues: 991
  helix:  0.97 (0.27), residues: 357
  sheet: -2.77 (0.44), residues: 109
  loop : -2.73 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.041   0.002   TRP A1076 
   HIS   0.004   0.001   HIS A 497 
   PHE   0.016   0.002   PHE A 870 
   TYR   0.032   0.002   TYR A 873 
   ARG   0.006   0.000   ARG A 144 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 241
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 27
  outliers final: 10
  residues processed: 255
  average time/residue: 0.2259
  time to fit residues: 75.7310
Evaluate side-chains
  234 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 224
  time to evaluate  : 0.915 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0787
  time to fit residues: 2.6487
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0050
   chunk 18 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0980
   chunk 50 optimal weight:    8.9990
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
A 471 GLN
A 596 ASN
A 889 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8052  Z= 0.197
  Angle     :  0.715  16.879  10883  Z= 0.351
  Chirality :  0.046   0.202   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  5.025  25.842   1101
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.49 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 33.41 %
    Favored  : 62.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.84 (0.26), residues: 991
  helix:  1.00 (0.27), residues: 359
  sheet: -2.67 (0.47), residues: 102
  loop : -2.65 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.027   0.001   TRP A1076 
   HIS   0.009   0.001   HIS A 889 
   PHE   0.032   0.002   PHE A 435 
   TYR   0.028   0.002   TYR A 873 
   ARG   0.006   0.000   ARG A 144 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 224
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 31
  outliers final: 20
  residues processed: 243
  average time/residue: 0.2201
  time to fit residues: 70.8766
Evaluate side-chains
  229 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 0.858 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0766
  time to fit residues: 4.0938
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 GLN
A 596 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8052  Z= 0.220
  Angle     :  0.747  15.775  10883  Z= 0.365
  Chirality :  0.047   0.199   1193
  Planarity :  0.005   0.053   1405
  Dihedral  :  5.152  26.866   1101
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.10 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 34.82 %
    Favored  : 62.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.84 (0.26), residues: 991
  helix:  0.99 (0.28), residues: 357
  sheet: -2.56 (0.47), residues: 104
  loop : -2.65 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP A1076 
   HIS   0.003   0.001   HIS A 173 
   PHE   0.030   0.002   PHE A 435 
   TYR   0.031   0.002   TYR A 873 
   ARG   0.007   0.001   ARG A 144 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 13
  residues processed: 232
  average time/residue: 0.2212
  time to fit residues: 68.5788
Evaluate side-chains
  221 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 208
  time to evaluate  : 1.788 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1093
  time to fit residues: 3.8473
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 GLN
A 614 ASN
A 686 GLN
A 706 ASN
A 889 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8052  Z= 0.266
  Angle     :  0.767  15.310  10883  Z= 0.385
  Chirality :  0.047   0.216   1193
  Planarity :  0.005   0.053   1405
  Dihedral  :  5.293  28.623   1101
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 19.85
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.60 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 35.64 %
    Favored  : 62.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.99 (0.26), residues: 991
  helix:  0.74 (0.27), residues: 358
  sheet: -2.54 (0.46), residues: 104
  loop : -2.66 (0.25), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.062   0.003   TRP A1076 
   HIS   0.009   0.001   HIS A 889 
   PHE   0.030   0.002   PHE A 435 
   TYR   0.018   0.002   TYR A 873 
   ARG   0.008   0.001   ARG A 144 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 223
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 8
  residues processed: 227
  average time/residue: 0.2126
  time to fit residues: 64.6690
Evaluate side-chains
  223 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 215
  time to evaluate  : 0.845 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0816
  time to fit residues: 2.5299
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0040
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 94 optimal weight:    0.0170
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6632

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 GLN
A 596 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8052  Z= 0.207
  Angle     :  0.782  14.195  10883  Z= 0.385
  Chirality :  0.046   0.226   1193
  Planarity :  0.005   0.053   1405
  Dihedral  :  5.133  27.531   1101
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 19.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 37.75 %
    Favored  : 61.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.87 (0.26), residues: 991
  helix:  0.78 (0.28), residues: 360
  sheet: -2.39 (0.47), residues: 104
  loop : -2.57 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.055   0.003   TRP A1076 
   HIS   0.005   0.001   HIS A 886 
   PHE   0.026   0.002   PHE A 870 
   TYR   0.023   0.002   TYR A 695 
   ARG   0.007   0.001   ARG A 144 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 219
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 224
  average time/residue: 0.2155
  time to fit residues: 64.6028
Evaluate side-chains
  214 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 210
  time to evaluate  : 0.947 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1563
  time to fit residues: 2.2036
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0570
   chunk 62 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0470
   overall best weight:    1.6200

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 GLN
A 497 HIS
A 596 ASN
A 686 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8052  Z= 0.257
  Angle     :  0.822  14.741  10883  Z= 0.407
  Chirality :  0.048   0.266   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  5.336  27.714   1101
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.11 %
    Favored  : 87.79 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 37.87 %
    Favored  : 60.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.98 (0.26), residues: 991
  helix:  0.66 (0.27), residues: 362
  sheet: -2.40 (0.47), residues: 103
  loop : -2.64 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.043   0.003   TRP A1076 
   HIS   0.025   0.001   HIS A 497 
   PHE   0.028   0.002   PHE A 435 
   TYR   0.041   0.002   TYR A 873 
   ARG   0.007   0.001   ARG A 144 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 214
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 5
  residues processed: 220
  average time/residue: 0.2147
  time to fit residues: 63.0341
Evaluate side-chains
  211 residues out of total 853 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 206
  time to evaluate  : 0.973 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1447
  time to fit residues: 2.3940
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 78 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.107251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096982 restraints weight = 18592.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 3.46
r_work: 0.3329 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   8052  Z= 0.274
  Angle     :  0.826  14.472  10883  Z= 0.409
  Chirality :  0.048   0.212   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  5.499  31.530   1101
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 21.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.31 %
    Favored  : 87.69 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 37.98 %
    Favored  : 60.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -2.02 (0.26), residues: 991
  helix:  0.60 (0.27), residues: 361
  sheet: -2.37 (0.47), residues: 104
  loop : -2.66 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.037   0.003   TRP A1092 
   HIS   0.005   0.001   HIS A1054 
   PHE   0.028   0.002   PHE A 435 
   TYR   0.020   0.002   TYR A 444 
   ARG   0.007   0.001   ARG A 144 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2269.10 seconds
wall clock time: 41 minutes 38.71 seconds (2498.71 seconds total)