Starting phenix.real_space_refine
on Fri Dec  8 12:24:42 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/12_2023/8h8b_34541.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/12_2023/8h8b_34541.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/12_2023/8h8b_34541.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/12_2023/8h8b_34541.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/12_2023/8h8b_34541.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/12_2023/8h8b_34541.pdb"
  }
  resolution = 3.16
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    5251      2.51       5
     N    1439      2.21       5
     O    1641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  146": "OE1" <-> "OE2"
    Residue "A GLU  162": "OE1" <-> "OE2"
    Residue "A ASP  168": "OD1" <-> "OD2"
    Residue "A GLU  170": "OE1" <-> "OE2"
    Residue "A ARG  182": "NH1" <-> "NH2"
    Residue "A ARG  188": "NH1" <-> "NH2"
    Residue "A GLU  203": "OE1" <-> "OE2"
    Residue "A ASP  209": "OD1" <-> "OD2"
    Residue "A ASP  222": "OD1" <-> "OD2"
    Residue "A GLU  226": "OE1" <-> "OE2"
    Residue "A PHE  249": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  267": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  268": "OE1" <-> "OE2"
    Residue "A ASP  272": "OD1" <-> "OD2"
    Residue "A ARG  293": "NH1" <-> "NH2"
    Residue "A ARG  296": "NH1" <-> "NH2"
    Residue "A GLU  299": "OE1" <-> "OE2"
    Residue "A ARG  305": "NH1" <-> "NH2"
    Residue "A GLU  309": "OE1" <-> "OE2"
    Residue "A GLU  320": "OE1" <-> "OE2"
    Residue "A GLU  337": "OE1" <-> "OE2"
    Residue "A ASP  339": "OD1" <-> "OD2"
    Residue "A ARG  367": "NH1" <-> "NH2"
    Residue "A PHE  371": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  376": "OE1" <-> "OE2"
    Residue "A PHE  390": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  399": "NH1" <-> "NH2"
    Residue "A TYR  409": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  414": "OD1" <-> "OD2"
    Residue "A ASP  422": "OD1" <-> "OD2"
    Residue "A GLU  423": "OE1" <-> "OE2"
    Residue "A GLU  429": "OE1" <-> "OE2"
    Residue "A ARG  447": "NH1" <-> "NH2"
    Residue "A ASP  455": "OD1" <-> "OD2"
    Residue "A TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  463": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  499": "OD1" <-> "OD2"
    Residue "A GLU  501": "OE1" <-> "OE2"
    Residue "A GLU  523": "OE1" <-> "OE2"
    Residue "A ARG  535": "NH1" <-> "NH2"
    Residue "A GLU  536": "OE1" <-> "OE2"
    Residue "A ASP  539": "OD1" <-> "OD2"
    Residue "A ASP  559": "OD1" <-> "OD2"
    Residue "A ARG  564": "NH1" <-> "NH2"
    Residue "A ASP  604": "OD1" <-> "OD2"
    Residue "A GLU  611": "OE1" <-> "OE2"
    Residue "A GLU  641": "OE1" <-> "OE2"
    Residue "A ASP  647": "OD1" <-> "OD2"
    Residue "A ARG  666": "NH1" <-> "NH2"
    Residue "A TYR  676": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  710": "OD1" <-> "OD2"
    Residue "A GLU  736": "OE1" <-> "OE2"
    Residue "A ARG  746": "NH1" <-> "NH2"
    Residue "A ARG  770": "NH1" <-> "NH2"
    Residue "A GLU  776": "OE1" <-> "OE2"
    Residue "A GLU  780": "OE1" <-> "OE2"
    Residue "A ARG  787": "NH1" <-> "NH2"
    Residue "A ASP  794": "OD1" <-> "OD2"
    Residue "A ASP  815": "OD1" <-> "OD2"
    Residue "A TYR  825": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  840": "NH1" <-> "NH2"
    Residue "A ARG  859": "NH1" <-> "NH2"
    Residue "A ASP  907": "OD1" <-> "OD2"
    Residue "A ASP  916": "OD1" <-> "OD2"
    Residue "A ARG  931": "NH1" <-> "NH2"
    Residue "A ARG  943": "NH1" <-> "NH2"
    Residue "A ARG  952": "NH1" <-> "NH2"
    Residue "A PHE  954": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  973": "OE1" <-> "OE2"
    Residue "A ARG  980": "NH1" <-> "NH2"
    Residue "A GLU  991": "OE1" <-> "OE2"
    Residue "A GLU  997": "OE1" <-> "OE2"
    Residue "A ARG 1009": "NH1" <-> "NH2"
    Residue "A GLU 1033": "OE1" <-> "OE2"
    Residue "A ASP 1035": "OD1" <-> "OD2"
    Residue "A ARG 1042": "NH1" <-> "NH2"
    Residue "A ARG 1070": "NH1" <-> "NH2"
    Residue "A ARG 1074": "NH1" <-> "NH2"
    Residue "A ARG 1100": "NH1" <-> "NH2"
    Residue "A ASP 1105": "OD1" <-> "OD2"
    Residue "A GLU 1134": "OE1" <-> "OE2"
    Residue "A GLU 1163": "OE1" <-> "OE2"
  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: 8344
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1027, 8344
          Classifications: {'peptide': 1027}
          Link IDs: {'PTRANS': 24, 'TRANS': 1002}
  Time building chain proxies: 4.55, per 1000 atoms: 0.55
  Number of scatterers: 8344
  At special positions: 0
  Unit cell: (76.56, 89.61, 119.19, 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      13     16.00
     O    1641      8.00
     N    1439      7.00
     C    5251      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1884

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 17 sheets defined
      2.8% alpha, 31.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 380 through 384
      removed outlier: 3.590A  pdb=" N   SER A 383 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1107 through 1112
    Processing helix  chain 'A' and resid 1139 through 1144
    Processing helix  chain 'A' and resid 1154 through 1165
    Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 170
      removed outlier: 6.677A  pdb=" N   TRP A 177 " --> pdb=" O   ASP A 168 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207
      removed outlier: 4.363A  pdb=" N   SER A 216 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251
      removed outlier: 5.891A  pdb=" N   CYS A 247 " --> pdb=" O   THR A 258 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   THR A 258 " --> pdb=" O   CYS A 247 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   PHE A 249 " --> pdb=" O   ILE A 256 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   ILE A 256 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASN A 251 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291
      removed outlier: 3.503A  pdb=" N   ARG A 290 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302
      removed outlier: 7.072A  pdb=" N   VAL A 300 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ARG A 305 " --> pdb=" O   HIS A 302 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335
      removed outlier: 3.665A  pdb=" N   ILE A 334 " --> pdb=" O   GLY A 343 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY A 343 " --> pdb=" O   ILE A 334 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356
    Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 377
      removed outlier: 3.554A  pdb=" N   GLU A 376 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 402
      removed outlier: 5.513A  pdb=" N   LEU A 428 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   GLU A 449 " --> pdb=" O   TYR A 461 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ILE A 470 " --> pdb=" O   TYR A 482 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLN A 481 " --> pdb=" O   VAL A 494 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL A 491 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   LYS A 502 " --> pdb=" O   ASP A 514 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ASP A 514 " --> pdb=" O   LYS A 502 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 544 through 547
      removed outlier: 6.464A  pdb=" N   ARG A 544 " --> pdb=" O   HIS A 556 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   HIS A 556 " --> pdb=" O   ARG A 544 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TRP A 546 " --> pdb=" O   VAL A 554 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   VAL A 554 " --> pdb=" O   TYR A 565 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   ASN A 574 " --> pdb=" O   ILE A 586 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   THR A 595 " --> pdb=" O   TYR A 612 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   ALA A 621 " --> pdb=" O   TYR A 632 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   THR A 662 " --> pdb=" O   PHE A 674 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 696 through 697
      removed outlier: 6.916A  pdb=" N   LYS A 696 " --> pdb=" O   ILE A 704 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 717
      removed outlier: 4.579A  pdb=" N   GLN A 724 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE A 726 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 758 through 763
      removed outlier: 7.257A  pdb=" N   GLN A 758 " --> pdb=" O   ARG A 770 " (cutoff:3.500A)
      removed outlier: 5.203A  pdb=" N   ARG A 770 " --> pdb=" O   GLN A 758 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   GLN A 760 " --> pdb=" O   THR A 768 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER A 762 " --> pdb=" O   HIS A 766 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   HIS A 766 " --> pdb=" O   SER A 762 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 799 through 803
      removed outlier: 6.049A  pdb=" N   ASP A 803 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   LEU A 808 " --> pdb=" O   ASP A 803 " (cutoff:3.500A)
      removed outlier: 11.855A  pdb=" N   ARG A 807 " --> pdb=" O   TYR A 825 " (cutoff:3.500A)
      removed outlier: 9.374A  pdb=" N   TYR A 825 " --> pdb=" O   ARG A 807 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   SER A 809 " --> pdb=" O   PHE A 823 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   PHE A 823 " --> pdb=" O   SER A 809 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   SER A 832 " --> pdb=" O   LYS A 843 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLU A 853 " --> pdb=" O   LEU A 844 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   VAL A 852 " --> pdb=" O   TYR A 863 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   SER A 872 " --> pdb=" O   TYR A 884 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY A 880 " --> pdb=" O   ASP A 876 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 918 through 919
      removed outlier: 6.526A  pdb=" N   LYS A 918 " --> pdb=" O   GLU A 925 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   GLU A 925 " --> pdb=" O   TYR A 932 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   VAL A 961 " --> pdb=" O   TYR A 972 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   HIS A 971 " --> pdb=" O   LYS A 983 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   LYS A 983 " --> pdb=" O   HIS A 971 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   GLU A 973 " --> pdb=" O   THR A 981 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   THR A 981 " --> pdb=" O   PHE A 992 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLU A 991 " --> pdb=" O   GLU A1002 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   GLU A1002 " --> pdb=" O   GLU A 991 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU A 993 " --> pdb=" O   LEU A1000 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ARG A 998 " --> pdb=" O   GLU A 995 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG A1009 " --> pdb=" O   GLU A1002 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG A1042 " --> pdb=" O   GLU A1033 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   GLU A1041 " --> pdb=" O   ALA A1054 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ASP A1045 " --> pdb=" O   ILE A1050 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE A1050 " --> pdb=" O   ASP A1045 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL A1066 " --> pdb=" O   SER A1053 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   SER A1055 " --> pdb=" O   ILE A1064 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ILE A1064 " --> pdb=" O   SER A1055 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1013 through 1014
      removed outlier: 6.205A  pdb=" N   ILE A1019 " --> pdb=" O   GLN A1014 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1079 through 1081
      removed outlier: 3.597A  pdb=" N   ARG A1100 " --> pdb=" O   ASP A1095 " (cutoff:3.500A)

    219 hydrogen bonds defined for protein.
    582 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: 3.75

  Time building geometry restraints manager: 3.28 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: 2805
        1.34 -     1.46: 2083
        1.46 -     1.58: 3641
        1.58 -     1.69: 0
        1.69 -     1.81: 17
  Bond restraints: 8546
  Sorted by residual:
  bond pdb=" CA  GLU A 271 "
       pdb=" C   GLU A 271 "
    ideal  model  delta    sigma   weight residual
    1.519  1.529 -0.009 1.01e-02 9.80e+03 8.60e-01
  bond pdb=" CA  ILE A1019 "
       pdb=" CB  ILE A1019 "
    ideal  model  delta    sigma   weight residual
    1.537  1.525  0.012 1.29e-02 6.01e+03 8.25e-01
  bond pdb=" N   THR A 332 "
       pdb=" CA  THR A 332 "
    ideal  model  delta    sigma   weight residual
    1.460  1.472 -0.012 1.42e-02 4.96e+03 6.85e-01
  bond pdb=" N   TYR A 242 "
       pdb=" CA  TYR A 242 "
    ideal  model  delta    sigma   weight residual
    1.460  1.471 -0.011 1.39e-02 5.18e+03 6.13e-01
  bond pdb=" CA  VAL A 735 "
       pdb=" C   VAL A 735 "
    ideal  model  delta    sigma   weight residual
    1.524  1.531 -0.007 1.01e-02 9.80e+03 5.14e-01
  ... (remaining 8541 not shown)

  Histogram of bond angle deviations from ideal:
      100.79 -   107.43: 208
      107.43 -   114.07: 4533
      114.07 -   120.71: 3431
      120.71 -   127.34: 3310
      127.34 -   133.98: 88
  Bond angle restraints: 11570
  Sorted by residual:
  angle pdb=" N   CYS A 147 "
        pdb=" CA  CYS A 147 "
        pdb=" C   CYS A 147 "
      ideal   model   delta    sigma   weight residual
     108.24  112.24   -4.00 1.32e+00 5.74e-01 9.20e+00
  angle pdb=" C   HIS A 302 "
        pdb=" N   ASN A 303 "
        pdb=" CA  ASN A 303 "
      ideal   model   delta    sigma   weight residual
     121.54  127.26   -5.72 1.91e+00 2.74e-01 8.98e+00
  angle pdb=" N   SER A 216 "
        pdb=" CA  SER A 216 "
        pdb=" C   SER A 216 "
      ideal   model   delta    sigma   weight residual
     108.32  112.95   -4.63 1.64e+00 3.72e-01 7.98e+00
  angle pdb=" N   ASP A 397 "
        pdb=" CA  ASP A 397 "
        pdb=" C   ASP A 397 "
      ideal   model   delta    sigma   weight residual
     107.93  111.54   -3.61 1.65e+00 3.67e-01 4.80e+00
  angle pdb=" CA  VAL A 319 "
        pdb=" C   VAL A 319 "
        pdb=" N   GLU A 320 "
      ideal   model   delta    sigma   weight residual
     116.60  119.55   -2.95 1.45e+00 4.76e-01 4.14e+00
  ... (remaining 11565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4587
       17.86 -    35.71: 329
       35.71 -    53.57: 58
       53.57 -    71.43: 18
       71.43 -    89.29: 6
  Dihedral angle restraints: 4998
    sinusoidal: 2018
      harmonic: 2980
  Sorted by residual:
  dihedral pdb=" CA  LYS A 304 "
           pdb=" C   LYS A 304 "
           pdb=" N   ARG A 305 "
           pdb=" CA  ARG A 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.03  -19.97     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CB  GLU A 429 "
           pdb=" CG  GLU A 429 "
           pdb=" CD  GLU A 429 "
           pdb=" OE1 GLU A 429 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.29   89.29     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CA  ASN A 303 "
           pdb=" C   ASN A 303 "
           pdb=" N   LYS A 304 "
           pdb=" CA  LYS A 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.26   15.74     0      5.00e+00 4.00e-02 9.91e+00
  ... (remaining 4995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 705
       0.027 -    0.054: 322
       0.054 -    0.081: 61
       0.081 -    0.108: 68
       0.108 -    0.135: 30
  Chirality restraints: 1186
  Sorted by residual:
  chirality pdb=" CA  THR A 332 "
            pdb=" N   THR A 332 "
            pdb=" C   THR A 332 "
            pdb=" CB  THR A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  ILE A 726 "
            pdb=" N   ILE A 726 "
            pdb=" C   ILE A 726 "
            pdb=" CB  ILE A 726 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CA  ILE A 597 "
            pdb=" N   ILE A 597 "
            pdb=" C   ILE A 597 "
            pdb=" CB  ILE A 597 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  ... (remaining 1183 not shown)

  Planarity restraints: 1528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 251 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.14e+00
        pdb=" N   PRO A 252 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 252 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 252 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 453 "    0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO A 454 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 454 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 454 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A1014 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO A1015 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A1015 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A1015 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1525 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1165
        2.76 -     3.30: 7163
        3.30 -     3.83: 12974
        3.83 -     4.37: 15555
        4.37 -     4.90: 27797
  Nonbonded interactions: 64654
  Sorted by model distance:
  nonbonded pdb=" O   SER A 587 "
            pdb=" OG1 THR A 595 "
     model   vdw
     2.226 2.440
  nonbonded pdb=" OG1 THR A 742 "
            pdb=" O   GLY A 745 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   ILE A 871 "
            pdb=" OH  TYR A 886 "
     model   vdw
     2.265 2.440
  nonbonded pdb=" O   THR A 796 "
            pdb=" OG  SER A 814 "
     model   vdw
     2.287 2.440
  nonbonded pdb=" O   GLY A 938 "
            pdb=" OH  TYR A1116 "
     model   vdw
     2.317 2.440
  ... (remaining 64649 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:             1.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          4.220
  Check model and map are aligned:         0.130
  Set scattering table:                    0.090
  Process input model:                     26.660
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
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      :  0.001   0.016   8546  Z= 0.096
  Angle     :  0.457   8.138  11570  Z= 0.276
  Chirality :  0.040   0.135   1186
  Planarity :  0.002   0.037   1528
  Dihedral  : 12.997  89.286   3114
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  6.86 %
    Favored  : 92.46 %
  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: -2.99 (0.23), residues: 1025
  helix: -1.91 (1.51), residues: 12
  sheet: -0.79 (0.37), residues: 188
  loop : -2.52 (0.18), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.003   0.000   TRP A 438 
   HIS   0.004   0.000   HIS A 444 
   PHE   0.006   0.000   PHE A 267 
   TYR   0.009   0.001   TYR A 242 
   ARG   0.001   0.000   ARG A 979 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 160
  time to evaluate  : 0.861 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 166
  average time/residue: 0.2601
  time to fit residues: 56.5004
Evaluate side-chains
  89 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.942 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0788
  time to fit residues: 1.7727
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN
A 264 GLN
A 421 HIS
A 456 ASN
A 529 HIS
A 585 GLN
A 622 GLN
A 633 GLN
A 639 GLN
A 737 ASN
A 760 GLN
A 772 GLN
A 799 ASN
A 854 GLN
A 855 GLN
A 937 GLN
A 959 GLN
A1082 GLN
A1089 ASN
A1148 GLN
A1160 GLN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8546  Z= 0.326
  Angle     :  0.657  14.887  11570  Z= 0.343
  Chirality :  0.046   0.160   1186
  Planarity :  0.004   0.043   1528
  Dihedral  :  4.674  29.736   1156
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.32 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 12.04 %
    Favored  : 85.38 %
  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: -2.46 (0.24), residues: 1025
  helix: -1.08 (1.47), residues: 13
  sheet: -0.33 (0.34), residues: 237
  loop : -2.27 (0.20), residues: 775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP A 856 
   HIS   0.008   0.002   HIS A 556 
   PHE   0.027   0.002   PHE A1075 
   TYR   0.023   0.002   TYR A1094 
   ARG   0.004   0.001   ARG A 436 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.886 
Fit side-chains
  outliers start: 23
  outliers final: 14
  residues processed: 117
  average time/residue: 0.2025
  time to fit residues: 33.6839
Evaluate side-chains
  96 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 1.005 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0864
  time to fit residues: 3.4397
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   chunk 77 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0770
   chunk 100 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.9542

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 868 GLN
A 937 GLN
A1121 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8546  Z= 0.283
  Angle     :  0.628  15.324  11570  Z= 0.325
  Chirality :  0.046   0.162   1186
  Planarity :  0.004   0.041   1528
  Dihedral  :  4.858  30.095   1156
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.52 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.25 (0.24), residues: 1025
  helix: -0.82 (1.48), residues: 13
  sheet: -0.18 (0.35), residues: 235
  loop : -2.11 (0.20), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP A 177 
   HIS   0.005   0.001   HIS A 766 
   PHE   0.017   0.002   PHE A1075 
   TYR   0.017   0.002   TYR A1094 
   ARG   0.003   0.001   ARG A 770 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.934 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 98
  average time/residue: 0.1836
  time to fit residues: 26.3628
Evaluate side-chains
  85 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.938 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0819
  time to fit residues: 1.9259
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 98 optimal weight:    0.0470
   chunk 88 optimal weight:    0.7980
   chunk 26 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.9682

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8546  Z= 0.161
  Angle     :  0.556  14.422  11570  Z= 0.286
  Chirality :  0.044   0.156   1186
  Planarity :  0.003   0.043   1528
  Dihedral  :  4.504  28.840   1156
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.41 %
    Favored  : 83.01 %
  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: -2.08 (0.25), residues: 1025
  helix: -0.25 (1.58), residues: 13
  sheet:  0.17 (0.36), residues: 223
  loop : -2.06 (0.20), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 177 
   HIS   0.004   0.001   HIS A 198 
   PHE   0.010   0.001   PHE A1075 
   TYR   0.014   0.001   TYR A1094 
   ARG   0.002   0.000   ARG A 830 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.964 
Fit side-chains
  outliers start: 14
  outliers final: 4
  residues processed: 98
  average time/residue: 0.2053
  time to fit residues: 28.8462
Evaluate side-chains
  78 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.961 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0827
  time to fit residues: 1.8690
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8546  Z= 0.335
  Angle     :  0.663  16.001  11570  Z= 0.344
  Chirality :  0.047   0.167   1186
  Planarity :  0.004   0.047   1528
  Dihedral  :  5.153  30.441   1156
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.10 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.54 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.12 (0.25), residues: 1025
  helix: -0.54 (1.50), residues: 13
  sheet:  0.00 (0.35), residues: 234
  loop : -2.06 (0.20), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP A 513 
   HIS   0.006   0.001   HIS A 766 
   PHE   0.019   0.002   PHE A1075 
   TYR   0.018   0.002   TYR A1094 
   ARG   0.003   0.000   ARG A 952 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 1.091 
Fit side-chains
  outliers start: 17
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1944
  time to fit residues: 28.6307
Evaluate side-chains
  89 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 1.030 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0875
  time to fit residues: 2.9928
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 8 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8546  Z= 0.248
  Angle     :  0.620  15.070  11570  Z= 0.319
  Chirality :  0.045   0.164   1186
  Planarity :  0.004   0.045   1528
  Dihedral  :  4.967  30.042   1156
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 18.79 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.03 (0.25), residues: 1025
  helix: -0.37 (1.51), residues: 13
  sheet:  0.18 (0.36), residues: 229
  loop : -2.02 (0.20), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP A 513 
   HIS   0.005   0.001   HIS A 198 
   PHE   0.015   0.001   PHE A1075 
   TYR   0.016   0.001   TYR A1094 
   ARG   0.003   0.000   ARG A 952 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.926 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 91
  average time/residue: 0.1752
  time to fit residues: 23.7815
Evaluate side-chains
  79 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.880 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0964
  time to fit residues: 1.9167
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8546  Z= 0.215
  Angle     :  0.600  15.014  11570  Z= 0.309
  Chirality :  0.045   0.160   1186
  Planarity :  0.003   0.045   1528
  Dihedral  :  4.864  29.424   1156
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 19.80 %
    Favored  : 79.42 %
  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: -2.00 (0.25), residues: 1025
  helix: -0.17 (1.55), residues: 13
  sheet:  0.19 (0.36), residues: 223
  loop : -1.99 (0.20), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP A 513 
   HIS   0.004   0.001   HIS A 198 
   PHE   0.013   0.001   PHE A1075 
   TYR   0.016   0.001   TYR A1094 
   ARG   0.002   0.000   ARG A 952 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.962 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1942
  time to fit residues: 26.3324
Evaluate side-chains
  83 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.974 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0881
  time to fit residues: 1.9975
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0670
   chunk 89 optimal weight:    0.4980
   chunk 94 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.4722

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8546  Z= 0.223
  Angle     :  0.607  14.930  11570  Z= 0.313
  Chirality :  0.045   0.159   1186
  Planarity :  0.003   0.045   1528
  Dihedral  :  4.882  29.363   1156
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 19.91 %
    Favored  : 79.64 %
  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: -1.97 (0.25), residues: 1025
  helix: -0.02 (1.56), residues: 13
  sheet:  0.22 (0.36), residues: 229
  loop : -1.98 (0.20), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP A 513 
   HIS   0.005   0.001   HIS A 198 
   PHE   0.014   0.001   PHE A1075 
   TYR   0.016   0.001   TYR A1094 
   ARG   0.002   0.000   ARG A 952 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.958 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 86
  average time/residue: 0.1900
  time to fit residues: 23.9838
Evaluate side-chains
  83 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.961 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0812
  time to fit residues: 1.7756
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 82 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 96 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0040
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 HIS
A 479 GLN
A 481 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8546  Z= 0.126
  Angle     :  0.547  13.344  11570  Z= 0.281
  Chirality :  0.043   0.157   1186
  Planarity :  0.003   0.042   1528
  Dihedral  :  4.393  27.766   1156
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 20.36 %
    Favored  : 79.08 %
  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: -1.83 (0.25), residues: 1025
  helix:  0.39 (1.64), residues: 13
  sheet:  0.34 (0.37), residues: 223
  loop : -1.88 (0.21), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 438 
   HIS   0.004   0.001   HIS A 444 
   PHE   0.009   0.001   PHE A 229 
   TYR   0.012   0.001   TYR A1094 
   ARG   0.002   0.000   ARG A 931 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.948 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 96
  average time/residue: 0.1975
  time to fit residues: 27.5112
Evaluate side-chains
  81 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.949 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0868
  time to fit residues: 1.5229
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0470
   overall best weight:    1.3282

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 HIS
A 479 GLN
A 481 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8546  Z= 0.209
  Angle     :  0.594  14.788  11570  Z= 0.306
  Chirality :  0.044   0.155   1186
  Planarity :  0.003   0.041   1528
  Dihedral  :  4.668  27.837   1156
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.02 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 20.58 %
    Favored  : 79.08 %
  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: -1.83 (0.25), residues: 1025
  helix:  0.20 (1.60), residues: 13
  sheet:  0.35 (0.37), residues: 223
  loop : -1.89 (0.21), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 513 
   HIS   0.004   0.001   HIS A 198 
   PHE   0.013   0.001   PHE A1075 
   TYR   0.015   0.001   TYR A1094 
   ARG   0.002   0.000   ARG A 952 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.961 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 87
  average time/residue: 0.1911
  time to fit residues: 24.5009
Evaluate side-chains
  82 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.969 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0862
  time to fit residues: 1.7341
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 10 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 HIS
A 479 GLN
A 481 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.151408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.131857 restraints weight = 10853.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.22
r_work: 0.3497 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8546  Z= 0.149
  Angle     :  0.565  13.954  11570  Z= 0.291
  Chirality :  0.043   0.155   1186
  Planarity :  0.003   0.042   1528
  Dihedral  :  4.485  27.651   1156
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 20.81 %
    Favored  : 78.85 %
  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: -1.76 (0.25), residues: 1025
  helix:  0.41 (1.64), residues: 13
  sheet:  0.44 (0.37), residues: 223
  loop : -1.85 (0.21), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP A 513 
   HIS   0.004   0.001   HIS A 198 
   PHE   0.009   0.001   PHE A 229 
   TYR   0.013   0.001   TYR A 591 
   ARG   0.002   0.000   ARG A 840 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1969.62 seconds
wall clock time: 36 minutes 11.68 seconds (2171.68 seconds total)