Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 09:35:44 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/04_2023/6nus_0521.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/04_2023/6nus_0521.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/04_2023/6nus_0521.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/04_2023/6nus_0521.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/04_2023/6nus_0521.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nus_0521/04_2023/6nus_0521.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      54      5.16       5
     C    4235      2.51       5
     N    1115      2.21       5
     O    1226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  149": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  286": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  287": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  326": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  348": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  456": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  458": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  479": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  480": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  483": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  516": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  521": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  594": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  595": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  606": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  653": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  732": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  766": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  782": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  828": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  831": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  833": "OD1" <-> "OD2"
    Residue "A PHE  859": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  884": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  916": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  147": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 6632
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 715, 5767
          Classifications: {'peptide': 715}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 689}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 863
          Classifications: {'peptide': 112}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1481  SG  CYS A 301      37.503  61.634  35.610  1.00 36.78           S
  ATOM   1522  SG  CYS A 306      37.698  60.632  32.501  1.00 62.98           S
  ATOM   1554  SG  CYS A 310      41.314  60.514  34.574  1.00 33.81           S
  ATOM   2658  SG  CYS A 487      19.463  58.580  43.739  1.00 37.60           S
  ATOM   3783  SG  CYS A 645      18.191  58.310  40.576  1.00 36.07           S
  ATOM   3789  SG  CYS A 646      21.574  60.826  41.973  1.00 36.63           S

  Time building chain proxies: 3.97, per 1000 atoms: 0.60
  Number of scatterers: 6632
  At special positions: 0
  Unit cell: (86.25, 93.15, 97.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      54     16.00
     O    1226      8.00
     N    1115      7.00
     C    4235      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: 2.67
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 301 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 310 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 306 "
        pdb="ZN    ZN A1001 " - pdb=" ND1 HIS A 295 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 645 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 487 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 646 "
        pdb="ZN    ZN A1002 " - pdb=" ND1 HIS A 642 "
      Number of angles added : 6


  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      52.4% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 153 through 159
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 178 through 199
    Processing helix  chain 'A' and resid 234 through 242
    Processing helix  chain 'A' and resid 243 through 245
      No H-bonds generated for 'chain 'A' and resid 243 through 245'
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 3.763A  pdb=" N   SER A 255 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 287
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.517A  pdb=" N   ILE A 307 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE A 313 " --> pdb=" O   HIS A 309 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 321
      No H-bonds generated for 'chain 'A' and resid 319 through 321'
    Processing helix  chain 'A' and resid 367 through 376
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 416 through 425
    Processing helix  chain 'A' and resid 465 through 479
      removed outlier: 3.505A  pdb=" N   PHE A 471 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 493
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 512 through 517
    Processing helix  chain 'A' and resid 520 through 531
    Processing helix  chain 'A' and resid 561 through 581
      removed outlier: 5.213A  pdb=" N   THR A 567 " --> pdb=" O   CYS A 563 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   GLN A 570 " --> pdb=" O   MET A 566 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   LYS A 574 " --> pdb=" O   GLN A 570 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   LEU A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 607
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 640 through 642
      No H-bonds generated for 'chain 'A' and resid 640 through 642'
    Processing helix  chain 'A' and resid 647 through 663
    Processing helix  chain 'A' and resid 686 through 709
      removed outlier: 4.206A  pdb=" N   SER A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 715
      removed outlier: 3.804A  pdb=" N   ILE A 715 " --> pdb=" O   GLY A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 729
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 768 through 772
    Processing helix  chain 'A' and resid 778 through 790
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 833 through 840
    Processing helix  chain 'A' and resid 855 through 867
    Processing helix  chain 'A' and resid 868 through 872
    Processing helix  chain 'A' and resid 874 through 891
      removed outlier: 4.068A  pdb=" N   VAL A 880 " --> pdb=" O   GLU A 876 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE A 881 " --> pdb=" O   TYR A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 910 through 915
    Processing helix  chain 'A' and resid 916 through 918
      No H-bonds generated for 'chain 'A' and resid 916 through 918'
    Processing helix  chain 'B' and resid 81 through 99
    Processing helix  chain 'B' and resid 100 through 109
    Processing helix  chain 'B' and resid 120 through 125
    Processing helix  chain 'B' and resid 134 through 140
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'B' and resid 176 through 180
    Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224
      removed outlier: 6.589A  pdb=" N   ILE A 201 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ILE A 233 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   GLY A 203 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 355
      removed outlier: 6.533A  pdb=" N   VAL A 335 " --> pdb=" O   PRO A 339 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   VAL A 341 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ILE A 333 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   SER A 343 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ARG A 331 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 345 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390
      removed outlier: 6.281A  pdb=" N   LEU A 387 " --> pdb=" O   MET B 129 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   VAL B 131 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A 389 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE B 185 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL B 159 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR B 187 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390
      removed outlier: 6.281A  pdb=" N   LEU A 387 " --> pdb=" O   MET B 129 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   VAL B 131 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A 389 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE B 185 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL B 159 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR B 187 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL B 159 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 400
      removed outlier: 6.189A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   VAL A 675 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 753 through 758
    Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 821

    319 hydrogen bonds defined for protein.
    864 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: 2.09

  Time building geometry restraints manager: 2.85 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1232
        1.32 -     1.45: 1957
        1.45 -     1.58: 3498
        1.58 -     1.70: 15
        1.70 -     1.83: 81
  Bond restraints: 6783
  Sorted by residual:
  bond pdb=" CB  TYR A 884 "
       pdb=" CG  TYR A 884 "
    ideal  model  delta    sigma   weight residual
    1.512  1.424  0.088 2.20e-02 2.07e+03 1.60e+01
  bond pdb=" NE  ARG A 365 "
       pdb=" CZ  ARG A 365 "
    ideal  model  delta    sigma   weight residual
    1.326  1.370 -0.044 1.10e-02 8.26e+03 1.58e+01
  bond pdb=" CB  ILE B 107 "
       pdb=" CG1 ILE B 107 "
    ideal  model  delta    sigma   weight residual
    1.530  1.609 -0.079 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" CB  LEU B  91 "
       pdb=" CG  LEU B  91 "
    ideal  model  delta    sigma   weight residual
    1.530  1.606 -0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" NE1 TRP A 290 "
       pdb=" CE2 TRP A 290 "
    ideal  model  delta    sigma   weight residual
    1.370  1.329  0.041 1.10e-02 8.26e+03 1.38e+01
  ... (remaining 6778 not shown)

  Histogram of bond angle deviations from ideal:
       99.75 -   106.59: 236
      106.59 -   113.43: 3439
      113.43 -   120.27: 2865
      120.27 -   127.10: 2605
      127.10 -   133.94: 65
  Bond angle restraints: 9210
  Sorted by residual:
  angle pdb=" C   ASP A 377 "
        pdb=" N   PRO A 378 "
        pdb=" CA  PRO A 378 "
      ideal   model   delta    sigma   weight residual
     119.56  127.07   -7.51 1.02e+00 9.61e-01 5.42e+01
  angle pdb=" C   MET A 626 "
        pdb=" N   PRO A 627 "
        pdb=" CA  PRO A 627 "
      ideal   model   delta    sigma   weight residual
     119.78  127.04   -7.26 1.03e+00 9.43e-01 4.96e+01
  angle pdb=" C   ASN A 168 "
        pdb=" N   PRO A 169 "
        pdb=" CA  PRO A 169 "
      ideal   model   delta    sigma   weight residual
     119.82  126.63   -6.81 9.80e-01 1.04e+00 4.83e+01
  angle pdb=" CA  ASP A 194 "
        pdb=" CB  ASP A 194 "
        pdb=" CG  ASP A 194 "
      ideal   model   delta    sigma   weight residual
     112.60  119.47   -6.87 1.00e+00 1.00e+00 4.72e+01
  angle pdb=" N   ILE A 757 "
        pdb=" CA  ILE A 757 "
        pdb=" C   ILE A 757 "
      ideal   model   delta    sigma   weight residual
     108.11  117.41   -9.30 1.40e+00 5.10e-01 4.41e+01
  ... (remaining 9205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 3896
       17.22 -    34.44: 103
       34.44 -    51.66: 16
       51.66 -    68.88: 9
       68.88 -    86.11: 5
  Dihedral angle restraints: 4029
    sinusoidal: 1576
      harmonic: 2453
  Sorted by residual:
  dihedral pdb=" C   HIS A 295 "
           pdb=" N   HIS A 295 "
           pdb=" CA  HIS A 295 "
           pdb=" CB  HIS A 295 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.98   -8.62     0      2.50e+00 1.60e-01 1.19e+01
  dihedral pdb=" N   ILE B 120 "
           pdb=" C   ILE B 120 "
           pdb=" CA  ILE B 120 "
           pdb=" CB  ILE B 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  131.72   -8.32     0      2.50e+00 1.60e-01 1.11e+01
  dihedral pdb=" CA  PRO A 830 "
           pdb=" C   PRO A 830 "
           pdb=" N   TYR A 831 "
           pdb=" CA  TYR A 831 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.43   16.57     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 4026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 623
       0.070 -    0.140: 281
       0.140 -    0.210: 89
       0.210 -    0.279: 29
       0.279 -    0.349: 4
  Chirality restraints: 1026
  Sorted by residual:
  chirality pdb=" CA  TYR A 867 "
            pdb=" N   TYR A 867 "
            pdb=" C   TYR A 867 "
            pdb=" CB  TYR A 867 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" CA  PHE B  92 "
            pdb=" N   PHE B  92 "
            pdb=" C   PHE B  92 "
            pdb=" CB  PHE B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  MET A 242 "
            pdb=" N   MET A 242 "
            pdb=" C   MET A 242 "
            pdb=" CB  MET A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.38e+00
  ... (remaining 1023 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 619 "    0.072 2.00e-02 2.50e+03   3.93e-02 3.09e+01
        pdb=" CG  TYR A 619 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 619 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 619 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 619 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 619 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 619 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 619 "    0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 509 "   -0.046 2.00e-02 2.50e+03   2.25e-02 1.26e+01
        pdb=" CG  TRP A 509 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 509 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 509 "    0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 509 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 509 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 509 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 509 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 509 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 237 "    0.048 2.00e-02 2.50e+03   2.50e-02 1.25e+01
        pdb=" CG  TYR A 237 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 237 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 237 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 237 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 237 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 237 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 237 "    0.034 2.00e-02 2.50e+03
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1997
        2.82 -     3.34: 6272
        3.34 -     3.86: 11632
        3.86 -     4.38: 14206
        4.38 -     4.90: 22527
  Nonbonded interactions: 56634
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 175 "
            pdb=" OH  TYR A 787 "
     model   vdw
     2.301 2.440
  nonbonded pdb=" OG1 THR A 189 "
            pdb=" OH  TYR A 237 "
     model   vdw
     2.418 2.440
  nonbonded pdb=" NZ  LYS A 478 "
            pdb=" OD1 ASP A 743 "
     model   vdw
     2.458 2.520
  nonbonded pdb=" N   ASP A 258 "
            pdb=" OD1 ASP A 258 "
     model   vdw
     2.460 2.520
  nonbonded pdb=" N   ASP B 112 "
            pdb=" OD1 ASP B 112 "
     model   vdw
     2.464 2.520
  ... (remaining 56629 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          4.200
  Check model and map are aligned:         0.090
  Set scattering table:                    0.060
  Process input model:                     23.040
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
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      :  0.016   0.094   6783  Z= 1.029
  Angle     :  1.568   9.299   9210  Z= 1.081
  Chirality :  0.090   0.349   1026
  Planarity :  0.009   0.039   1176
  Dihedral  :  9.782  86.106   2445
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer Outliers :  0.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.28), residues: 811
  helix: -0.34 (0.24), residues: 354
  sheet:  0.55 (0.60), residues: 63
  loop :  0.94 (0.32), residues: 394

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 264
  average time/residue: 0.2095
  time to fit residues: 71.1209
Evaluate side-chains
  168 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.784 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1016
  time to fit residues: 1.2696
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 34 optimal weight:    0.1980
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 210 GLN
A 572 HIS
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN
A 752 HIS
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6783  Z= 0.220
  Angle     :  0.604   6.558   9210  Z= 0.329
  Chirality :  0.043   0.220   1026
  Planarity :  0.005   0.045   1176
  Dihedral  :  4.610  21.288    907
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer Outliers :  2.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.29), residues: 811
  helix:  0.79 (0.27), residues: 359
  sheet:  0.48 (0.60), residues: 72
  loop :  0.63 (0.33), residues: 380

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 172
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 11
  residues processed: 180
  average time/residue: 0.1899
  time to fit residues: 45.2058
Evaluate side-chains
  158 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.815 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0643
  time to fit residues: 2.4430
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 73 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 210 GLN
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6783  Z= 0.172
  Angle     :  0.532   6.078   9210  Z= 0.285
  Chirality :  0.041   0.150   1026
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.425  22.104    907
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer Outliers :  0.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.30), residues: 811
  helix:  0.99 (0.28), residues: 361
  sheet:  0.44 (0.58), residues: 68
  loop :  0.36 (0.33), residues: 382

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 161
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 162
  average time/residue: 0.1727
  time to fit residues: 38.2347
Evaluate side-chains
  143 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 141
  time to evaluate  : 0.784 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0676
  time to fit residues: 1.3970
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 613 HIS
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6783  Z= 0.217
  Angle     :  0.543   6.582   9210  Z= 0.293
  Chirality :  0.042   0.136   1026
  Planarity :  0.004   0.044   1176
  Dihedral  :  4.442  25.177    907
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer Outliers :  2.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.29), residues: 811
  helix:  0.78 (0.28), residues: 364
  sheet:  0.18 (0.56), residues: 69
  loop :  0.21 (0.33), residues: 378

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 12
  residues processed: 151
  average time/residue: 0.1589
  time to fit residues: 33.6908
Evaluate side-chains
  152 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.793 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0666
  time to fit residues: 2.5640
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.5077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6783  Z= 0.195
  Angle     :  0.524   6.609   9210  Z= 0.279
  Chirality :  0.041   0.122   1026
  Planarity :  0.004   0.044   1176
  Dihedral  :  4.382  24.296    907
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer Outliers :  1.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.30), residues: 811
  helix:  0.89 (0.28), residues: 365
  sheet:  0.13 (0.54), residues: 69
  loop :  0.17 (0.33), residues: 377

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 152
  average time/residue: 0.1590
  time to fit residues: 33.8199
Evaluate side-chains
  143 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.825 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0733
  time to fit residues: 1.8540
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0970
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.5365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6783  Z= 0.163
  Angle     :  0.538   9.173   9210  Z= 0.274
  Chirality :  0.042   0.330   1026
  Planarity :  0.004   0.044   1176
  Dihedral  :  4.285  25.731    907
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer Outliers :  1.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.30), residues: 811
  helix:  0.86 (0.28), residues: 367
  sheet:  0.28 (0.54), residues: 73
  loop :  0.25 (0.33), residues: 371

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 9
  residues processed: 144
  average time/residue: 0.1526
  time to fit residues: 31.3356
Evaluate side-chains
  144 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.845 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0627
  time to fit residues: 2.1402
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    0.0570
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0020
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.4306

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

Flipped N/Q/H residues before XYZ refinement:
A 416 ASN
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 ASN
A 815 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6783  Z= 0.149
  Angle     :  0.518  10.710   9210  Z= 0.265
  Chirality :  0.041   0.282   1026
  Planarity :  0.004   0.041   1176
  Dihedral  :  4.156  25.117    907
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer Outliers :  0.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.30), residues: 811
  helix:  0.82 (0.27), residues: 378
  sheet:  0.21 (0.55), residues: 69
  loop :  0.39 (0.34), residues: 364

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 152
  average time/residue: 0.1641
  time to fit residues: 35.1197
Evaluate side-chains
  147 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 0.804 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0990
  time to fit residues: 1.6428
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 53 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 381 HIS
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.5720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6783  Z= 0.187
  Angle     :  0.545   7.987   9210  Z= 0.279
  Chirality :  0.042   0.245   1026
  Planarity :  0.004   0.044   1176
  Dihedral  :  4.161  24.493    907
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer Outliers :  1.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.30), residues: 811
  helix:  0.77 (0.27), residues: 379
  sheet:  0.27 (0.56), residues: 69
  loop :  0.34 (0.34), residues: 363

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 8
  residues processed: 148
  average time/residue: 0.1554
  time to fit residues: 32.9321
Evaluate side-chains
  149 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 0.798 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0700
  time to fit residues: 2.1237
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0470
   chunk 48 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.5840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6783  Z= 0.178
  Angle     :  0.538   8.469   9210  Z= 0.276
  Chirality :  0.042   0.241   1026
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.164  24.123    907
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer Outliers :  1.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.30), residues: 811
  helix:  0.90 (0.28), residues: 377
  sheet:  0.32 (0.56), residues: 69
  loop :  0.29 (0.34), residues: 365

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 142
  average time/residue: 0.1496
  time to fit residues: 30.6167
Evaluate side-chains
  143 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.838 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0685
  time to fit residues: 1.6468
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0040
   chunk 75 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 6 optimal weight:    0.3980
   chunk 50 optimal weight:    0.0270
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.4050

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.5948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6783  Z= 0.152
  Angle     :  0.555   8.815   9210  Z= 0.281
  Chirality :  0.042   0.221   1026
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.162  23.185    907
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer Outliers :  0.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.30), residues: 811
  helix:  0.92 (0.28), residues: 377
  sheet:  0.19 (0.56), residues: 69
  loop :  0.37 (0.34), residues: 365

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 147
  time to evaluate  : 0.846 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 147
  average time/residue: 0.1588
  time to fit residues: 32.8396
Evaluate side-chains
  141 residues out of total 729 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 138
  time to evaluate  : 0.727 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0745
  time to fit residues: 1.4393
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0470
   chunk 66 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.7880

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.182717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.160427 restraints weight = 8728.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.164664 restraints weight = 4243.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.167179 restraints weight = 2525.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.6042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6783  Z= 0.186
  Angle     :  0.560   8.615   9210  Z= 0.286
  Chirality :  0.042   0.215   1026
  Planarity :  0.004   0.049   1176
  Dihedral  :  4.168  23.456    907
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer Outliers :  0.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.30), residues: 811
  helix:  0.88 (0.28), residues: 377
  sheet:  0.19 (0.56), residues: 69
  loop :  0.29 (0.34), residues: 365

===============================================================================
Job complete
usr+sys time: 1629.41 seconds
wall clock time: 30 minutes 16.13 seconds (1816.13 seconds total)