Starting phenix.real_space_refine
on Fri Aug 22 19:27:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qyc_18750/08_2025/8qyc_18750.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qyc_18750/08_2025/8qyc_18750.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qyc_18750/08_2025/8qyc_18750.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qyc_18750/08_2025/8qyc_18750.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qyc_18750/08_2025/8qyc_18750.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qyc_18750/08_2025/8qyc_18750.map"
  }
  resolution = 2.75
  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
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=   0.110
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
     P       3      5.49       5
     S      16      5.16       5
     C    4592      2.51       5
     N    1246      2.21       5
     O    1341      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7198
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 893, 7167
          Classifications: {'peptide': 893}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 50, 'TRANS': 842}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.35, per 1000 atoms: 0.33
  Number of scatterers: 7198
  At special positions: 0
  Unit cell: (83.2, 119.808, 94.848, 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)
     S      16     16.00
     P       3     15.00
     O    1341      8.00
     N    1246      7.00
     C    4592      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  - 3.00
        Amino acid           : True  - 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: 0.59
  Conformation dependent library (CDL) restraints added in 484.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 9 sheets defined
      49.9% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 40
    Processing helix  chain 'A' and resid 43 through 56
    Processing helix  chain 'A' and resid 70 through 79
    Processing helix  chain 'A' and resid 85 through 89
    Processing helix  chain 'A' and resid 147 through 165
      removed outlier: 3.579A  pdb=" N   ILE A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 188
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 233 through 241
      removed outlier: 3.623A  pdb=" N   SER A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 275
      removed outlier: 3.768A  pdb=" N   VAL A 269 " --> pdb=" O   GLU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 278
      No H-bonds generated for 'chain 'A' and resid 276 through 278'
    Processing helix  chain 'A' and resid 283 through 292
    Processing helix  chain 'A' and resid 292 through 298
      removed outlier: 4.234A  pdb=" N   PHE A 296 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 305
      removed outlier: 4.192A  pdb=" N   SER A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 317
    Processing helix  chain 'A' and resid 360 through 377
      removed outlier: 3.813A  pdb=" N   LEU A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 414
    Processing helix  chain 'A' and resid 581 through 596
    Processing helix  chain 'A' and resid 614 through 630
    Processing helix  chain 'A' and resid 641 through 656
      removed outlier: 3.774A  pdb=" N   ASN A 647 " --> pdb=" O   SER A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 675
    Processing helix  chain 'A' and resid 682 through 687
    Processing helix  chain 'A' and resid 708 through 715
    Processing helix  chain 'A' and resid 715 through 720
    Processing helix  chain 'A' and resid 732 through 736
    Processing helix  chain 'A' and resid 740 through 749
    Processing helix  chain 'A' and resid 765 through 777
      removed outlier: 4.250A  pdb=" N   LEU A 769 " --> pdb=" O   THR A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 792
    Processing helix  chain 'A' and resid 804 through 813
    Processing helix  chain 'A' and resid 836 through 840
    Processing helix  chain 'A' and resid 844 through 864
    Processing helix  chain 'A' and resid 875 through 888
    Processing helix  chain 'A' and resid 888 through 893
      removed outlier: 3.921A  pdb=" N   VAL A 892 " --> pdb=" O   HIS A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 900
    Processing helix  chain 'A' and resid 902 through 919
    Processing helix  chain 'A' and resid 929 through 945
    Processing helix  chain 'A' and resid 958 through 975
      removed outlier: 4.861A  pdb=" N   SER A 964 " --> pdb=" O   GLN A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1017
    Processing helix  chain 'A' and resid 1042 through 1059
    Processing helix  chain 'A' and resid 1069 through 1074
    Processing helix  chain 'A' and resid 1075 through 1079
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 3.716A  pdb=" N   ARG A  65 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104
      removed outlier: 6.195A  pdb=" N   SER A 102 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   ILE A 116 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ARG A 104 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   VAL A 114 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   TRP A 119 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 138
    Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 201
    Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 213
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.076A  pdb=" N   GLU A 338 " --> pdb=" O   GLN A 329 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 663 through 665
      removed outlier: 6.440A  pdb=" N   LEU A 664 " --> pdb=" O   LEU A 706 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   SER A 725 " --> pdb=" O   ALA A 751 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   CYS A 605 " --> pdb=" O   ALA A 756 " (cutoff:3.500A)
      removed outlier: 9.053A  pdb=" N   LEU A 818 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   LEU A 606 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 834
      removed outlier: 6.900A  pdb=" N   ASN A 998 " --> pdb=" O   TYR A1029 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   TYR A1031 " --> pdb=" O   ASN A 998 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL A1000 " --> pdb=" O   TYR A1031 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS A 922 " --> pdb=" O   ALA A 997 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   VAL A 949 " --> pdb=" O   ILE A 982 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 841 through 842
      removed outlier: 5.937A  pdb=" N   LEU A 841 " --> pdb=" O   ARG A1036 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    355 hydrogen bonds defined for protein.
    1008 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: 0.96

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.23 -     1.37: 2485
        1.37 -     1.52: 2245
        1.52 -     1.66: 2616
        1.66 -     1.80: 13
        1.80 -     1.95: 8
  Bond restraints: 7367
  Sorted by residual:
  bond pdb=" C4' AGS A1101 "
       pdb=" O4' AGS A1101 "
    ideal  model  delta    sigma   weight residual
    1.444  1.435  0.009 1.20e-02 6.94e+03 6.09e-01
  bond pdb=" C   SER A 598 "
       pdb=" N   PRO A 599 "
    ideal  model  delta    sigma   weight residual
    1.336  1.345 -0.009 1.20e-02 6.94e+03 5.06e-01
  bond pdb=" C2' AGS A1101 "
       pdb=" C3' AGS A1101 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.30e-02 5.92e+03 4.62e-01
  bond pdb=" CA  VAL A 994 "
       pdb=" CB  VAL A 994 "
    ideal  model  delta    sigma   weight residual
    1.532  1.539 -0.007 1.08e-02 8.57e+03 4.29e-01
  bond pdb=" CA  ILE A 982 "
       pdb=" CB  ILE A 982 "
    ideal  model  delta    sigma   weight residual
    1.540  1.531  0.009 1.36e-02 5.41e+03 4.04e-01
  ... (remaining 7362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 9778
        1.13 -     2.26: 179
        2.26 -     3.39: 53
        3.39 -     4.52: 12
        4.52 -     5.65: 2
  Bond angle restraints: 10024
  Sorted by residual:
  angle pdb=" N   SER A 598 "
        pdb=" CA  SER A 598 "
        pdb=" C   SER A 598 "
      ideal   model   delta    sigma   weight residual
     109.81  114.31   -4.50 2.21e+00 2.05e-01 4.15e+00
  angle pdb=" CA  TRP A 177 "
        pdb=" CB  TRP A 177 "
        pdb=" CG  TRP A 177 "
      ideal   model   delta    sigma   weight residual
     113.60  109.75    3.85 1.90e+00 2.77e-01 4.11e+00
  angle pdb=" C1' AGS A1101 "
        pdb=" C2' AGS A1101 "
        pdb=" C3' AGS A1101 "
      ideal   model   delta    sigma   weight residual
     101.46  103.84   -2.38 1.19e+00 7.12e-01 4.05e+00
  angle pdb=" N   ASP A 828 "
        pdb=" CA  ASP A 828 "
        pdb=" C   ASP A 828 "
      ideal   model   delta    sigma   weight residual
     111.81  109.00    2.81 1.44e+00 4.82e-01 3.81e+00
  angle pdb=" C   LEU A 809 "
        pdb=" N   ARG A 810 "
        pdb=" CA  ARG A 810 "
      ideal   model   delta    sigma   weight residual
     120.31  123.18   -2.87 1.52e+00 4.33e-01 3.57e+00
  ... (remaining 10019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 4214
       17.43 -    34.86: 181
       34.86 -    52.29: 38
       52.29 -    69.72: 9
       69.72 -    87.15: 6
  Dihedral angle restraints: 4448
    sinusoidal: 1836
      harmonic: 2612
  Sorted by residual:
  dihedral pdb=" CA  PHE A 130 "
           pdb=" C   PHE A 130 "
           pdb=" N   SER A 131 "
           pdb=" CA  SER A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.90   17.10     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASP A1017 "
           pdb=" C   ASP A1017 "
           pdb=" N   ARG A1018 "
           pdb=" CA  ARG A1018 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" N   LEU A 620 "
           pdb=" CA  LEU A 620 "
           pdb=" CB  LEU A 620 "
           pdb=" CG  LEU A 620 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.63   59.63     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 4445 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 757
       0.031 -    0.063: 250
       0.063 -    0.094: 49
       0.094 -    0.125: 63
       0.125 -    0.157: 4
  Chirality restraints: 1123
  Sorted by residual:
  chirality pdb=" CA  ILE A 681 "
            pdb=" N   ILE A 681 "
            pdb=" C   ILE A 681 "
            pdb=" CB  ILE A 681 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.14e-01
  chirality pdb=" CA  VAL A  91 "
            pdb=" N   VAL A  91 "
            pdb=" C   VAL A  91 "
            pdb=" CB  VAL A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  ILE A 570 "
            pdb=" N   ILE A 570 "
            pdb=" C   ILE A 570 "
            pdb=" CB  ILE A 570 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1120 not shown)

  Planarity restraints: 1294
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 598 "    0.032 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO A 599 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 599 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 599 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 893 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO A 894 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 894 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 894 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 681 "   -0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO A 682 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 682 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 682 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1291 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 182
        2.71 -     3.26: 6996
        3.26 -     3.80: 11977
        3.80 -     4.35: 15869
        4.35 -     4.90: 26231
  Nonbonded interactions: 61255
  Sorted by model distance:
  nonbonded pdb=" O1A AGS A1101 "
            pdb=" O2B AGS A1101 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   HIS A 583 "
            pdb=" NH1 ARG A 820 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" OD1 ASP A 646 "
            pdb=" NZ  LYS A 665 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" NZ  LYS A 904 "
            pdb=" OE2 GLU A1044 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   VAL A 244 "
            pdb=" NZ  LYS A 267 "
     model   vdw
     2.304 3.120
  ... (remaining 61250 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.760
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:6.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
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      :  0.002   0.019   7367  Z= 0.108
  Angle     :  0.443   5.653  10024  Z= 0.237
  Chirality :  0.040   0.157   1123
  Planarity :  0.004   0.048   1294
  Dihedral  : 11.072  87.151   2742
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  3.21 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.29), residues: 885
  helix:  1.70 (0.27), residues: 381
  sheet:  0.54 (0.45), residues: 123
  loop : -0.01 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 897 
 TYR   0.010   0.001   TYR A 676 
 PHE   0.010   0.001   PHE A 622 
 TRP   0.015   0.001   TRP A 177 
 HIS   0.002   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 7367)
  covalent geometry    : angle       0.44257 (10024)
  hydrogen bonds       : bond        0.16904 (  355)
  hydrogen bonds       : angle       6.74150 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7004 (m-30) cc_final: 0.6792 (m-30)
REVERT: A  118 GLU cc_start: 0.7227 (pt0) cc_final: 0.6939 (pt0)
REVERT: A  222 GLU cc_start: 0.7079 (pp20) cc_final: 0.6875 (tm-30)
REVERT: A  268 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6400 (pt0)
REVERT: A  369 GLN cc_start: 0.7867 (mm110) cc_final: 0.7507 (mm110)
REVERT: A  790 GLN cc_start: 0.7181 (tt0) cc_final: 0.6896 (tt0)
REVERT: A  942 GLN cc_start: 0.7773 (mt0) cc_final: 0.7570 (mt0)
REVERT: A  970 ASP cc_start: 0.7183 (m-30) cc_final: 0.6753 (m-30)
REVERT: A  993 ASN cc_start: 0.8058 (p0) cc_final: 0.7856 (p0)
REVERT: A  996 LYS cc_start: 0.7483 (mmtp) cc_final: 0.6852 (mptt)
REVERT: A 1014 GLN cc_start: 0.7931 (mm110) cc_final: 0.7519 (tp40)
REVERT: A 1018 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.7719 (mmp-170)
  outliers start: 10
  outliers final: 1
  residues processed: 149
  average time/residue: 0.6860
  time to fit residues: 107.0800
Evaluate side-chains
  110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0570
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7102

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
A 259 HIS
A 312 GLN
A 995 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1052 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.166906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.136478 restraints weight = 7609.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 1.73
r_work: 0.3449 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7367  Z= 0.156
  Angle     :  0.525   6.709  10024  Z= 0.274
  Chirality :  0.043   0.217   1123
  Planarity :  0.005   0.049   1294
  Dihedral  :  5.729  71.704    976
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.90 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.29), residues: 885
  helix:  1.61 (0.27), residues: 385
  sheet:  0.61 (0.45), residues: 121
  loop : -0.03 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 820 
 TYR   0.013   0.002   TYR A 667 
 PHE   0.011   0.002   PHE A 773 
 TRP   0.014   0.001   TRP A 177 
 HIS   0.004   0.001   HIS A 999 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7367)
  covalent geometry    : angle       0.52468 (10024)
  hydrogen bonds       : bond        0.04511 (  355)
  hydrogen bonds       : angle       5.19518 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.6887 (tm-30)
REVERT: A  104 ARG cc_start: 0.7643 (ptt90) cc_final: 0.7351 (ptt90)
REVERT: A  181 ARG cc_start: 0.7427 (ttt90) cc_final: 0.7119 (ttt-90)
REVERT: A  222 GLU cc_start: 0.6977 (pp20) cc_final: 0.6737 (tm-30)
REVERT: A  280 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7875 (mtm110)
REVERT: A  369 GLN cc_start: 0.7975 (mm110) cc_final: 0.7646 (mm110)
REVERT: A  611 MET cc_start: 0.7987 (tpp) cc_final: 0.7711 (mmp)
REVERT: A  827 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7668 (pmm-80)
REVERT: A  970 ASP cc_start: 0.7398 (m-30) cc_final: 0.6937 (m-30)
REVERT: A  996 LYS cc_start: 0.7718 (mmtp) cc_final: 0.7144 (mptt)
  outliers start: 16
  outliers final: 6
  residues processed: 133
  average time/residue: 0.5757
  time to fit residues: 80.4879
Evaluate side-chains
  116 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  804 GLU
Chi-restraints excluded: chain A residue 1075 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    0.0770
   chunk 57 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   chunk 62 optimal weight:    0.1980
   chunk 49 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
A 995 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1052 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.162869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.130234 restraints weight = 7708.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.04
r_work: 0.3387 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7367  Z= 0.117
  Angle     :  0.485   5.488  10024  Z= 0.253
  Chirality :  0.042   0.219   1123
  Planarity :  0.004   0.044   1294
  Dihedral  :  5.786  72.952    976
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.18 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.29), residues: 885
  helix:  1.79 (0.27), residues: 386
  sheet: -0.08 (0.43), residues: 133
  loop :  0.15 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1059 
 TYR   0.017   0.002   TYR A 667 
 PHE   0.017   0.001   PHE A 898 
 TRP   0.016   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7367)
  covalent geometry    : angle       0.48521 (10024)
  hydrogen bonds       : bond        0.03845 (  355)
  hydrogen bonds       : angle       4.83183 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   65 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6595 (ttp-170)
REVERT: A   80 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6605 (tm-30)
REVERT: A  104 ARG cc_start: 0.7462 (ptt90) cc_final: 0.7177 (ptt90)
REVERT: A  223 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8122 (mp)
REVERT: A  280 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7494 (mtm110)
REVERT: A  369 GLN cc_start: 0.7668 (mm110) cc_final: 0.7243 (mm110)
REVERT: A  710 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7562 (mt-10)
REVERT: A  790 GLN cc_start: 0.7017 (tt0) cc_final: 0.6510 (mm-40)
REVERT: A  805 ARG cc_start: 0.6599 (mmp-170) cc_final: 0.6016 (mmp-170)
REVERT: A  827 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.7387 (pmm-80)
REVERT: A  970 ASP cc_start: 0.6872 (m-30) cc_final: 0.6350 (m-30)
REVERT: A  996 LYS cc_start: 0.7425 (mmtp) cc_final: 0.6764 (mptt)
  outliers start: 24
  outliers final: 5
  residues processed: 119
  average time/residue: 0.5875
  time to fit residues: 73.5837
Evaluate side-chains
  112 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ARG
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  710 GLU
Chi-restraints excluded: chain A residue  804 GLU
Chi-restraints excluded: chain A residue  837 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 166 GLN
A 995 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1052 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.160551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127696 restraints weight = 7865.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.07
r_work: 0.3356 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7367  Z= 0.159
  Angle     :  0.520   6.760  10024  Z= 0.268
  Chirality :  0.043   0.234   1123
  Planarity :  0.004   0.049   1294
  Dihedral  :  5.892  71.616    976
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 12.08 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.29), residues: 885
  helix:  1.72 (0.26), residues: 386
  sheet:  0.07 (0.42), residues: 123
  loop : -0.06 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 181 
 TYR   0.014   0.002   TYR A 294 
 PHE   0.019   0.002   PHE A 898 
 TRP   0.013   0.002   TRP A 177 
 HIS   0.004   0.001   HIS A 999 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7367)
  covalent geometry    : angle       0.51988 (10024)
  hydrogen bonds       : bond        0.03991 (  355)
  hydrogen bonds       : angle       4.78631 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6641 (tm-30)
REVERT: A  104 ARG cc_start: 0.7454 (ptt90) cc_final: 0.7160 (ptt90)
REVERT: A  280 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7585 (mtm110)
REVERT: A  369 GLN cc_start: 0.7681 (mm110) cc_final: 0.7239 (mm110)
REVERT: A  611 MET cc_start: 0.7864 (tpp) cc_final: 0.7552 (mmp)
REVERT: A  710 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7574 (mt-10)
REVERT: A  790 GLN cc_start: 0.7070 (tt0) cc_final: 0.6632 (mm-40)
REVERT: A  805 ARG cc_start: 0.6684 (mmp-170) cc_final: 0.6118 (mmp-170)
REVERT: A  827 ARG cc_start: 0.7898 (ptp-170) cc_final: 0.7430 (pmm-80)
REVERT: A  970 ASP cc_start: 0.6903 (m-30) cc_final: 0.6372 (m-30)
REVERT: A  996 LYS cc_start: 0.7517 (mmtp) cc_final: 0.6933 (mptt)
REVERT: A 1048 ASP cc_start: 0.7426 (t70) cc_final: 0.7177 (t70)
  outliers start: 24
  outliers final: 8
  residues processed: 119
  average time/residue: 0.5643
  time to fit residues: 70.7117
Evaluate side-chains
  111 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  710 GLU
Chi-restraints excluded: chain A residue  837 SER
Chi-restraints excluded: chain A residue 1075 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 71 optimal weight:    0.4980
   chunk 80 optimal weight:    0.0070
   chunk 33 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 166 GLN
A 995 GLN
** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1052 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.160163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.127348 restraints weight = 7814.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.06
r_work: 0.3350 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7367  Z= 0.158
  Angle     :  0.517   6.560  10024  Z= 0.267
  Chirality :  0.043   0.248   1123
  Planarity :  0.004   0.045   1294
  Dihedral  :  6.008  72.606    976
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 12.85 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.29), residues: 885
  helix:  1.73 (0.27), residues: 385
  sheet:  0.07 (0.42), residues: 125
  loop : -0.06 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 181 
 TYR   0.014   0.002   TYR A 294 
 PHE   0.020   0.002   PHE A 898 
 TRP   0.017   0.002   TRP A 177 
 HIS   0.004   0.001   HIS A 999 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7367)
  covalent geometry    : angle       0.51702 (10024)
  hydrogen bonds       : bond        0.03937 (  355)
  hydrogen bonds       : angle       4.74375 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6608 (tm-30)
REVERT: A  104 ARG cc_start: 0.7435 (ptt90) cc_final: 0.7119 (ptt90)
REVERT: A  223 ILE cc_start: 0.8290 (mt) cc_final: 0.8074 (mp)
REVERT: A  280 ARG cc_start: 0.7750 (mtm180) cc_final: 0.7522 (mtm110)
REVERT: A  369 GLN cc_start: 0.7643 (mm110) cc_final: 0.7188 (mm110)
REVERT: A  710 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7507 (mt-10)
REVERT: A  790 GLN cc_start: 0.7022 (tt0) cc_final: 0.6568 (mm-40)
REVERT: A  805 ARG cc_start: 0.6671 (mmp-170) cc_final: 0.6064 (mmp-170)
REVERT: A  827 ARG cc_start: 0.7889 (ptp-170) cc_final: 0.7496 (pmm-80)
REVERT: A  970 ASP cc_start: 0.6887 (m-30) cc_final: 0.6318 (m-30)
REVERT: A  996 LYS cc_start: 0.7500 (mmtp) cc_final: 0.6641 (mptt)
REVERT: A 1048 ASP cc_start: 0.7406 (t70) cc_final: 0.7105 (t70)
  outliers start: 26
  outliers final: 14
  residues processed: 118
  average time/residue: 0.5560
  time to fit residues: 68.8529
Evaluate side-chains
  120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  670 THR
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  710 GLU
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  804 GLU
Chi-restraints excluded: chain A residue  837 SER
Chi-restraints excluded: chain A residue  998 ASN
Chi-restraints excluded: chain A residue 1075 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 51 optimal weight:    0.1980
   chunk 33 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 60 optimal weight:    0.3980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 166 GLN
A 995 GLN
** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1052 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.160992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.128559 restraints weight = 7819.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.04
r_work: 0.3365 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7367  Z= 0.134
  Angle     :  0.494   5.948  10024  Z= 0.256
  Chirality :  0.042   0.258   1123
  Planarity :  0.004   0.047   1294
  Dihedral  :  5.991  71.303    976
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.75 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 885
  helix:  1.81 (0.27), residues: 386
  sheet: -0.35 (0.42), residues: 135
  loop :  0.08 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 325 
 TYR   0.013   0.001   TYR A 294 
 PHE   0.019   0.001   PHE A 898 
 TRP   0.016   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A 999 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7367)
  covalent geometry    : angle       0.49434 (10024)
  hydrogen bonds       : bond        0.03729 (  355)
  hydrogen bonds       : angle       4.59577 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6630 (tm-30)
REVERT: A  181 ARG cc_start: 0.7231 (ttt90) cc_final: 0.6971 (ttt90)
REVERT: A  223 ILE cc_start: 0.8268 (mt) cc_final: 0.8037 (mp)
REVERT: A  271 ASN cc_start: 0.8026 (m-40) cc_final: 0.7667 (m-40)
REVERT: A  280 ARG cc_start: 0.7765 (mtm180) cc_final: 0.7554 (mtm110)
REVERT: A  369 GLN cc_start: 0.7672 (mm110) cc_final: 0.7219 (mm110)
REVERT: A  710 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7561 (mt-10)
REVERT: A  790 GLN cc_start: 0.7089 (tt0) cc_final: 0.6632 (mm-40)
REVERT: A  805 ARG cc_start: 0.6699 (mmp-170) cc_final: 0.6104 (mmp-170)
REVERT: A  819 ARG cc_start: 0.8465 (tpt170) cc_final: 0.8251 (tpt90)
REVERT: A  827 ARG cc_start: 0.7922 (ptp-170) cc_final: 0.7548 (pmm-80)
REVERT: A  970 ASP cc_start: 0.6922 (m-30) cc_final: 0.6372 (m-30)
REVERT: A  996 LYS cc_start: 0.7555 (mmtp) cc_final: 0.6687 (mptt)
REVERT: A 1026 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7470 (ptmt)
REVERT: A 1048 ASP cc_start: 0.7481 (t70) cc_final: 0.7157 (t70)
  outliers start: 20
  outliers final: 14
  residues processed: 120
  average time/residue: 0.5291
  time to fit residues: 66.6901
Evaluate side-chains
  122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  670 THR
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  710 GLU
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  804 GLU
Chi-restraints excluded: chain A residue  837 SER
Chi-restraints excluded: chain A residue  998 ASN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1026 LYS
Chi-restraints excluded: chain A residue 1075 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 60 optimal weight:    0.0870
   chunk 59 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 77 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 166 GLN
A 995 GLN
** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1052 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.160756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.128290 restraints weight = 7819.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.04
r_work: 0.3364 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7367  Z= 0.139
  Angle     :  0.502   6.031  10024  Z= 0.259
  Chirality :  0.042   0.271   1123
  Planarity :  0.004   0.045   1294
  Dihedral  :  6.012  69.523    976
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.14 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.29), residues: 885
  helix:  1.96 (0.27), residues: 379
  sheet: -0.00 (0.43), residues: 127
  loop : -0.01 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 325 
 TYR   0.014   0.001   TYR A 294 
 PHE   0.021   0.002   PHE A 898 
 TRP   0.018   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A 999 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7367)
  covalent geometry    : angle       0.50232 (10024)
  hydrogen bonds       : bond        0.03721 (  355)
  hydrogen bonds       : angle       4.55508 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   65 ARG cc_start: 0.7108 (ttp-170) cc_final: 0.6903 (ttp-170)
REVERT: A   80 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6659 (tm-30)
REVERT: A  104 ARG cc_start: 0.7513 (ptt90) cc_final: 0.7230 (ptt90)
REVERT: A  223 ILE cc_start: 0.8276 (mt) cc_final: 0.8046 (mp)
REVERT: A  271 ASN cc_start: 0.8041 (m-40) cc_final: 0.7689 (m-40)
REVERT: A  280 ARG cc_start: 0.7780 (mtm180) cc_final: 0.7578 (mtm110)
REVERT: A  369 GLN cc_start: 0.7698 (mm110) cc_final: 0.7223 (mm110)
REVERT: A  586 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6509 (tm-30)
REVERT: A  710 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7578 (mt-10)
REVERT: A  819 ARG cc_start: 0.8478 (tpt170) cc_final: 0.8254 (tpt90)
REVERT: A  827 ARG cc_start: 0.7924 (ptp-170) cc_final: 0.7557 (pmm-80)
REVERT: A  970 ASP cc_start: 0.6810 (m-30) cc_final: 0.6286 (m-30)
REVERT: A  996 LYS cc_start: 0.7589 (mmtp) cc_final: 0.6718 (mptt)
REVERT: A 1048 ASP cc_start: 0.7471 (t70) cc_final: 0.7133 (t70)
  outliers start: 22
  outliers final: 16
  residues processed: 119
  average time/residue: 0.5068
  time to fit residues: 63.2825
Evaluate side-chains
  122 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  670 THR
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  710 GLU
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  804 GLU
Chi-restraints excluded: chain A residue  837 SER
Chi-restraints excluded: chain A residue  998 ASN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1075 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 166 GLN
** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 790 GLN
A 995 GLN
A1052 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.159457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.126907 restraints weight = 7866.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.06
r_work: 0.3344 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7367  Z= 0.171
  Angle     :  0.535   6.898  10024  Z= 0.275
  Chirality :  0.044   0.286   1123
  Planarity :  0.004   0.047   1294
  Dihedral  :  6.144  69.281    976
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.04 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.29), residues: 885
  helix:  1.73 (0.26), residues: 385
  sheet:  0.06 (0.43), residues: 125
  loop : -0.11 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 325 
 TYR   0.014   0.002   TYR A 294 
 PHE   0.021   0.002   PHE A 898 
 TRP   0.016   0.002   TRP A 177 
 HIS   0.004   0.001   HIS A 880 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7367)
  covalent geometry    : angle       0.53540 (10024)
  hydrogen bonds       : bond        0.03948 (  355)
  hydrogen bonds       : angle       4.63408 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6646 (tm-30)
REVERT: A  104 ARG cc_start: 0.7501 (ptt90) cc_final: 0.7188 (ptt90)
REVERT: A  181 ARG cc_start: 0.7132 (ttt90) cc_final: 0.6827 (ttt90)
REVERT: A  223 ILE cc_start: 0.8228 (mt) cc_final: 0.8002 (mp)
REVERT: A  369 GLN cc_start: 0.7644 (mm110) cc_final: 0.7227 (mm110)
REVERT: A  586 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6396 (tm-30)
REVERT: A  710 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7516 (mt-10)
REVERT: A  819 ARG cc_start: 0.8495 (tpt170) cc_final: 0.8264 (tpt90)
REVERT: A  827 ARG cc_start: 0.7902 (ptp-170) cc_final: 0.7502 (pmm-80)
REVERT: A  970 ASP cc_start: 0.6775 (m-30) cc_final: 0.6190 (m-30)
REVERT: A  996 LYS cc_start: 0.7577 (mmtp) cc_final: 0.6689 (mptt)
REVERT: A 1048 ASP cc_start: 0.7456 (t70) cc_final: 0.7115 (t70)
  outliers start: 21
  outliers final: 15
  residues processed: 121
  average time/residue: 0.4916
  time to fit residues: 62.7046
Evaluate side-chains
  123 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  670 THR
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  710 GLU
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  837 SER
Chi-restraints excluded: chain A residue  998 ASN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1075 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 166 GLN
A 790 GLN
A1052 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.160473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.128178 restraints weight = 7806.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.04
r_work: 0.3359 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7367  Z= 0.139
  Angle     :  0.507   6.106  10024  Z= 0.262
  Chirality :  0.043   0.303   1123
  Planarity :  0.004   0.044   1294
  Dihedral  :  6.121  68.235    976
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.52 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.29), residues: 885
  helix:  1.94 (0.27), residues: 379
  sheet: -0.38 (0.43), residues: 137
  loop :  0.10 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 325 
 TYR   0.014   0.001   TYR A 294 
 PHE   0.021   0.002   PHE A 898 
 TRP   0.018   0.002   TRP A 177 
 HIS   0.003   0.001   HIS A 999 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7367)
  covalent geometry    : angle       0.50726 (10024)
  hydrogen bonds       : bond        0.03723 (  355)
  hydrogen bonds       : angle       4.54250 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6640 (tm-30)
REVERT: A  104 ARG cc_start: 0.7559 (ptt90) cc_final: 0.7233 (ptt90)
REVERT: A  181 ARG cc_start: 0.7218 (ttt90) cc_final: 0.6957 (ttt90)
REVERT: A  223 ILE cc_start: 0.8231 (mt) cc_final: 0.7996 (mp)
REVERT: A  271 ASN cc_start: 0.8003 (m-40) cc_final: 0.7640 (m-40)
REVERT: A  369 GLN cc_start: 0.7696 (mm110) cc_final: 0.7219 (mm110)
REVERT: A  586 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6474 (tm-30)
REVERT: A  647 ASN cc_start: 0.7533 (t0) cc_final: 0.7272 (t0)
REVERT: A  710 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7543 (mt-10)
REVERT: A  819 ARG cc_start: 0.8486 (tpt170) cc_final: 0.8245 (tpt90)
REVERT: A  827 ARG cc_start: 0.7938 (ptp-170) cc_final: 0.7558 (pmm-80)
REVERT: A  970 ASP cc_start: 0.6845 (m-30) cc_final: 0.6281 (m-30)
REVERT: A  996 LYS cc_start: 0.7627 (mmtp) cc_final: 0.6754 (mptt)
REVERT: A 1048 ASP cc_start: 0.7383 (t70) cc_final: 0.7040 (t70)
  outliers start: 23
  outliers final: 15
  residues processed: 120
  average time/residue: 0.5644
  time to fit residues: 71.1426
Evaluate side-chains
  124 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  670 THR
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  710 GLU
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  837 SER
Chi-restraints excluded: chain A residue  998 ASN
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1075 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    0.0870
   chunk 73 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0270
   chunk 86 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.3416

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 166 GLN
A 790 GLN
A1052 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.161865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.129649 restraints weight = 7760.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.04
r_work: 0.3378 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7367  Z= 0.112
  Angle     :  0.487   5.276  10024  Z= 0.253
  Chirality :  0.042   0.299   1123
  Planarity :  0.004   0.045   1294
  Dihedral  :  6.082  66.583    976
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.30 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.29), residues: 885
  helix:  2.05 (0.26), residues: 380
  sheet: -0.34 (0.43), residues: 137
  loop :  0.12 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 325 
 TYR   0.013   0.001   TYR A 294 
 PHE   0.021   0.001   PHE A 898 
 TRP   0.019   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A 880 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7367)
  covalent geometry    : angle       0.48675 (10024)
  hydrogen bonds       : bond        0.03513 (  355)
  hydrogen bonds       : angle       4.46849 ( 1008)

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6561 (tm-30)
REVERT: A  104 ARG cc_start: 0.7526 (ptt90) cc_final: 0.7202 (ptt90)
REVERT: A  181 ARG cc_start: 0.7168 (ttt90) cc_final: 0.6889 (ttt90)
REVERT: A  223 ILE cc_start: 0.8189 (mt) cc_final: 0.7956 (mp)
REVERT: A  271 ASN cc_start: 0.7853 (m-40) cc_final: 0.7494 (m-40)
REVERT: A  369 GLN cc_start: 0.7622 (mm110) cc_final: 0.7150 (mm110)
REVERT: A  586 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6407 (tm-30)
REVERT: A  710 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7509 (mt-10)
REVERT: A  819 ARG cc_start: 0.8424 (tpt170) cc_final: 0.8209 (tpt90)
REVERT: A  823 GLU cc_start: 0.6776 (pp20) cc_final: 0.6290 (mm-30)
REVERT: A  827 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7522 (pmm-80)
REVERT: A  970 ASP cc_start: 0.6698 (m-30) cc_final: 0.6165 (m-30)
REVERT: A  996 LYS cc_start: 0.7566 (mmtp) cc_final: 0.6672 (mptt)
REVERT: A 1048 ASP cc_start: 0.7298 (t70) cc_final: 0.6958 (t70)
  outliers start: 16
  outliers final: 12
  residues processed: 111
  average time/residue: 0.5731
  time to fit residues: 66.6100
Evaluate side-chains
  120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  670 THR
Chi-restraints excluded: chain A residue  676 TYR
Chi-restraints excluded: chain A residue  710 GLU
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  837 SER
Chi-restraints excluded: chain A residue  998 ASN
Chi-restraints excluded: chain A residue 1004 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0070
   chunk 76 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A 166 GLN
A 654 ASN
A 790 GLN
A 995 GLN
A1052 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.160777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.128370 restraints weight = 7878.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.05
r_work: 0.3363 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7367  Z= 0.143
  Angle     :  0.510   6.022  10024  Z= 0.263
  Chirality :  0.043   0.300   1123
  Planarity :  0.004   0.045   1294
  Dihedral  :  6.106  65.620    976
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.30 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.29), residues: 885
  helix:  1.99 (0.26), residues: 379
  sheet: -0.28 (0.43), residues: 135
  loop :  0.08 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 325 
 TYR   0.014   0.001   TYR A 294 
 PHE   0.020   0.002   PHE A 898 
 TRP   0.017   0.002   TRP A 177 
 HIS   0.003   0.001   HIS A 880 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7367)
  covalent geometry    : angle       0.51011 (10024)
  hydrogen bonds       : bond        0.03687 (  355)
  hydrogen bonds       : angle       4.50083 ( 1008)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2552.62 seconds
wall clock time: 44 minutes 5.75 seconds (2645.75 seconds total)