Starting phenix.real_space_refine
on Wed Sep 17 23:20:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mn7_48415/09_2025/9mn7_48415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mn7_48415/09_2025/9mn7_48415.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mn7_48415/09_2025/9mn7_48415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mn7_48415/09_2025/9mn7_48415.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mn7_48415/09_2025/9mn7_48415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mn7_48415/09_2025/9mn7_48415.cif"
  }
  resolution = 2.65
  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=   0.001 sd=   0.021
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: 6
    Type Number    sf(0)   Gaussians
     P      69      5.49       5
     Mg      1      5.21       5
     S      63      5.16       5
     C    7300      2.51       5
     N    2112      2.21       5
     O    2243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11788
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2440
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 19, 'TRANS': 281}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 7953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 997, 7953
          Classifications: {'peptide': 997}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 64, 'TRANS': 932}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 618
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "R"
      Number of atoms: 133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 133
          Classifications: {'RNA': 6}
          Modifications used: {'rna3p_pur': 5}
          Link IDs: {'rna3p': 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "T"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 612
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "E"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.99, per 1000 atoms: 0.25
  Number of scatterers: 11788
  At special positions: 0
  Unit cell: (94.17, 129.94, 110.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P      69     15.00
     Mg      1     11.99
     O    2243      8.00
     N    2112      7.00
     C    7300      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: 1.04
  Conformation dependent library (CDL) restraints added in 511.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2462

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 11 sheets defined
      56.2% alpha, 6.2% beta
      23 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'B' and resid 80 through 90
    Processing helix  chain 'B' and resid 107 through 115
    Processing helix  chain 'B' and resid 129 through 135
      removed outlier: 3.778A  pdb=" N   LEU B 133 " --> pdb=" O   PHE B 129 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU B 134 " --> pdb=" O   ILE B 130 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER B 135 " --> pdb=" O   PRO B 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 129 through 135'
    Processing helix  chain 'B' and resid 168 through 177
    Processing helix  chain 'B' and resid 199 through 213
      removed outlier: 3.902A  pdb=" N   SER B 213 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 219
    Processing helix  chain 'B' and resid 231 through 237
    Processing helix  chain 'B' and resid 248 through 258
    Processing helix  chain 'B' and resid 316 through 328
      removed outlier: 3.535A  pdb=" N   HIS B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU B 323 " --> pdb=" O   ILE B 319 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   HIS B 326 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 343
      removed outlier: 3.538A  pdb=" N   HIS B 338 " --> pdb=" O   THR B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 355
    Processing helix  chain 'B' and resid 366 through 379
      removed outlier: 3.632A  pdb=" N   PHE B 370 " --> pdb=" O   HIS B 366 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS B 371 " --> pdb=" O   PRO B 367 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE B 377 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   GLU B 378 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ARG B 379 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 236
    Processing helix  chain 'E' and resid 238 through 249
      removed outlier: 3.582A  pdb=" N   ALA E 242 " --> pdb=" O   GLN E 238 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 274
    Processing helix  chain 'E' and resid 277 through 290
      removed outlier: 3.522A  pdb=" N   ALA E 290 " --> pdb=" O   MET E 286 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 295 through 309
    Processing helix  chain 'E' and resid 312 through 327
      removed outlier: 3.783A  pdb=" N   GLY E 327 " --> pdb=" O   MET E 323 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 329 through 336
      removed outlier: 3.910A  pdb=" N   PHE E 334 " --> pdb=" O   LEU E 330 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   THR E 335 " --> pdb=" O   GLN E 331 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 340 through 353
    Processing helix  chain 'E' and resid 392 through 410
    Processing helix  chain 'E' and resid 424 through 462
    Processing helix  chain 'E' and resid 467 through 472
    Processing helix  chain 'E' and resid 475 through 489
    Processing helix  chain 'E' and resid 497 through 520
      removed outlier: 3.758A  pdb=" N   VAL E 514 " --> pdb=" O   SER E 510 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 521 through 538
      removed outlier: 3.550A  pdb=" N   ALA E 525 " --> pdb=" O   GLY E 521 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LYS E 532 " --> pdb=" O   ASN E 528 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   CYS E 535 " --> pdb=" O   ARG E 531 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   LEU E 536 " --> pdb=" O   LYS E 532 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   LEU E 537 " --> pdb=" O   TYR E 533 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 548 through 556
    Processing helix  chain 'E' and resid 568 through 587
    Processing helix  chain 'E' and resid 624 through 634
    Processing helix  chain 'E' and resid 644 through 646
      No H-bonds generated for 'chain 'E' and resid 644 through 646'
    Processing helix  chain 'E' and resid 679 through 687
      removed outlier: 3.721A  pdb=" N   CYS E 687 " --> pdb=" O   LEU E 683 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 692 through 704
    Processing helix  chain 'E' and resid 710 through 723
      removed outlier: 3.718A  pdb=" N   ALA E 723 " --> pdb=" O   GLN E 719 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 758 through 789
    Processing helix  chain 'E' and resid 818 through 824
    Processing helix  chain 'E' and resid 836 through 850
      removed outlier: 3.884A  pdb=" N   TRP E 840 " --> pdb=" O   HIS E 836 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY E 850 " --> pdb=" O   VAL E 846 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 856 through 867
    Processing helix  chain 'E' and resid 867 through 877
    Processing helix  chain 'E' and resid 883 through 888
      removed outlier: 3.561A  pdb=" N   MET E 886 " --> pdb=" O   LYS E 883 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 890 through 906
    Processing helix  chain 'E' and resid 925 through 936
    Processing helix  chain 'E' and resid 937 through 944
    Processing helix  chain 'E' and resid 954 through 971
      removed outlier: 3.926A  pdb=" N   GLY E 958 " --> pdb=" O   ASP E 954 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 975 through 982
      removed outlier: 4.364A  pdb=" N   GLN E 979 " --> pdb=" O   MET E 975 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLU E 982 " --> pdb=" O   ALA E 978 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 986 through 997
      removed outlier: 3.848A  pdb=" N   VAL E 990 " --> pdb=" O   THR E 986 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLN E 992 " --> pdb=" O   LYS E 988 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   THR E 993 " --> pdb=" O   VAL E 989 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1004 through 1010
      removed outlier: 3.863A  pdb=" N   LEU E1008 " --> pdb=" O   TYR E1004 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1011 through 1016
    Processing helix  chain 'E' and resid 1024 through 1034
    Processing helix  chain 'E' and resid 1036 through 1041
    Processing helix  chain 'E' and resid 1044 through 1064
    Processing helix  chain 'E' and resid 1111 through 1141
      Proline residue:  E1120  - end of helix
      removed outlier: 3.841A  pdb=" N   ILE E1124 " --> pdb=" O   PRO E1120 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG E1141 " --> pdb=" O   LEU E1137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1159 through 1177
      removed outlier: 3.954A  pdb=" N   GLU E1177 " --> pdb=" O   ARG E1173 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1178 through 1192
    Processing helix  chain 'E' and resid 1196 through 1200
      removed outlier: 3.761A  pdb=" N   LEU E1199 " --> pdb=" O   GLN E1196 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1201 through 1209
    Processing helix  chain 'E' and resid 1218 through 1225
      removed outlier: 3.524A  pdb=" N   GLN E1221 " --> pdb=" O   ASP E1218 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 120 through 122
      removed outlier: 5.799A  pdb=" N   LEU B  99 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL B 192 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY B 193 " --> pdb=" O   ASN B 226 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   HIS B 264 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 411 through 415
    Processing sheet with id=AA3, first strand: chain 'E' and resid 495 through 496
      removed outlier: 3.741A  pdb=" N   GLU E 495 " --> pdb=" O   LEU E 621 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 588 through 590
    Processing sheet with id=AA5, first strand: chain 'E' and resid 794 through 795
    Processing sheet with id=AA6, first strand: chain 'E' and resid 798 through 800
    Processing sheet with id=AA7, first strand: chain 'E' and resid 831 through 832
    Processing sheet with id=AA8, first strand: chain 'E' and resid 1146 through 1149
    Processing sheet with id=AA9, first strand: chain 'E' and resid 1069 through 1071
    Processing sheet with id=AB1, first strand: chain 'E' and resid 1083 through 1084
      removed outlier: 4.580A  pdb=" N   LYS E1109 " --> pdb=" O   LEU E1084 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 1087 through 1090
      removed outlier: 3.811A  pdb=" N   LYS E1087 " --> pdb=" O   HIS E1102 " (cutoff:3.500A)

    514 hydrogen bonds defined for protein.
    1500 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      57 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 2.73

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2913
        1.33 -     1.45: 2588
        1.45 -     1.57: 6475
        1.57 -     1.69: 134
        1.69 -     1.81: 96
  Bond restraints: 12206
  Sorted by residual:
  bond pdb=" C   VAL B 181 "
       pdb=" N   PRO B 182 "
    ideal  model  delta    sigma   weight residual
    1.333  1.374 -0.041 1.20e-02 6.94e+03 1.16e+01
  bond pdb=" N   LEU B 154 "
       pdb=" CA  LEU B 154 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 4.95e+00
  bond pdb=" C   PRO B  95 "
       pdb=" N   PRO B  96 "
    ideal  model  delta    sigma   weight residual
    1.336  1.361 -0.025 1.25e-02 6.40e+03 4.13e+00
  bond pdb=" C3'  DA N  46 "
       pdb=" O3'  DA N  46 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.81e+00
  bond pdb=" CB  ASP E1151 "
       pdb=" CG  ASP E1151 "
    ideal  model  delta    sigma   weight residual
    1.516  1.557 -0.041 2.50e-02 1.60e+03 2.69e+00
  ... (remaining 12201 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 16502
        2.85 -     5.69: 278
        5.69 -     8.54: 44
        8.54 -    11.39: 10
       11.39 -    14.24: 1
  Bond angle restraints: 16835
  Sorted by residual:
  angle pdb=" C   HIS E1150 "
        pdb=" N   ASP E1151 "
        pdb=" CA  ASP E1151 "
      ideal   model   delta    sigma   weight residual
     126.32  136.40  -10.08 1.74e+00 3.30e-01 3.36e+01
  angle pdb=" N   VAL E1149 "
        pdb=" CA  VAL E1149 "
        pdb=" C   VAL E1149 "
      ideal   model   delta    sigma   weight residual
     110.05  104.06    5.99 1.09e+00 8.42e-01 3.02e+01
  angle pdb=" N   PRO B  95 "
        pdb=" CA  PRO B  95 "
        pdb=" C   PRO B  95 "
      ideal   model   delta    sigma   weight residual
     110.70  116.74   -6.04 1.22e+00 6.72e-01 2.45e+01
  angle pdb=" CA  PRO B  95 "
        pdb=" C   PRO B  95 "
        pdb=" N   PRO B  96 "
      ideal   model   delta    sigma   weight residual
     117.93  123.86   -5.93 1.20e+00 6.94e-01 2.44e+01
  angle pdb=" N   ASP B 240 "
        pdb=" CA  ASP B 240 "
        pdb=" C   ASP B 240 "
      ideal   model   delta    sigma   weight residual
     109.81   99.70   10.11 2.21e+00 2.05e-01 2.09e+01
  ... (remaining 16830 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.68: 6663
       25.68 -    51.36: 482
       51.36 -    77.03: 109
       77.03 -   102.71: 7
      102.71 -   128.39: 1
  Dihedral angle restraints: 7262
    sinusoidal: 3469
      harmonic: 3793
  Sorted by residual:
  dihedral pdb=" CA  GLN B 357 "
           pdb=" C   GLN B 357 "
           pdb=" N   GLU B 358 "
           pdb=" CA  GLU B 358 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.50   31.50     0      5.00e+00 4.00e-02 3.97e+01
  dihedral pdb=" CA  VAL E 944 "
           pdb=" C   VAL E 944 "
           pdb=" N   ASN E 945 "
           pdb=" CA  ASN E 945 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.52  -26.48     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" CA  SER E1148 "
           pdb=" C   SER E1148 "
           pdb=" N   VAL E1149 "
           pdb=" CA  VAL E1149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.85   26.15     0      5.00e+00 4.00e-02 2.73e+01
  ... (remaining 7259 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1461
       0.056 -    0.113: 337
       0.113 -    0.169: 64
       0.169 -    0.225: 6
       0.225 -    0.282: 3
  Chirality restraints: 1871
  Sorted by residual:
  chirality pdb=" C3'  DA N  35 "
            pdb=" C4'  DA N  35 "
            pdb=" O3'  DA N  35 "
            pdb=" C2'  DA N  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.38   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" P    DG N  37 "
            pdb=" OP1  DG N  37 "
            pdb=" OP2  DG N  37 "
            pdb=" O5'  DG N  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.58   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CB  ILE E1010 "
            pdb=" CA  ILE E1010 "
            pdb=" CG1 ILE E1010 "
            pdb=" CG2 ILE E1010 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1868 not shown)

  Planarity restraints: 1924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN E1165 "   -0.015 2.00e-02 2.50e+03   2.92e-02 8.51e+00
        pdb=" C   GLN E1165 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLN E1165 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL E1166 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS E1167 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.93e+00
        pdb=" C   CYS E1167 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   CYS E1167 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ARG E1168 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 225 "   -0.013 2.00e-02 2.50e+03   2.66e-02 7.08e+00
        pdb=" C   VAL B 225 "    0.046 2.00e-02 2.50e+03
        pdb=" O   VAL B 225 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASN B 226 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1921 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1906
        2.77 -     3.30: 10692
        3.30 -     3.83: 20086
        3.83 -     4.37: 23787
        4.37 -     4.90: 38893
  Nonbonded interactions: 95364
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 236 "
            pdb=" OG  SER B 251 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OH  TYR E 956 "
            pdb=" O1B ATP E1301 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   PRO E1121 "
            pdb=" ND1 HIS E1125 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OH  TYR E 530 "
            pdb=" O   PRO E 651 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" NE2 GLN E1165 "
            pdb=" OE2 GLU E1169 "
     model   vdw
     2.300 3.120
  ... (remaining 95359 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             3.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.010
  Find NCS groups from input model:        0.050
  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:7.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4802
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      :  0.005   0.064  12206  Z= 0.219
  Angle     :  0.933  14.236  16835  Z= 0.494
  Chirality :  0.050   0.282   1871
  Planarity :  0.008   0.084   1924
  Dihedral  : 17.445 128.389   4800
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.29 (0.21), residues: 1290
  helix: -0.56 (0.18), residues: 668
  sheet: -0.17 (0.58), residues: 75
  loop : -1.20 (0.24), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 516 
 TYR   0.034   0.003   TYR B 212 
 PHE   0.038   0.003   PHE E 229 
 TRP   0.025   0.002   TRP E1026 
 HIS   0.011   0.002   HIS E1131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (12206)
  covalent geometry    : angle       0.93301 (16835)
  hydrogen bonds       : bond        0.13951 (  571)
  hydrogen bonds       : angle       5.84372 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  229 PHE cc_start: 0.7003 (t80) cc_final: 0.6739 (t80)
REVERT: E  401 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6518 (mm-30)
REVERT: E  411 ARG cc_start: 0.6325 (ptp-170) cc_final: 0.6076 (ptp-170)
REVERT: E  632 GLU cc_start: 0.6321 (mp0) cc_final: 0.6114 (mp0)
REVERT: E  776 ARG cc_start: 0.6821 (ttt90) cc_final: 0.6417 (ttt180)
REVERT: E  975 MET cc_start: 0.5430 (mtm) cc_final: 0.4913 (ptm)
REVERT: E 1084 LEU cc_start: 0.6717 (pt) cc_final: 0.6466 (pt)
REVERT: E 1165 GLN cc_start: 0.6255 (tm-30) cc_final: 0.6047 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.6306
  time to fit residues: 111.4976
Evaluate side-chains
  145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
B 255 GLN
B 300 GLN
E 252 GLN
E 309 GLN
E 369 ASN
E 512 HIS
E 528 ASN
E 877 GLN
E 921 GLN
E 945 ASN
E 992 GLN
E1009 GLN
E1022 GLN
E1030 HIS
E1051 GLN
E1111 ASN
E1115 GLN
E1138 HIS

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.199686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.163599 restraints weight = 16420.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 1.87
r_work: 0.3930 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3788 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.1112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099  12206  Z= 0.193
  Angle     :  0.667   9.241  16835  Z= 0.345
  Chirality :  0.042   0.158   1871
  Planarity :  0.006   0.054   1924
  Dihedral  : 19.117 122.850   2191
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  6.43 %
    Favored  : 91.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.41 (0.22), residues: 1290
  helix:  0.28 (0.19), residues: 690
  sheet: -0.34 (0.56), residues: 82
  loop : -0.89 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  78 
 TYR   0.026   0.002   TYR B 212 
 PHE   0.027   0.002   PHE E1229 
 TRP   0.018   0.002   TRP E1026 
 HIS   0.006   0.001   HIS E1175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (12206)
  covalent geometry    : angle       0.66749 (16835)
  hydrogen bonds       : bond        0.05035 (  571)
  hydrogen bonds       : angle       4.58278 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: B  352 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7327 (mpp)
REVERT: E  238 GLN cc_start: 0.7872 (mt0) cc_final: 0.7645 (mt0)
REVERT: E 1007 ARG cc_start: 0.6883 (ttp80) cc_final: 0.6612 (ttp-110)
REVERT: E 1084 LEU cc_start: 0.7386 (pt) cc_final: 0.7183 (pt)
  outliers start: 18
  outliers final: 7
  residues processed: 157
  average time/residue: 0.6337
  time to fit residues: 107.5476
Evaluate side-chains
  156 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  415 VAL
Chi-restraints excluded: chain E residue  433 THR
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  659 HIS
Chi-restraints excluded: chain E residue 1064 MET
Chi-restraints excluded: chain E residue 1211 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 133 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 120 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 134 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 112 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B 148 HIS
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 528 ASN
E 877 GLN
** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 953 GLN
E1111 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.198032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.161602 restraints weight = 16524.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.4013 rms_B_bonded: 1.88
r_work: 0.3904 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3761 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12206  Z= 0.207
  Angle     :  0.652   8.271  16835  Z= 0.338
  Chirality :  0.043   0.169   1871
  Planarity :  0.006   0.059   1924
  Dihedral  : 18.985 121.784   2191
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.60 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.20 (0.23), residues: 1290
  helix:  0.47 (0.20), residues: 689
  sheet: -0.39 (0.55), residues: 82
  loop : -0.81 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 447 
 TYR   0.030   0.002   TYR B 212 
 PHE   0.026   0.002   PHE E1229 
 TRP   0.014   0.002   TRP B 254 
 HIS   0.010   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (12206)
  covalent geometry    : angle       0.65168 (16835)
  hydrogen bonds       : bond        0.04916 (  571)
  hydrogen bonds       : angle       4.51721 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: E  318 ARG cc_start: 0.7260 (tmt-80) cc_final: 0.6701 (tpt90)
REVERT: E 1083 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7697 (mtt-85)
  outliers start: 19
  outliers final: 8
  residues processed: 161
  average time/residue: 0.6030
  time to fit residues: 105.3574
Evaluate side-chains
  161 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 152
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  372 LYS
Chi-restraints excluded: chain E residue  415 VAL
Chi-restraints excluded: chain E residue  433 THR
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  659 HIS
Chi-restraints excluded: chain E residue 1064 MET
Chi-restraints excluded: chain E residue 1083 ARG
Chi-restraints excluded: chain E residue 1211 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 102 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 132 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
E 369 ASN
E 528 ASN
E 877 GLN
E1103 ASN
E1111 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.198049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.161554 restraints weight = 16618.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 1.89
r_work: 0.3907 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12206  Z= 0.180
  Angle     :  0.635  10.994  16835  Z= 0.323
  Chirality :  0.041   0.200   1871
  Planarity :  0.005   0.058   1924
  Dihedral  : 18.902 121.101   2191
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.00 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.09 (0.23), residues: 1290
  helix:  0.66 (0.20), residues: 686
  sheet: -0.54 (0.54), residues: 82
  loop : -0.85 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 458 
 TYR   0.025   0.002   TYR B 212 
 PHE   0.014   0.002   PHE E1229 
 TRP   0.011   0.002   TRP E 707 
 HIS   0.006   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (12206)
  covalent geometry    : angle       0.63514 (16835)
  hydrogen bonds       : bond        0.04570 (  571)
  hydrogen bonds       : angle       4.45500 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: E  318 ARG cc_start: 0.7290 (tmt-80) cc_final: 0.6687 (tpt90)
REVERT: E  445 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8031 (mm)
REVERT: E 1083 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7747 (mtt-85)
  outliers start: 28
  outliers final: 9
  residues processed: 159
  average time/residue: 0.6122
  time to fit residues: 105.7148
Evaluate side-chains
  158 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  398 CYS
Chi-restraints excluded: chain E residue  415 VAL
Chi-restraints excluded: chain E residue  445 LEU
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  659 HIS
Chi-restraints excluded: chain E residue 1064 MET
Chi-restraints excluded: chain E residue 1083 ARG
Chi-restraints excluded: chain E residue 1211 VAL
Chi-restraints excluded: chain E residue 1219 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 96 optimal weight:    0.6980
   chunk 104 optimal weight:    0.0970
   chunk 108 optimal weight:    0.7980
   chunk 133 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0470
   chunk 91 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
E 304 GLN
E 528 ASN
E 877 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.198826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.162560 restraints weight = 16608.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 1.88
r_work: 0.3922 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3780 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12206  Z= 0.144
  Angle     :  0.589   7.353  16835  Z= 0.304
  Chirality :  0.039   0.151   1871
  Planarity :  0.005   0.061   1924
  Dihedral  : 18.852 120.578   2191
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.50 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.17 (0.23), residues: 1290
  helix:  0.93 (0.20), residues: 687
  sheet: -0.55 (0.54), residues: 82
  loop : -0.81 (0.27), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 447 
 TYR   0.017   0.001   TYR B 212 
 PHE   0.012   0.001   PHE E 802 
 TRP   0.011   0.001   TRP B 254 
 HIS   0.005   0.001   HIS E1125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12206)
  covalent geometry    : angle       0.58919 (16835)
  hydrogen bonds       : bond        0.04263 (  571)
  hydrogen bonds       : angle       4.30363 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
REVERT: B  167 MET cc_start: 0.6303 (mtp) cc_final: 0.5792 (mtp)
REVERT: E  318 ARG cc_start: 0.7231 (tmt-80) cc_final: 0.6644 (tpt90)
REVERT: E  445 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7983 (mm)
REVERT: E 1083 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7722 (mtt-85)
  outliers start: 26
  outliers final: 11
  residues processed: 159
  average time/residue: 0.5808
  time to fit residues: 100.2827
Evaluate side-chains
  162 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  240 ASP
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  398 CYS
Chi-restraints excluded: chain E residue  415 VAL
Chi-restraints excluded: chain E residue  445 LEU
Chi-restraints excluded: chain E residue  504 LEU
Chi-restraints excluded: chain E residue  659 HIS
Chi-restraints excluded: chain E residue  673 THR
Chi-restraints excluded: chain E residue 1083 ARG
Chi-restraints excluded: chain E residue 1211 VAL
Chi-restraints excluded: chain E residue 1219 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0770
   chunk 40 optimal weight:    0.7980
   chunk 119 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 75 optimal weight:    0.4980
   chunk 34 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:
** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 528 ASN
E 877 GLN
E1111 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.198700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.162956 restraints weight = 16539.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 1.83
r_work: 0.3923 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3782 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12206  Z= 0.149
  Angle     :  0.597   8.628  16835  Z= 0.305
  Chirality :  0.040   0.175   1871
  Planarity :  0.005   0.059   1924
  Dihedral  : 18.833 119.879   2191
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.68 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.26 (0.23), residues: 1290
  helix:  0.96 (0.20), residues: 694
  sheet: -0.53 (0.54), residues: 82
  loop : -0.72 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 458 
 TYR   0.018   0.001   TYR B 212 
 PHE   0.030   0.002   PHE E 229 
 TRP   0.011   0.001   TRP E 707 
 HIS   0.005   0.001   HIS E1125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12206)
  covalent geometry    : angle       0.59673 (16835)
  hydrogen bonds       : bond        0.04232 (  571)
  hydrogen bonds       : angle       4.24700 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: B  167 MET cc_start: 0.6308 (mtp) cc_final: 0.5815 (mtp)
REVERT: E  318 ARG cc_start: 0.7251 (tmt-80) cc_final: 0.6639 (tpt90)
REVERT: E  445 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8056 (mm)
REVERT: E  458 ARG cc_start: 0.6945 (ttp80) cc_final: 0.6721 (ttp80)
REVERT: E 1083 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7718 (mtt-85)
REVERT: E 1151 ASP cc_start: 0.6269 (p0) cc_final: 0.5998 (p0)
  outliers start: 28
  outliers final: 10
  residues processed: 159
  average time/residue: 0.5775
  time to fit residues: 99.9853
Evaluate side-chains
  161 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  240 ASP
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  415 VAL
Chi-restraints excluded: chain E residue  445 LEU
Chi-restraints excluded: chain E residue  504 LEU
Chi-restraints excluded: chain E residue  659 HIS
Chi-restraints excluded: chain E residue  673 THR
Chi-restraints excluded: chain E residue 1083 ARG
Chi-restraints excluded: chain E residue 1211 VAL
Chi-restraints excluded: chain E residue 1219 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 130 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   chunk 120 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
E 304 GLN
E 528 ASN
E 877 GLN
E1111 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.197317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.160814 restraints weight = 16490.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 1.87
r_work: 0.3898 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3753 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12206  Z= 0.196
  Angle     :  0.628   8.687  16835  Z= 0.321
  Chirality :  0.042   0.205   1871
  Planarity :  0.006   0.072   1924
  Dihedral  : 18.849 119.309   2191
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.29 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.12 (0.23), residues: 1290
  helix:  0.83 (0.20), residues: 693
  sheet: -0.56 (0.53), residues: 82
  loop : -0.76 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 447 
 TYR   0.024   0.002   TYR B 212 
 PHE   0.030   0.002   PHE E 229 
 TRP   0.015   0.002   TRP B 254 
 HIS   0.006   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (12206)
  covalent geometry    : angle       0.62808 (16835)
  hydrogen bonds       : bond        0.04581 (  571)
  hydrogen bonds       : angle       4.37482 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: B  167 MET cc_start: 0.6402 (mtp) cc_final: 0.5889 (mtp)
REVERT: B  301 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7712 (mmt)
REVERT: E  318 ARG cc_start: 0.7266 (tmt-80) cc_final: 0.6655 (tpt90)
REVERT: E  445 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8064 (mm)
REVERT: E  955 VAL cc_start: 0.8081 (m) cc_final: 0.7827 (t)
REVERT: E 1083 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7759 (mtt-85)
  outliers start: 29
  outliers final: 10
  residues processed: 167
  average time/residue: 0.5693
  time to fit residues: 103.6353
Evaluate side-chains
  162 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  240 ASP
Chi-restraints excluded: chain B residue  301 MET
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  398 CYS
Chi-restraints excluded: chain E residue  415 VAL
Chi-restraints excluded: chain E residue  445 LEU
Chi-restraints excluded: chain E residue  504 LEU
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  673 THR
Chi-restraints excluded: chain E residue 1083 ARG
Chi-restraints excluded: chain E residue 1084 LEU
Chi-restraints excluded: chain E residue 1211 VAL
Chi-restraints excluded: chain E residue 1219 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 103 optimal weight:    0.3980
   chunk 51 optimal weight:    0.6980
   chunk 106 optimal weight:    0.0030
   chunk 8 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0970
   chunk 31 optimal weight:    0.5980
   chunk 131 optimal weight:   10.0000
   chunk 50 optimal weight:    0.6980
   chunk 114 optimal weight:    0.4980
   overall best weight:    0.3188

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

Flipped N/Q/H residues before XYZ refinement:
** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 528 ASN
E 877 GLN
E1111 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.199548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.163803 restraints weight = 16605.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 1.85
r_work: 0.3934 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3797 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12206  Z= 0.128
  Angle     :  0.587   8.872  16835  Z= 0.298
  Chirality :  0.039   0.232   1871
  Planarity :  0.005   0.058   1924
  Dihedral  : 18.780 118.374   2191
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.35 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.44 (0.24), residues: 1290
  helix:  1.19 (0.20), residues: 686
  sheet: -0.52 (0.53), residues: 82
  loop : -0.71 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG E 458 
 TYR   0.010   0.001   TYR B 212 
 PHE   0.032   0.001   PHE E 229 
 TRP   0.011   0.001   TRP E 707 
 HIS   0.005   0.001   HIS E1175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (12206)
  covalent geometry    : angle       0.58675 (16835)
  hydrogen bonds       : bond        0.04011 (  571)
  hydrogen bonds       : angle       4.17439 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: B  167 MET cc_start: 0.6252 (mtp) cc_final: 0.5775 (mtp)
REVERT: B  301 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7527 (mmt)
REVERT: E  318 ARG cc_start: 0.7199 (tmt-80) cc_final: 0.6643 (tpt90)
REVERT: E  445 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7993 (mm)
REVERT: E 1083 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7686 (mtt-85)
REVERT: E 1151 ASP cc_start: 0.6243 (p0) cc_final: 0.5950 (p0)
  outliers start: 22
  outliers final: 10
  residues processed: 158
  average time/residue: 0.5902
  time to fit residues: 101.1934
Evaluate side-chains
  165 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  240 ASP
Chi-restraints excluded: chain B residue  301 MET
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  445 LEU
Chi-restraints excluded: chain E residue  500 LEU
Chi-restraints excluded: chain E residue  504 LEU
Chi-restraints excluded: chain E residue  673 THR
Chi-restraints excluded: chain E residue 1083 ARG
Chi-restraints excluded: chain E residue 1211 VAL
Chi-restraints excluded: chain E residue 1219 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 129 optimal weight:   10.0000
   chunk 16 optimal weight:    0.1980
   chunk 105 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0270
   chunk 108 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
B 311 ASN
E 304 GLN
E 528 ASN
E 877 GLN
E1111 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.199305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.163459 restraints weight = 16406.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 1.84
r_work: 0.3930 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3791 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12206  Z= 0.136
  Angle     :  0.594   8.889  16835  Z= 0.299
  Chirality :  0.039   0.252   1871
  Planarity :  0.005   0.062   1924
  Dihedral  : 18.755 117.560   2191
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 15.14 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.51 (0.24), residues: 1290
  helix:  1.18 (0.20), residues: 694
  sheet: -0.43 (0.53), residues: 82
  loop : -0.62 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG E 447 
 TYR   0.013   0.001   TYR B 212 
 PHE   0.033   0.002   PHE E 229 
 TRP   0.010   0.001   TRP E1026 
 HIS   0.004   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (12206)
  covalent geometry    : angle       0.59385 (16835)
  hydrogen bonds       : bond        0.04032 (  571)
  hydrogen bonds       : angle       4.14494 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: B  167 MET cc_start: 0.6227 (mtp) cc_final: 0.5722 (mtp)
REVERT: B  301 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7621 (mmt)
REVERT: E  445 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7955 (mm)
REVERT: E 1083 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7705 (mtt-85)
  outliers start: 16
  outliers final: 8
  residues processed: 159
  average time/residue: 0.6240
  time to fit residues: 107.4832
Evaluate side-chains
  154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  240 ASP
Chi-restraints excluded: chain B residue  301 MET
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  445 LEU
Chi-restraints excluded: chain E residue  504 LEU
Chi-restraints excluded: chain E residue  673 THR
Chi-restraints excluded: chain E residue 1083 ARG
Chi-restraints excluded: chain E residue 1211 VAL
Chi-restraints excluded: chain E residue 1219 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 125 optimal weight:    0.0980
   chunk 84 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 129 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0370
   chunk 78 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
E 528 ASN
E 877 GLN
E1111 ASN
E1165 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.198583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.163018 restraints weight = 16482.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 1.82
r_work: 0.3928 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3788 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12206  Z= 0.145
  Angle     :  0.595   9.004  16835  Z= 0.302
  Chirality :  0.040   0.248   1871
  Planarity :  0.005   0.059   1924
  Dihedral  : 18.732 116.730   2191
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.32 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.48 (0.23), residues: 1290
  helix:  1.13 (0.20), residues: 695
  sheet: -0.42 (0.53), residues: 82
  loop : -0.60 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG E 447 
 TYR   0.015   0.001   TYR B 212 
 PHE   0.032   0.002   PHE E 229 
 TRP   0.012   0.001   TRP B 254 
 HIS   0.004   0.001   HIS E1175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (12206)
  covalent geometry    : angle       0.59540 (16835)
  hydrogen bonds       : bond        0.04089 (  571)
  hydrogen bonds       : angle       4.14154 ( 1614)

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

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

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2580 Ramachandran restraints generated.
    1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: B  167 MET cc_start: 0.6286 (mtp) cc_final: 0.5781 (mtp)
REVERT: B  227 MET cc_start: 0.6174 (pp-130) cc_final: 0.5916 (ppp)
REVERT: B  301 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7656 (mmt)
REVERT: E  445 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8001 (mm)
REVERT: E 1083 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7712 (mtt-85)
  outliers start: 14
  outliers final: 8
  residues processed: 151
  average time/residue: 0.6631
  time to fit residues: 108.1076
Evaluate side-chains
  159 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  240 ASP
Chi-restraints excluded: chain B residue  301 MET
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  445 LEU
Chi-restraints excluded: chain E residue  504 LEU
Chi-restraints excluded: chain E residue  673 THR
Chi-restraints excluded: chain E residue 1083 ARG
Chi-restraints excluded: chain E residue 1211 VAL
Chi-restraints excluded: chain E residue 1219 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 134 optimal weight:    6.9990
   chunk 105 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 120 optimal weight:    0.5980
   chunk 80 optimal weight:    0.0970
   chunk 24 optimal weight:    0.5980
   chunk 123 optimal weight:    0.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
E 304 GLN
E 528 ASN
E 877 GLN
E1111 ASN
E1165 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.198077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.162287 restraints weight = 16402.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 1.83
r_work: 0.3917 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3777 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12206  Z= 0.165
  Angle     :  0.621  10.397  16835  Z= 0.314
  Chirality :  0.041   0.250   1871
  Planarity :  0.006   0.062   1924
  Dihedral  : 18.730 116.082   2191
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.32 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.44 (0.23), residues: 1290
  helix:  1.08 (0.20), residues: 695
  sheet: -0.44 (0.53), residues: 82
  loop : -0.60 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG E 447 
 TYR   0.019   0.001   TYR B 212 
 PHE   0.032   0.002   PHE E 229 
 TRP   0.016   0.002   TRP B 254 
 HIS   0.006   0.001   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (12206)
  covalent geometry    : angle       0.62078 (16835)
  hydrogen bonds       : bond        0.04254 (  571)
  hydrogen bonds       : angle       4.20469 ( 1614)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5327.07 seconds
wall clock time: 91 minutes 19.21 seconds (5479.21 seconds total)