Starting phenix.real_space_refine
on Wed Mar 12 19:37:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k77_36935/03_2025/8k77_36935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k77_36935/03_2025/8k77_36935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k77_36935/03_2025/8k77_36935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k77_36935/03_2025/8k77_36935.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k77_36935/03_2025/8k77_36935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k77_36935/03_2025/8k77_36935.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.097
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    5294      2.51       5
     N    1362      2.21       5
     O    1489      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8192
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4674
          Classifications: {'peptide': 592}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 576}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3437
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411}
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 43
          Unusual residues: {'NAG': 2, 'VLX': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.92, per 1000 atoms: 0.60
  Number of scatterers: 8192
  At special positions: 0
  Unit cell: (84.66, 83.83, 146.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1489      8.00
     N    1362      7.00
     C    5294      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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 801 " - " ASN A 498 "
      " NAG A 802 " - " ASN A 548 "
      " NAG C   1 " - " ASN A 573 "
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 867.9 milliseconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1866

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 5 sheets defined
      43.5% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 137 through 160
    Processing helix  chain 'A' and resid 162 through 183
      removed outlier: 3.700A  pdb=" N   ASP A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 197
      Proline residue:  A 191  - end of helix
      removed outlier: 4.108A  pdb=" N   LYS A 195 " --> pdb=" O   PRO A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 230
      removed outlier: 4.435A  pdb=" N   VAL A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   TYR A 212 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE A 220 " --> pdb=" O   MET A 216 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ASP A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ARG A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 250
    Processing helix  chain 'A' and resid 255 through 271
      removed outlier: 4.491A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.568A  pdb=" N   ILE A 275 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLU A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 284
      No H-bonds generated for 'chain 'A' and resid 283 through 284'
    Processing helix  chain 'A' and resid 285 through 288
      removed outlier: 3.711A  pdb=" N   LYS A 288 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 285 through 288'
    Processing helix  chain 'A' and resid 289 through 295
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.826A  pdb=" N   MET A 301 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.725A  pdb=" N   VAL A 335 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 3.669A  pdb=" N   PHE A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 386
    Processing helix  chain 'A' and resid 419 through 439
    Processing helix  chain 'A' and resid 444 through 483
      Proline residue:  A 469  - end of helix
    Processing helix  chain 'A' and resid 562 through 564
      No H-bonds generated for 'chain 'A' and resid 562 through 564'
    Processing helix  chain 'A' and resid 593 through 619
      removed outlier: 3.729A  pdb=" N   VAL A 597 " --> pdb=" O   GLY A 593 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A 608 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A 609 " --> pdb=" O   THR A 605 " (cutoff:3.500A)
      Proline residue:  A 610  - end of helix
      removed outlier: 3.530A  pdb=" N   ILE A 613 " --> pdb=" O   LEU A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 642
      removed outlier: 3.836A  pdb=" N   MET A 634 " --> pdb=" O   GLY A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 676
      removed outlier: 3.791A  pdb=" N   ILE A 663 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   ALA A 664 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   SER A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 707
    Processing helix  chain 'A' and resid 712 through 731
      removed outlier: 4.000A  pdb=" N   ILE A 716 " --> pdb=" O   LYS A 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 929 through 933
      removed outlier: 3.888A  pdb=" N   VAL B 933 " --> pdb=" O   ASN B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 958
      removed outlier: 3.639A  pdb=" N   LEU B 958 " --> pdb=" O   LYS B 955 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1080 through 1092
    Processing helix  chain 'B' and resid 1265 through 1273
    Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 485 through 492
    current: chain 'A' and resid 514 through 527
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 514 through 527
    current: chain 'B' and resid 1142 through 1144
    Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884
      removed outlier: 3.720A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 887 through 890
    current: chain 'B' and resid 914 through 917
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 914 through 917
    current: chain 'B' and resid 1015 through 1021
      removed outlier: 3.856A  pdb=" N   ASP B1037 " --> pdb=" O   ILE B1029 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ILE B1031 " --> pdb=" O   LEU B1035 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   LEU B1035 " --> pdb=" O   ILE B1031 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 897 through 900
      removed outlier: 7.659A  pdb=" N   MET B1054 " --> pdb=" O   CYS B 967 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   CYS B 967 " --> pdb=" O   MET B1054 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   LYS B1056 " --> pdb=" O   ILE B 965 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ILE B 965 " --> pdb=" O   LYS B1056 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   THR B 963 " --> pdb=" O   LEU B 978 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LEU B 978 " --> pdb=" O   THR B 963 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TRP B 974 " --> pdb=" O   CYS B 967 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1112 through 1115
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1122 through 1125
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1134 through 1137
    current: chain 'B' and resid 1179 through 1186
      removed outlier: 5.618A  pdb=" N   ILE B1182 " --> pdb=" O   LEU B1193 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1189 through 1194
    current: chain 'B' and resid 1232 through 1240
      removed outlier: 27.341A  pdb=" N   ASN B1233 " --> pdb=" O   LEU B1254 " (cutoff:3.500A)
      removed outlier: 23.656A  pdb=" N   LEU B1254 " --> pdb=" O   ASN B1233 " (cutoff:3.500A)
      removed outlier: 15.969A  pdb=" N   CYS B1235 " --> pdb=" O   PHE B1252 " (cutoff:3.500A)
      removed outlier: 11.261A  pdb=" N   PHE B1252 " --> pdb=" O   CYS B1235 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   MET B1237 " --> pdb=" O   ILE B1250 " (cutoff:3.500A)

    367 hydrogen bonds defined for protein.
    1071 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.02 -     1.18: 2
        1.18 -     1.34: 2535
        1.34 -     1.49: 2386
        1.49 -     1.65: 3387
        1.65 -     1.81: 76
  Bond restraints: 8386
  Sorted by residual:
  bond pdb=" CG  PRO A 343 "
       pdb=" CD  PRO A 343 "
    ideal  model  delta    sigma   weight residual
    1.503  1.158  0.345 3.40e-02 8.65e+02 1.03e+02
  bond pdb=" CB  PRO A 343 "
       pdb=" CG  PRO A 343 "
    ideal  model  delta    sigma   weight residual
    1.492  1.021  0.471 5.00e-02 4.00e+02 8.89e+01
  bond pdb=" C6  VLX A 803 "
       pdb=" N1  VLX A 803 "
    ideal  model  delta    sigma   weight residual
    1.351  1.500 -0.149 2.00e-02 2.50e+03 5.54e+01
  bond pdb=" C9  VLX A 803 "
       pdb=" N2  VLX A 803 "
    ideal  model  delta    sigma   weight residual
    1.339  1.448 -0.109 2.00e-02 2.50e+03 2.99e+01
  bond pdb=" N   PRO A 343 "
       pdb=" CA  PRO A 343 "
    ideal  model  delta    sigma   weight residual
    1.471  1.525 -0.054 1.32e-02 5.74e+03 1.67e+01
  ... (remaining 8381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.77: 11336
       14.77 -    29.54: 2
       29.54 -    44.31: 0
       44.31 -    59.08: 0
       59.08 -    73.85: 1
  Bond angle restraints: 11339
  Sorted by residual:
  angle pdb=" CB  PRO A 343 "
        pdb=" CG  PRO A 343 "
        pdb=" CD  PRO A 343 "
      ideal   model   delta    sigma   weight residual
     106.10  179.95  -73.85 3.20e+00 9.77e-02 5.33e+02
  angle pdb=" N   PRO A 343 "
        pdb=" CD  PRO A 343 "
        pdb=" CG  PRO A 343 "
      ideal   model   delta    sigma   weight residual
     103.20   76.47   26.73 1.50e+00 4.44e-01 3.18e+02
  angle pdb=" CA  PRO A 343 "
        pdb=" CB  PRO A 343 "
        pdb=" CG  PRO A 343 "
      ideal   model   delta    sigma   weight residual
     104.50   75.32   29.18 1.90e+00 2.77e-01 2.36e+02
  angle pdb=" CA  PRO A 343 "
        pdb=" N   PRO A 343 "
        pdb=" CD  PRO A 343 "
      ideal   model   delta    sigma   weight residual
     112.00  101.62   10.38 1.40e+00 5.10e-01 5.50e+01
  angle pdb=" N   PRO A 343 "
        pdb=" CA  PRO A 343 "
        pdb=" C   PRO A 343 "
      ideal   model   delta    sigma   weight residual
     113.84  120.10   -6.26 1.30e+00 5.92e-01 2.32e+01
  ... (remaining 11334 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 4257
       16.65 -    33.31: 502
       33.31 -    49.96: 161
       49.96 -    66.62: 34
       66.62 -    83.27: 15
  Dihedral angle restraints: 4969
    sinusoidal: 2046
      harmonic: 2923
  Sorted by residual:
  dihedral pdb=" CA  ASP A 528 "
           pdb=" CB  ASP A 528 "
           pdb=" CG  ASP A 528 "
           pdb=" OD1 ASP A 528 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.32   54.32     1      2.00e+01 2.50e-03 1.00e+01
  dihedral pdb=" CA  ASP A 620 "
           pdb=" CB  ASP A 620 "
           pdb=" CG  ASP A 620 "
           pdb=" OD1 ASP A 620 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.03   54.03     1      2.00e+01 2.50e-03 9.90e+00
  dihedral pdb=" CG  ARG B 996 "
           pdb=" CD  ARG B 996 "
           pdb=" NE  ARG B 996 "
           pdb=" CZ  ARG B 996 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.49  -42.49     2      1.50e+01 4.44e-03 9.73e+00
  ... (remaining 4966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1217
       0.113 -    0.226: 26
       0.226 -    0.338: 1
       0.338 -    0.451: 0
       0.451 -    0.564: 1
  Chirality restraints: 1245
  Sorted by residual:
  chirality pdb=" C1  NAG A 801 "
            pdb=" ND2 ASN A 498 "
            pdb=" C2  NAG A 801 "
            pdb=" O5  NAG A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.84   -0.56 2.00e-01 2.50e+01 7.94e+00
  chirality pdb=" C1  NAG A 802 "
            pdb=" ND2 ASN A 548 "
            pdb=" C2  NAG A 802 "
            pdb=" O5  NAG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.38   -0.02 2.00e-02 2.50e+03 1.53e+00
  ... (remaining 1242 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 440 "   -0.070 5.00e-02 4.00e+02   1.06e-01 1.78e+01
        pdb=" N   PRO A 441 "    0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO A 441 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 441 "   -0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 342 "   -0.071 5.00e-02 4.00e+02   9.80e-02 1.54e+01
        pdb=" N   PRO A 343 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO A 343 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 343 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 343 "    0.013 2.00e-02 2.50e+03   2.54e-02 6.44e+00
        pdb=" C   PRO A 343 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   PRO A 343 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER A 344 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 223
        2.71 -     3.26: 8033
        3.26 -     3.80: 13167
        3.80 -     4.35: 16905
        4.35 -     4.90: 28823
  Nonbonded interactions: 67151
  Sorted by model distance:
  nonbonded pdb=" O   GLY B1129 "
            pdb=" OG  SER B1207 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" O   PRO A 355 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OH  TYR B 934 "
            pdb=" O   GLU B 939 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NH2 ARG B 903 "
            pdb=" OH  TYR B 905 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OG1 THR B1195 "
            pdb=" O   ILE B1205 "
     model   vdw
     2.263 3.040
  ... (remaining 67146 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.940
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
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      :  0.008   0.471   8386  Z= 0.545
  Angle     :  0.987  73.852  11339  Z= 0.450
  Chirality :  0.047   0.564   1245
  Planarity :  0.005   0.106   1428
  Dihedral  : 16.518  83.272   3103
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.11 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.27), residues: 1006
  helix:  1.90 (0.26), residues: 407
  sheet:  0.20 (0.33), residues: 243
  loop : -0.79 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 467 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.019   0.001   PHE A 342 
 TYR   0.016   0.001   TYR A 306 
 ARG   0.014   0.001   ARG B 903 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2523
  time to fit residues: 35.3385
Evaluate side-chains
  105 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 76 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0470
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0570
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 434 ASN
A 504 GLN
A 568 ASN
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 970 ASN
B 988 GLN
B1003 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.206212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.162281 restraints weight = 8994.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 2.33
r_work: 0.3655 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.0623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   8386  Z= 0.160
  Angle     :  0.472   5.893  11339  Z= 0.257
  Chirality :  0.043   0.418   1245
  Planarity :  0.003   0.062   1428
  Dihedral  :  5.591  52.919   1226
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.29 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.27), residues: 1006
  helix:  2.43 (0.26), residues: 412
  sheet:  0.21 (0.33), residues: 243
  loop : -0.69 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 467 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.010   0.001   PHE A 459 
 TYR   0.011   0.001   TYR A 306 
 ARG   0.002   0.000   ARG A 737 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: A  442 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7668 (mt-10)
REVERT: A  535 TYR cc_start: 0.8307 (t80) cc_final: 0.7953 (t80)
REVERT: B  903 ARG cc_start: 0.7439 (mmm160) cc_final: 0.7083 (mmm160)
REVERT: B 1058 ASP cc_start: 0.7412 (m-30) cc_final: 0.7096 (m-30)
  outliers start: 17
  outliers final: 8
  residues processed: 118
  average time/residue: 0.2282
  time to fit residues: 36.7118
Evaluate side-chains
  113 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue  988 GLN
Chi-restraints excluded: chain B residue 1003 GLN
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN
A 354 GLN
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1003 GLN
B1022 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.200080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.156590 restraints weight = 9068.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 2.28
r_work: 0.3613 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8386  Z= 0.214
  Angle     :  0.482   5.336  11339  Z= 0.261
  Chirality :  0.043   0.341   1245
  Planarity :  0.003   0.043   1428
  Dihedral  :  5.439  53.189   1226
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.61 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.27), residues: 1006
  helix:  2.40 (0.26), residues: 413
  sheet:  0.20 (0.33), residues: 236
  loop : -0.74 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 467 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.011   0.001   PHE A 499 
 TYR   0.015   0.001   TYR A 306 
 ARG   0.002   0.000   ARG B1175 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6318 (mtt) cc_final: 0.5075 (ttm)
REVERT: A  442 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7700 (mt-10)
REVERT: A  523 SER cc_start: 0.8746 (m) cc_final: 0.8310 (p)
REVERT: B  903 ARG cc_start: 0.7521 (mmm160) cc_final: 0.7288 (mmm160)
REVERT: B  988 GLN cc_start: 0.7371 (tt0) cc_final: 0.7020 (tt0)
REVERT: B 1058 ASP cc_start: 0.7412 (m-30) cc_final: 0.7077 (m-30)
REVERT: B 1085 LYS cc_start: 0.7588 (tppp) cc_final: 0.7157 (tppt)
  outliers start: 23
  outliers final: 16
  residues processed: 128
  average time/residue: 0.2326
  time to fit residues: 40.0629
Evaluate side-chains
  119 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue  997 VAL
Chi-restraints excluded: chain B residue 1003 GLN
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 54 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0470
   chunk 90 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 988 GLN
B1003 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.203615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.159054 restraints weight = 9102.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 2.35
r_work: 0.3626 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8386  Z= 0.161
  Angle     :  0.455   7.676  11339  Z= 0.246
  Chirality :  0.042   0.314   1245
  Planarity :  0.003   0.035   1428
  Dihedral  :  5.045  47.600   1226
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.41 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.27), residues: 1006
  helix:  2.49 (0.26), residues: 411
  sheet:  0.20 (0.33), residues: 236
  loop : -0.72 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 467 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.010   0.001   PHE A 459 
 TYR   0.013   0.001   TYR A 306 
 ARG   0.004   0.000   ARG B1064 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6389 (mtt) cc_final: 0.5114 (ttm)
REVERT: A  442 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7729 (mt-10)
REVERT: A  523 SER cc_start: 0.8763 (m) cc_final: 0.8327 (p)
REVERT: A  742 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7215 (tm-30)
REVERT: B 1058 ASP cc_start: 0.7444 (m-30) cc_final: 0.7101 (m-30)
REVERT: B 1085 LYS cc_start: 0.7571 (tppp) cc_final: 0.7165 (tppt)
REVERT: B 1094 SER cc_start: 0.7987 (p) cc_final: 0.7600 (t)
  outliers start: 23
  outliers final: 15
  residues processed: 126
  average time/residue: 0.2204
  time to fit residues: 37.1724
Evaluate side-chains
  121 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1003 GLN
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 988 GLN
B1003 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.200276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155515 restraints weight = 9026.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 2.35
r_work: 0.3583 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8386  Z= 0.225
  Angle     :  0.482   7.108  11339  Z= 0.260
  Chirality :  0.043   0.305   1245
  Planarity :  0.003   0.030   1428
  Dihedral  :  5.009  46.919   1226
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.29 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.28), residues: 1006
  helix:  2.50 (0.26), residues: 410
  sheet:  0.18 (0.33), residues: 236
  loop : -0.70 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 467 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.012   0.001   PHE A 459 
 TYR   0.016   0.001   TYR A 306 
 ARG   0.003   0.000   ARG B 903 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6467 (mtt) cc_final: 0.5147 (ttm)
REVERT: A  442 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7778 (mt-10)
REVERT: A  471 MET cc_start: 0.7855 (tpp) cc_final: 0.7654 (tpt)
REVERT: A  523 SER cc_start: 0.8774 (m) cc_final: 0.8364 (p)
REVERT: A  608 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.7853 (t)
REVERT: B  903 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7538 (mmm160)
REVERT: B  910 ASP cc_start: 0.7915 (t0) cc_final: 0.7694 (t70)
REVERT: B 1058 ASP cc_start: 0.7448 (m-30) cc_final: 0.7111 (m-30)
REVERT: B 1085 LYS cc_start: 0.7566 (tppp) cc_final: 0.7144 (tppt)
REVERT: B 1094 SER cc_start: 0.8129 (p) cc_final: 0.7757 (t)
  outliers start: 29
  outliers final: 22
  residues processed: 131
  average time/residue: 0.2133
  time to fit residues: 38.2689
Evaluate side-chains
  127 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1003 GLN
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1226 LYS
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0770
   chunk 58 optimal weight:    0.0000
   chunk 81 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5342

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

Flipped N/Q/H residues before XYZ refinement:
B 960 ASN
** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1003 GLN
B1233 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.202356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.157516 restraints weight = 9028.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 2.25
r_work: 0.3613 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8386  Z= 0.155
  Angle     :  0.452   7.108  11339  Z= 0.245
  Chirality :  0.042   0.300   1245
  Planarity :  0.003   0.030   1428
  Dihedral  :  4.727  46.863   1226
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.75 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.28), residues: 1006
  helix:  2.48 (0.26), residues: 411
  sheet:  0.21 (0.33), residues: 236
  loop : -0.70 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.014   0.001   PHE A 499 
 TYR   0.012   0.001   TYR A 306 
 ARG   0.003   0.000   ARG B1064 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6471 (mtt) cc_final: 0.5018 (ttm)
REVERT: A  442 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7755 (mt-10)
REVERT: A  523 SER cc_start: 0.8734 (m) cc_final: 0.8342 (p)
REVERT: A  596 MET cc_start: 0.6360 (tpp) cc_final: 0.6149 (mmm)
REVERT: A  693 CYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8042 (t)
REVERT: B  903 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7572 (mmm160)
REVERT: B 1058 ASP cc_start: 0.7392 (m-30) cc_final: 0.7043 (m-30)
REVERT: B 1085 LYS cc_start: 0.7497 (tppp) cc_final: 0.7070 (tppt)
  outliers start: 25
  outliers final: 17
  residues processed: 124
  average time/residue: 0.2170
  time to fit residues: 36.7105
Evaluate side-chains
  120 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue  997 VAL
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1226 LYS
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0070
   chunk 78 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 77 optimal weight:    0.4980
   chunk 90 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.200939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155967 restraints weight = 8952.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.25
r_work: 0.3612 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8386  Z= 0.154
  Angle     :  0.446   7.161  11339  Z= 0.241
  Chirality :  0.042   0.289   1245
  Planarity :  0.003   0.030   1428
  Dihedral  :  4.563  45.663   1226
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.66 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.27), residues: 1006
  helix:  2.53 (0.26), residues: 410
  sheet:  0.25 (0.34), residues: 231
  loop : -0.73 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 467 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.011   0.001   PHE A 499 
 TYR   0.012   0.001   TYR A 306 
 ARG   0.006   0.000   ARG A 163 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: A  442 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7784 (mt-10)
REVERT: A  523 SER cc_start: 0.8735 (m) cc_final: 0.8333 (p)
REVERT: A  693 CYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8110 (t)
REVERT: B  903 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7545 (mmm160)
REVERT: B 1058 ASP cc_start: 0.7383 (m-30) cc_final: 0.7030 (m-30)
REVERT: B 1064 ARG cc_start: 0.6986 (mtt180) cc_final: 0.6351 (ttt180)
REVERT: B 1085 LYS cc_start: 0.7597 (tppp) cc_final: 0.7314 (tppt)
REVERT: B 1087 LEU cc_start: 0.7029 (tp) cc_final: 0.6802 (tp)
REVERT: B 1094 SER cc_start: 0.8147 (p) cc_final: 0.7783 (t)
  outliers start: 23
  outliers final: 19
  residues processed: 125
  average time/residue: 0.1970
  time to fit residues: 34.2565
Evaluate side-chains
  126 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.197821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.152853 restraints weight = 9177.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.36
r_work: 0.3551 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8386  Z= 0.253
  Angle     :  0.506   7.197  11339  Z= 0.272
  Chirality :  0.044   0.295   1245
  Planarity :  0.003   0.028   1428
  Dihedral  :  4.959  44.349   1226
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.09 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.27), residues: 1006
  helix:  2.38 (0.26), residues: 410
  sheet:  0.18 (0.34), residues: 211
  loop : -0.71 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 333 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.013   0.001   PHE A 459 
 TYR   0.018   0.001   TYR A 306 
 ARG   0.003   0.000   ARG A 491 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6427 (mtt) cc_final: 0.4946 (ttm)
REVERT: A  442 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7824 (mt-10)
REVERT: A  449 MET cc_start: 0.6784 (mtp) cc_final: 0.6538 (mtp)
REVERT: A  523 SER cc_start: 0.8767 (m) cc_final: 0.8342 (p)
REVERT: A  693 CYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8110 (t)
REVERT: B 1058 ASP cc_start: 0.7466 (m-30) cc_final: 0.7110 (m-30)
REVERT: B 1064 ARG cc_start: 0.7001 (mtt180) cc_final: 0.6395 (ttt180)
REVERT: B 1077 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6589 (mttp)
REVERT: B 1085 LYS cc_start: 0.7594 (tppp) cc_final: 0.7308 (tppt)
  outliers start: 28
  outliers final: 24
  residues processed: 124
  average time/residue: 0.2617
  time to fit residues: 44.9842
Evaluate side-chains
  128 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  247 PHE
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue  997 VAL
Chi-restraints excluded: chain B residue 1077 LYS
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1226 LYS
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 61 optimal weight:    6.9990
   chunk 99 optimal weight:    5.9990
   chunk 83 optimal weight:    0.4980
   chunk 91 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 18 optimal weight:    0.3980
   chunk 65 optimal weight:    7.9990
   overall best weight:    0.6182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.199814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.155280 restraints weight = 9041.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.26
r_work: 0.3587 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8386  Z= 0.163
  Angle     :  0.467   7.007  11339  Z= 0.252
  Chirality :  0.042   0.279   1245
  Planarity :  0.003   0.031   1428
  Dihedral  :  4.606  44.358   1226
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 18.77 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.27), residues: 1006
  helix:  2.45 (0.26), residues: 410
  sheet:  0.23 (0.35), residues: 211
  loop : -0.74 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.012   0.001   PHE A 499 
 TYR   0.012   0.001   TYR A 306 
 ARG   0.003   0.000   ARG B 903 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LYS cc_start: 0.6843 (tmtt) cc_final: 0.6044 (ttmm)
REVERT: A  442 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7810 (mt-10)
REVERT: A  449 MET cc_start: 0.6654 (mtp) cc_final: 0.6426 (mtp)
REVERT: A  523 SER cc_start: 0.8744 (m) cc_final: 0.8308 (p)
REVERT: A  693 CYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8104 (t)
REVERT: B 1058 ASP cc_start: 0.7451 (m-30) cc_final: 0.7078 (m-30)
REVERT: B 1064 ARG cc_start: 0.7002 (mtt180) cc_final: 0.6481 (ttt180)
REVERT: B 1077 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6511 (mttp)
REVERT: B 1085 LYS cc_start: 0.7612 (tppp) cc_final: 0.7338 (tppt)
REVERT: B 1245 ASN cc_start: 0.7762 (m-40) cc_final: 0.7105 (t0)
  outliers start: 25
  outliers final: 21
  residues processed: 129
  average time/residue: 0.2107
  time to fit residues: 37.7948
Evaluate side-chains
  130 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1077 LYS
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1164 LYS
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1226 LYS
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.197439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.152260 restraints weight = 8915.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 2.30
r_work: 0.3554 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8386  Z= 0.192
  Angle     :  0.483   6.828  11339  Z= 0.261
  Chirality :  0.043   0.276   1245
  Planarity :  0.003   0.029   1428
  Dihedral  :  4.619  43.244   1226
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.57 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.27), residues: 1006
  helix:  2.39 (0.26), residues: 411
  sheet:  0.23 (0.35), residues: 208
  loop : -0.73 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 333 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.012   0.001   PHE A 499 
 TYR   0.015   0.001   TYR A 306 
 ARG   0.002   0.000   ARG A 491 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6400 (mtt) cc_final: 0.6175 (mtt)
REVERT: A  375 LYS cc_start: 0.6843 (tmtt) cc_final: 0.6021 (ttmm)
REVERT: A  442 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7824 (mt-10)
REVERT: A  449 MET cc_start: 0.6630 (mtp) cc_final: 0.6402 (mtp)
REVERT: A  523 SER cc_start: 0.8739 (m) cc_final: 0.8303 (p)
REVERT: A  693 CYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8096 (t)
REVERT: B 1058 ASP cc_start: 0.7429 (m-30) cc_final: 0.7053 (m-30)
REVERT: B 1077 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6517 (mttp)
REVERT: B 1087 LEU cc_start: 0.6990 (tp) cc_final: 0.6785 (tp)
REVERT: B 1245 ASN cc_start: 0.7768 (m-40) cc_final: 0.7109 (t0)
  outliers start: 23
  outliers final: 21
  residues processed: 123
  average time/residue: 0.2088
  time to fit residues: 35.3132
Evaluate side-chains
  127 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  693 CYS
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  954 SER
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue  997 VAL
Chi-restraints excluded: chain B residue 1077 LYS
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1164 LYS
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1226 LYS
Chi-restraints excluded: chain B residue 1270 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 56 optimal weight:    0.4980
   chunk 85 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.198397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.154064 restraints weight = 9021.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.22
r_work: 0.3555 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8386  Z= 0.199
  Angle     :  0.489   6.841  11339  Z= 0.264
  Chirality :  0.043   0.268   1245
  Planarity :  0.003   0.038   1428
  Dihedral  :  4.667  42.947   1226
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.45 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.27), residues: 1006
  helix:  2.38 (0.26), residues: 411
  sheet:  0.22 (0.35), residues: 208
  loop : -0.73 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 333 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.013   0.001   PHE A 499 
 TYR   0.015   0.001   TYR A 306 
 ARG   0.003   0.000   ARG B1064 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4259.42 seconds
wall clock time: 75 minutes 7.91 seconds (4507.91 seconds total)