Starting phenix.real_space_refine
on Sun Jun 15 05:26:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bwm_30233/06_2025/7bwm_30233.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bwm_30233/06_2025/7bwm_30233.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bwm_30233/06_2025/7bwm_30233.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bwm_30233/06_2025/7bwm_30233.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bwm_30233/06_2025/7bwm_30233.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bwm_30233/06_2025/7bwm_30233.cif"
  }
  resolution = 2.9
  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=   0.001 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9352 atoms to isotropic.
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       8      5.16       5
     C    5997      2.51       5
     N    1674      2.21       5
     O    1853      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-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9532
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9532
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1219, 9473
          Classifications: {'peptide': 1219}
          Link IDs: {'PCIS': 2, 'PTRANS': 75, 'TRANS': 1141}
          Chain breaks: 12
      Conformer: "B"
        Number of residues, atoms: 1219, 9473
          Classifications: {'peptide': 1219}
          Link IDs: {'PCIS': 2, 'PTRANS': 75, 'TRANS': 1141}
          Chain breaks: 12
          bond proxies already assigned to first conformer: 9640
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  AARG A 385 " occ=0.70
      ... (20 atoms not shown)
      pdb=" NH2BARG A 385 " occ=0.30
    residue:
      pdb=" N  AASN A 911 " occ=0.50
      ... (14 atoms not shown)
      pdb=" ND2BASN A 911 " occ=0.50
    residue:
      pdb=" N  ATRP A1025 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP A1025 " occ=0.50
    residue:
      pdb=" N  AGLN A1188 " occ=0.70
      ... (16 atoms not shown)
      pdb=" NE2BGLN A1188 " occ=0.30
    residue:
      pdb=" N  AASP A1257 " occ=0.50
      ... (14 atoms not shown)
      pdb=" OD2BASP A1257 " occ=0.50
    residue:
      pdb=" N  AGLU A1371 " occ=0.70
      ... (16 atoms not shown)
      pdb=" OE2BGLU A1371 " occ=0.30
  Time building chain proxies: 9.97, per 1000 atoms: 1.05
  Number of scatterers: 9532
  At special positions: 0
  Unit cell: (80.04, 100.05, 120.06, 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       8     16.00
     O    1853      8.00
     N    1674      7.00
     C    5997      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: 2.18
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2258

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 15 sheets defined
      25.6% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 112 through 124
    Processing helix  chain 'A' and resid 176 through 181
      removed outlier: 3.619A  pdb=" N   VAL A 180 " --> pdb=" O   GLN A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 209
      removed outlier: 3.835A  pdb=" N   VAL A 208 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 209'
    Processing helix  chain 'A' and resid 210 through 213
    Processing helix  chain 'A' and resid 248 through 254
      removed outlier: 3.607A  pdb=" N   SER A 251 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   ASN A 252 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LYS A 254 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 312
      No H-bonds generated for 'chain 'A' and resid 310 through 312'
    Processing helix  chain 'A' and resid 328 through 333
      removed outlier: 3.744A  pdb=" N   PHE A 332 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 365
      removed outlier: 3.556A  pdb=" N   ILE A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 395 through 401
      removed outlier: 3.899A  pdb=" N   MET A 399 " --> pdb=" O   ASP A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.777A  pdb=" N   THR A 409 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 426
      removed outlier: 4.105A  pdb=" N   ASP A 419 " --> pdb=" O   HIS A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 442
      removed outlier: 3.821A  pdb=" N   TRP A 441 " --> pdb=" O   HIS A 438 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE A 442 " --> pdb=" O   PRO A 439 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 438 through 442'
    Processing helix  chain 'A' and resid 483 through 490
    Processing helix  chain 'A' and resid 542 through 546
    Processing helix  chain 'A' and resid 607 through 610
      removed outlier: 3.572A  pdb=" N   SER A 610 " --> pdb=" O   GLU A 607 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 607 through 610'
    Processing helix  chain 'A' and resid 611 through 619
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 3.894A  pdb=" N   GLY A 633 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TRP A 634 " --> pdb=" O   PRO A 631 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 630 through 634'
    Processing helix  chain 'A' and resid 641 through 645
    Processing helix  chain 'A' and resid 662 through 666
      removed outlier: 3.772A  pdb=" N   GLN A 666 " --> pdb=" O   PRO A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 678
    Processing helix  chain 'A' and resid 701 through 710
    Processing helix  chain 'A' and resid 739 through 744
    Processing helix  chain 'A' and resid 753 through 757
      removed outlier: 3.511A  pdb=" N   ASN A 756 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU A 757 " --> pdb=" O   LYS A 754 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 753 through 757'
    Processing helix  chain 'A' and resid 761 through 767
      removed outlier: 3.676A  pdb=" N   ARG A 765 " --> pdb=" O   ASN A 761 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE A 766 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN A 767 " --> pdb=" O   TYR A 763 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 761 through 767'
    Processing helix  chain 'A' and resid 779 through 785
      removed outlier: 3.932A  pdb=" N   PHE A 783 " --> pdb=" O   TRP A 780 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   SER A 784 " --> pdb=" O   SER A 781 " (cutoff:3.500A)
      Proline residue:  A 785  - end of helix
    Processing helix  chain 'A' and resid 797 through 808
      removed outlier: 3.624A  pdb=" N   ASP A 802 " --> pdb=" O   GLY A 798 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLN A 803 " --> pdb=" O   SER A 799 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL A 804 " --> pdb=" O   VAL A 800 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASP A 806 " --> pdb=" O   ASP A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 826
      removed outlier: 3.557A  pdb=" N   ASP A 826 " --> pdb=" O   GLY A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 919
    Processing helix  chain 'A' and resid 981 through 985
      removed outlier: 3.524A  pdb=" N   PHE A 984 " --> pdb=" O   ALA A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 1002
      removed outlier: 3.929A  pdb=" N   GLN A 994 " --> pdb=" O   ALA A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1023
      removed outlier: 3.605A  pdb=" N   GLN A1023 " --> pdb=" O   ALA A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1031
    Processing helix  chain 'A' and resid 1049 through 1059
    Processing helix  chain 'A' and resid 1067 through 1071
      removed outlier: 4.354A  pdb=" N   THR A1071 " --> pdb=" O   SER A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1154
    Processing helix  chain 'A' and resid 1179 through 1187
    Processing helix  chain 'A' and resid 1195 through 1201
    Processing helix  chain 'A' and resid 1218 through 1223
      removed outlier: 3.580A  pdb=" N   LYS A1223 " --> pdb=" O   SER A1220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1255 through 1260
    Processing helix  chain 'A' and resid 1263 through 1275
      removed outlier: 3.780A  pdb=" N   VAL A1267 " --> pdb=" O   ASP A1263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1302 through 1307
      removed outlier: 3.534A  pdb=" N   SER A1307 " --> pdb=" O   SER A1303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1326 through 1338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68
    Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68
      removed outlier: 3.574A  pdb=" N   VAL A  92 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU A 128 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   ASP A 140 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ARG A 130 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 191
      removed outlier: 6.577A  pdb=" N   LEU A 201 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   VAL A 188 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ALA A 199 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   GLN A 190 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   ARG A 197 " --> pdb=" O   GLN A 190 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   TYR A 196 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ARG A 390 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   TYR A 377 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
      removed outlier: 5.609A  pdb=" N   ILE A 388 " --> pdb=" O   TYR A 377 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 246
    Processing sheet with id=AA6, first strand: chain 'A' and resid 257 through 259
      removed outlier: 5.857A  pdb=" N   ALA A 286 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 257 through 259
      removed outlier: 5.857A  pdb=" N   ALA A 286 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 319 through 320
      removed outlier: 3.681A  pdb=" N   GLN A 323 " --> pdb=" O   GLU A 320 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 497
    Processing sheet with id=AB1, first strand: chain 'A' and resid 574 through 582
      removed outlier: 5.110A  pdb=" N   VAL A 576 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   THR A 591 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLY A 578 " --> pdb=" O   ALA A 589 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LEU A 586 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ARG A 789 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 862 through 863
    Processing sheet with id=AB3, first strand: chain 'A' and resid 913 through 914
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1006 through 1008
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1107 through 1109
      removed outlier: 8.658A  pdb=" N   GLY A1367 " --> pdb=" O   LEU A1137 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   LEU A1139 " --> pdb=" O   GLY A1367 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1162 through 1167
      removed outlier: 5.466A  pdb=" N   VAL A1176 " --> pdb=" O   ARG A1163 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   SER A1165 " --> pdb=" O   GLU A1174 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   GLU A1174 " --> pdb=" O   SER A1165 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   SER A1287 " --> pdb=" O   MET A1377 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    567 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.70

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3173
        1.34 -     1.46: 1638
        1.46 -     1.57: 4947
        1.57 -     1.69: 0
        1.69 -     1.80: 16
  Bond restraints: 9774
  Sorted by residual:
  bond pdb=" C   PHE A 850 "
       pdb=" N   LEU A 851 "
    ideal  model  delta    sigma   weight residual
    1.329  1.270  0.059 1.86e-02 2.89e+03 1.01e+01
  bond pdb=" C   PHE A 722 "
       pdb=" N   VAL A 723 "
    ideal  model  delta    sigma   weight residual
    1.329  1.301  0.028 1.31e-02 5.83e+03 4.42e+00
  bond pdb=" C   SER A 784 "
       pdb=" N   PRO A 785 "
    ideal  model  delta    sigma   weight residual
    1.334  1.351 -0.017 8.40e-03 1.42e+04 4.27e+00
  bond pdb=" CA  SER A 799 "
       pdb=" C   SER A 799 "
    ideal  model  delta    sigma   weight residual
    1.523  1.500  0.023 1.35e-02 5.49e+03 2.99e+00
  bond pdb=" N   HIS A 653 "
       pdb=" CA  HIS A 653 "
    ideal  model  delta    sigma   weight residual
    1.456  1.476 -0.020 1.25e-02 6.40e+03 2.65e+00
  ... (remaining 9769 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 13020
        2.16 -     4.32: 269
        4.32 -     6.49: 31
        6.49 -     8.65: 8
        8.65 -    10.81: 3
  Bond angle restraints: 13331
  Sorted by residual:
  angle pdb=" N   VAL A1363 "
        pdb=" CA  VAL A1363 "
        pdb=" C   VAL A1363 "
      ideal   model   delta    sigma   weight residual
     113.71  107.50    6.21 9.50e-01 1.11e+00 4.27e+01
  angle pdb=" C   THR A 950 "
        pdb=" CA  THR A 950 "
        pdb=" CB  THR A 950 "
      ideal   model   delta    sigma   weight residual
     109.83  105.02    4.81 9.90e-01 1.02e+00 2.36e+01
  angle pdb=" C   SER A 948 "
        pdb=" N   LEU A 949 "
        pdb=" CA  LEU A 949 "
      ideal   model   delta    sigma   weight residual
     121.54  130.73   -9.19 1.91e+00 2.74e-01 2.32e+01
  angle pdb=" N   THR A 950 "
        pdb=" CA  THR A 950 "
        pdb=" C   THR A 950 "
      ideal   model   delta    sigma   weight residual
     113.51  120.67   -7.16 1.52e+00 4.33e-01 2.22e+01
  angle pdb=" C   ASP A 667 "
        pdb=" N   ARG A 668 "
        pdb=" CA  ARG A 668 "
      ideal   model   delta    sigma   weight residual
     122.21  111.72   10.49 2.87e+00 1.21e-01 1.34e+01
  ... (remaining 13326 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.57: 5373
       19.57 -    39.14: 287
       39.14 -    58.71: 92
       58.71 -    78.29: 15
       78.29 -    97.86: 6
  Dihedral angle restraints: 5773
    sinusoidal: 2261
      harmonic: 3512
  Sorted by residual:
  dihedral pdb=" CA  GLN A1282 "
           pdb=" C   GLN A1282 "
           pdb=" N   PRO A1283 "
           pdb=" CA  PRO A1283 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   34.48  -34.48     0      5.00e+00 4.00e-02 4.76e+01
  dihedral pdb=" CA  THR A 951 "
           pdb=" C   THR A 951 "
           pdb=" N   GLN A 952 "
           pdb=" CA  GLN A 952 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.58   33.42     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  THR A 950 "
           pdb=" C   THR A 950 "
           pdb=" N   THR A 951 "
           pdb=" CA  THR A 951 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.25   30.75     0      5.00e+00 4.00e-02 3.78e+01
  ... (remaining 5770 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1005
       0.043 -    0.086: 324
       0.086 -    0.128: 108
       0.128 -    0.171: 6
       0.171 -    0.214: 3
  Chirality restraints: 1446
  Sorted by residual:
  chirality pdb=" CA  GLN A 960 "
            pdb=" N   GLN A 960 "
            pdb=" C   GLN A 960 "
            pdb=" CB  GLN A 960 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  THR A 950 "
            pdb=" N   THR A 950 "
            pdb=" C   THR A 950 "
            pdb=" CB  THR A 950 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  PRO A1283 "
            pdb=" N   PRO A1283 "
            pdb=" C   PRO A1283 "
            pdb=" CB  PRO A1283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.02e-01
  ... (remaining 1443 not shown)

  Planarity restraints: 1761
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 973 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.83e+00
        pdb=" N   PRO A 974 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 974 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 974 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1099 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.68e+00
        pdb=" N   PRO A1100 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A1100 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1100 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 478 "    0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO A 479 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 479 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 479 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1758 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 139
        2.62 -     3.19: 8094
        3.19 -     3.76: 14707
        3.76 -     4.33: 22272
        4.33 -     4.90: 35629
  Nonbonded interactions: 80841
  Sorted by model distance:
  nonbonded pdb=" O   THR A 950 "
            pdb=" OG1 THR A 951 "
     model   vdw
     2.048 3.040
  nonbonded pdb=" OH  TYR A 139 "
            pdb=" OD1 ASP A 378 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" O   LEU A1271 "
            pdb=" OG  SER A1274 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" O   LEU A 120 "
            pdb=" OG1 THR A 124 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OD1 ASP A 142 "
            pdb=" OG  SER A 144 "
     model   vdw
     2.193 3.040
  ... (remaining 80836 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     31.190
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.070
  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:13.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   46.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
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   0.059   9774  Z= 0.233
  Angle     :  0.784  10.810  13331  Z= 0.467
  Chirality :  0.046   0.214   1446
  Planarity :  0.005   0.042   1761
  Dihedral  : 14.238  97.857   3515
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.78 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  7.21 %
    Allowed  :  7.12 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.30 %
    Twisted General : 0.18 %

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: -3.28 (0.20), residues: 1211
  helix: -2.75 (0.26), residues: 213
  sheet: -1.23 (0.36), residues: 169
  loop : -2.38 (0.18), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 496 
 HIS   0.003   0.001   HIS A 414 
 PHE   0.009   0.001   PHE A 488 
 TYR   0.013   0.002   TYR A 696 
 ARG   0.003   0.001   ARG A1157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21892 (  220)
  hydrogen bonds       : angle       8.68831 (  567)
  covalent geometry    : bond        0.00500 ( 9774)
  covalent geometry    : angle       0.78437 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 118
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7638 (mp)
REVERT: A  287 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8750 (mp)
REVERT: A  293 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8068 (pttp)
REVERT: A  309 ASP cc_start: 0.7783 (m-30) cc_final: 0.7557 (m-30)
REVERT: A  323 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5932 (pm20)
REVERT: A  513 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8287 (m)
REVERT: A  914 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7813 (mptt)
REVERT: A  960 GLN cc_start: 0.5955 (OUTLIER) cc_final: 0.5614 (pm20)
  outliers start: 74
  outliers final: 23
  residues processed: 183
  average time/residue: 1.1460
  time to fit residues: 225.4041
Evaluate side-chains
  106 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 76
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  293 LYS
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  803 GLN
Chi-restraints excluded: chain A residue  820 ASN
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  907 GLN
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue  944 LYS
Chi-restraints excluded: chain A residue  960 GLN
Chi-restraints excluded: chain A residue  972 LEU
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1148 THR
Chi-restraints excluded: chain A residue 1255 ASP
Chi-restraints excluded: chain A residue 1256 ASP
Chi-restraints excluded: chain A residue 1288 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0470
   overall best weight:    0.8082

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 323 GLN
A 469 GLN
A 490 ASN
A 661 ASN
A 685 ASN
A 716 GLN
A1192 GLN
A1279 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.163263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.129017 restraints weight = 44314.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 7.21
r_work: 0.3005 rms_B_bonded: 7.15 restraints_weight: 2.0000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2995
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2995
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9774  Z= 0.122
  Angle     :  0.619  10.211  13331  Z= 0.318
  Chirality :  0.044   0.222   1446
  Planarity :  0.004   0.048   1761
  Dihedral  :  8.898  79.715   1370
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.20 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 13.16 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.30 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.21), residues: 1211
  helix: -1.52 (0.31), residues: 218
  sheet: -0.60 (0.38), residues: 159
  loop : -1.67 (0.19), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 418 
 HIS   0.002   0.001   HIS A 912 
 PHE   0.019   0.001   PHE A 126 
 TYR   0.008   0.001   TYR A1042 
 ARG   0.011   0.001   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  220)
  hydrogen bonds       : angle       6.18224 (  567)
  covalent geometry    : bond        0.00272 ( 9774)
  covalent geometry    : angle       0.61902 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 86
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7736 (mp)
REVERT: A  287 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8897 (mp)
REVERT: A  293 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8325 (pttm)
REVERT: A  309 ASP cc_start: 0.7986 (m-30) cc_final: 0.7712 (m-30)
REVERT: A  323 GLN cc_start: 0.6079 (OUTLIER) cc_final: 0.5830 (pm20)
REVERT: A  465 LYS cc_start: 0.7859 (mttt) cc_final: 0.7576 (mmtm)
REVERT: A  513 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8309 (m)
REVERT: A  687 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7503 (tppt)
REVERT: A  914 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8044 (mmtm)
REVERT: A  960 GLN cc_start: 0.6016 (OUTLIER) cc_final: 0.5700 (pm20)
REVERT: A 1256 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7465 (t0)
REVERT: A 1366 VAL cc_start: 0.8368 (t) cc_final: 0.7672 (p)
  outliers start: 44
  outliers final: 17
  residues processed: 121
  average time/residue: 1.2420
  time to fit residues: 162.0881
Evaluate side-chains
  102 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  293 LYS
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  490 ASN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  513 SER
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  907 GLN
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue  944 LYS
Chi-restraints excluded: chain A residue  960 GLN
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1148 THR
Chi-restraints excluded: chain A residue 1255 ASP
Chi-restraints excluded: chain A residue 1256 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 93 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 490 ASN
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.161226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.124874 restraints weight = 52303.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 8.66
r_work: 0.2989 rms_B_bonded: 6.91 restraints_weight: 2.0000
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9774  Z= 0.175
  Angle     :  0.642  10.572  13331  Z= 0.326
  Chirality :  0.046   0.229   1446
  Planarity :  0.004   0.034   1761
  Dihedral  :  8.216  85.301   1355
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.70 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 14.33 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.30 %
    Twisted General : 0.18 %

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: -1.78 (0.22), residues: 1211
  helix: -1.08 (0.33), residues: 217
  sheet: -0.37 (0.40), residues: 157
  loop : -1.44 (0.20), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1098 
 HIS   0.003   0.001   HIS A1241 
 PHE   0.018   0.001   PHE A1115 
 TYR   0.011   0.001   TYR A 696 
 ARG   0.004   0.001   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03921 (  220)
  hydrogen bonds       : angle       6.00297 (  567)
  covalent geometry    : bond        0.00417 ( 9774)
  covalent geometry    : angle       0.64156 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 77
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7747 (mp)
REVERT: A  247 ASP cc_start: 0.7509 (t0) cc_final: 0.7084 (p0)
REVERT: A  287 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8965 (mp)
REVERT: A  293 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8285 (pttm)
REVERT: A  309 ASP cc_start: 0.7968 (m-30) cc_final: 0.7687 (m-30)
REVERT: A  323 GLN cc_start: 0.6071 (OUTLIER) cc_final: 0.5810 (pm20)
REVERT: A  687 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7402 (mppt)
REVERT: A  862 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8571 (tmtt)
REVERT: A  914 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8014 (mptt)
REVERT: A  960 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5810 (pm20)
REVERT: A 1253 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7365 (ptmm)
REVERT: A 1255 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6371 (p0)
REVERT: A 1256 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7318 (t0)
REVERT: A 1377 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.5144 (mtp)
  outliers start: 41
  outliers final: 15
  residues processed: 111
  average time/residue: 1.6005
  time to fit residues: 191.2229
Evaluate side-chains
  100 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  293 LYS
Chi-restraints excluded: chain A residue  323 GLN
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  862 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue  944 LYS
Chi-restraints excluded: chain A residue  960 GLN
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1148 THR
Chi-restraints excluded: chain A residue 1253 LYS
Chi-restraints excluded: chain A residue 1255 ASP
Chi-restraints excluded: chain A residue 1256 ASP
Chi-restraints excluded: chain A residue 1377 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 490 ASN
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.163478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.127626 restraints weight = 36133.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 6.47
r_work: 0.3063 rms_B_bonded: 6.13 restraints_weight: 2.0000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9774  Z= 0.112
  Angle     :  0.585   9.606  13331  Z= 0.297
  Chirality :  0.044   0.217   1446
  Planarity :  0.004   0.034   1761
  Dihedral  :  7.746  85.072   1350
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.11 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.79 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.30 %
    Twisted General : 0.18 %

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: -1.46 (0.22), residues: 1211
  helix: -0.78 (0.34), residues: 223
  sheet: -0.14 (0.41), residues: 156
  loop : -1.24 (0.20), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 418 
 HIS   0.002   0.000   HIS A 414 
 PHE   0.015   0.001   PHE A1115 
 TYR   0.008   0.001   TYR A1042 
 ARG   0.007   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03037 (  220)
  hydrogen bonds       : angle       5.72505 (  567)
  covalent geometry    : bond        0.00257 ( 9774)
  covalent geometry    : angle       0.58461 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 75
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8030 (mppt) cc_final: 0.7486 (tmtt)
REVERT: A  146 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7823 (mp)
REVERT: A  247 ASP cc_start: 0.7409 (t0) cc_final: 0.6931 (p0)
REVERT: A  292 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7300 (mtmp)
REVERT: A  293 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8403 (pptt)
REVERT: A  309 ASP cc_start: 0.7868 (m-30) cc_final: 0.7498 (m-30)
REVERT: A  465 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7365 (mtpp)
REVERT: A  687 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7420 (mppt)
REVERT: A  914 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8026 (mptt)
REVERT: A 1256 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7285 (t0)
  outliers start: 33
  outliers final: 13
  residues processed: 101
  average time/residue: 1.2317
  time to fit residues: 134.6647
Evaluate side-chains
  96 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  293 LYS
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1148 THR
Chi-restraints excluded: chain A residue 1255 ASP
Chi-restraints excluded: chain A residue 1256 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 120 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 ASN
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.160993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.126636 restraints weight = 49628.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 8.11
r_work: 0.2966 rms_B_bonded: 7.24 restraints_weight: 2.0000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2939
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9774  Z= 0.185
  Angle     :  0.659  11.214  13331  Z= 0.336
  Chirality :  0.047   0.222   1446
  Planarity :  0.004   0.038   1761
  Dihedral  :  6.970  54.278   1337
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.78 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.08 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.47 (0.22), residues: 1211
  helix: -0.75 (0.34), residues: 222
  sheet: -0.23 (0.40), residues: 158
  loop : -1.25 (0.20), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1098 
 HIS   0.003   0.001   HIS A1241 
 PHE   0.016   0.002   PHE A1115 
 TYR   0.012   0.001   TYR A 696 
 ARG   0.010   0.001   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03834 (  220)
  hydrogen bonds       : angle       5.80526 (  567)
  covalent geometry    : bond        0.00443 ( 9774)
  covalent geometry    : angle       0.65936 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 76
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7858 (mp)
REVERT: A  247 ASP cc_start: 0.7555 (t0) cc_final: 0.7022 (p0)
REVERT: A  309 ASP cc_start: 0.8041 (m-30) cc_final: 0.7621 (m-30)
REVERT: A  671 GLN cc_start: 0.7375 (tp40) cc_final: 0.7173 (tp40)
REVERT: A  687 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7329 (mppt)
REVERT: A  776 GLN cc_start: 0.7315 (tp-100) cc_final: 0.7011 (tp40)
REVERT: A  862 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8523 (tmtt)
REVERT: A  914 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7991 (mptt)
  outliers start: 31
  outliers final: 16
  residues processed: 100
  average time/residue: 1.2505
  time to fit residues: 134.2192
Evaluate side-chains
  95 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  862 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1148 THR
Chi-restraints excluded: chain A residue 1255 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 94 optimal weight:    0.0980
   chunk 46 optimal weight:    0.1980
   chunk 99 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 115 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 ASN
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.161135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123854 restraints weight = 40663.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 7.24
r_work: 0.3003 rms_B_bonded: 6.51 restraints_weight: 2.0000
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9774  Z= 0.180
  Angle     :  0.646  10.295  13331  Z= 0.330
  Chirality :  0.046   0.220   1446
  Planarity :  0.004   0.038   1761
  Dihedral  :  6.926  54.031   1331
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.89 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.48 (0.22), residues: 1211
  helix: -0.70 (0.34), residues: 222
  sheet: -0.27 (0.40), residues: 158
  loop : -1.27 (0.20), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1098 
 HIS   0.003   0.001   HIS A 414 
 PHE   0.015   0.001   PHE A1115 
 TYR   0.011   0.001   TYR A 696 
 ARG   0.007   0.001   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  220)
  hydrogen bonds       : angle       5.77596 (  567)
  covalent geometry    : bond        0.00433 ( 9774)
  covalent geometry    : angle       0.64632 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 76
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A   98 LYS cc_start: 0.8103 (mppt) cc_final: 0.7507 (tmtt)
REVERT: A  146 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7886 (mp)
REVERT: A  164 PHE cc_start: 0.7946 (m-80) cc_final: 0.7662 (m-80)
REVERT: A  247 ASP cc_start: 0.7557 (t0) cc_final: 0.7039 (p0)
REVERT: A  309 ASP cc_start: 0.7979 (m-30) cc_final: 0.7558 (m-30)
REVERT: A  675 ASP cc_start: 0.7965 (m-30) cc_final: 0.7724 (m-30)
REVERT: A  687 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7270 (mppt)
REVERT: A  776 GLN cc_start: 0.7318 (tp-100) cc_final: 0.6915 (tp40)
REVERT: A  862 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8540 (tmtt)
REVERT: A  914 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7972 (mptt)
REVERT: A 1253 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7515 (ptmm)
REVERT: A 1255 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6471 (p0)
  outliers start: 35
  outliers final: 21
  residues processed: 103
  average time/residue: 1.1237
  time to fit residues: 125.0563
Evaluate side-chains
  100 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  862 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1073 SER
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1148 THR
Chi-restraints excluded: chain A residue 1253 LYS
Chi-restraints excluded: chain A residue 1255 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0470
   chunk 44 optimal weight:    0.9990
   chunk 59 optimal weight:    8.9990
   chunk 119 optimal weight:    0.0000
   chunk 103 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0050
   chunk 82 optimal weight:    0.2980
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.2698

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

Flipped N/Q/H residues before XYZ refinement:
A 490 ASN
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.165253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.130455 restraints weight = 46059.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 7.48
r_work: 0.3052 rms_B_bonded: 7.04 restraints_weight: 2.0000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   9774  Z= 0.098
  Angle     :  0.572   9.902  13331  Z= 0.291
  Chirality :  0.042   0.196   1446
  Planarity :  0.004   0.044   1761
  Dihedral  :  6.355  55.314   1331
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.35 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    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: -1.17 (0.23), residues: 1211
  helix: -0.41 (0.35), residues: 228
  sheet: -0.02 (0.41), residues: 155
  loop : -1.07 (0.20), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 418 
 HIS   0.001   0.000   HIS A 414 
 PHE   0.017   0.001   PHE A 126 
 TYR   0.006   0.001   TYR A 658 
 ARG   0.011   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02700 (  220)
  hydrogen bonds       : angle       5.48485 (  567)
  covalent geometry    : bond        0.00217 ( 9774)
  covalent geometry    : angle       0.57152 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8017 (mppt) cc_final: 0.7347 (tptt)
REVERT: A  162 ASN cc_start: 0.7965 (t0) cc_final: 0.7693 (t0)
REVERT: A  164 PHE cc_start: 0.7956 (m-80) cc_final: 0.7680 (m-80)
REVERT: A  247 ASP cc_start: 0.7388 (t0) cc_final: 0.6816 (p0)
REVERT: A  292 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6988 (mptp)
REVERT: A  687 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7268 (mppt)
REVERT: A  776 GLN cc_start: 0.7362 (tp-100) cc_final: 0.6926 (tp40)
REVERT: A  914 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8063 (mptt)
REVERT: A 1146 ASP cc_start: 0.7989 (t70) cc_final: 0.7785 (t0)
  outliers start: 25
  outliers final: 15
  residues processed: 105
  average time/residue: 1.2129
  time to fit residues: 137.1562
Evaluate side-chains
  98 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  490 ASN
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue 1148 THR
Chi-restraints excluded: chain A residue 1255 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 25 optimal weight:    0.6980
   chunk 94 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 ASN
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.161812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.126482 restraints weight = 46047.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 7.06
r_work: 0.2987 rms_B_bonded: 6.99 restraints_weight: 2.0000
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9774  Z= 0.185
  Angle     :  0.639  11.246  13331  Z= 0.325
  Chirality :  0.046   0.191   1446
  Planarity :  0.004   0.054   1761
  Dihedral  :  6.388  54.744   1328
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.35 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    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: -1.22 (0.22), residues: 1211
  helix: -0.45 (0.35), residues: 222
  sheet: -0.05 (0.40), residues: 155
  loop : -1.11 (0.20), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1098 
 HIS   0.003   0.001   HIS A 414 
 PHE   0.020   0.002   PHE A1115 
 TYR   0.011   0.002   TYR A 696 
 ARG   0.013   0.001   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  220)
  hydrogen bonds       : angle       5.62605 (  567)
  covalent geometry    : bond        0.00447 ( 9774)
  covalent geometry    : angle       0.63876 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.8021 (mppt) cc_final: 0.7486 (tmtt)
REVERT: A  162 ASN cc_start: 0.7972 (t0) cc_final: 0.7654 (t0)
REVERT: A  164 PHE cc_start: 0.7975 (m-80) cc_final: 0.7668 (m-80)
REVERT: A  247 ASP cc_start: 0.7509 (t0) cc_final: 0.6931 (p0)
REVERT: A  292 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7080 (mptp)
REVERT: A  687 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7277 (mppt)
REVERT: A  776 GLN cc_start: 0.7401 (tp-100) cc_final: 0.6933 (tp40)
REVERT: A  914 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8003 (mptt)
  outliers start: 26
  outliers final: 17
  residues processed: 98
  average time/residue: 1.3531
  time to fit residues: 143.4360
Evaluate side-chains
  97 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue 1073 SER
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1148 THR
Chi-restraints excluded: chain A residue 1255 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 111 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0040
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 ASN
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.164570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.129092 restraints weight = 45890.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 7.15
r_work: 0.3025 rms_B_bonded: 6.93 restraints_weight: 2.0000
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9774  Z= 0.108
  Angle     :  0.581  10.528  13331  Z= 0.296
  Chirality :  0.043   0.189   1446
  Planarity :  0.004   0.051   1761
  Dihedral  :  6.132  55.562   1328
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.13 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    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: -1.09 (0.23), residues: 1211
  helix: -0.32 (0.35), residues: 223
  sheet: -0.03 (0.40), residues: 155
  loop : -1.00 (0.20), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 418 
 HIS   0.002   0.000   HIS A 414 
 PHE   0.018   0.001   PHE A1115 
 TYR   0.007   0.001   TYR A1239 
 ARG   0.011   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02971 (  220)
  hydrogen bonds       : angle       5.49463 (  567)
  covalent geometry    : bond        0.00251 ( 9774)
  covalent geometry    : angle       0.58118 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 1.065 
Fit side-chains
REVERT: A   98 LYS cc_start: 0.7971 (mppt) cc_final: 0.7469 (tmtt)
REVERT: A  136 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7905 (ttp-110)
REVERT: A  162 ASN cc_start: 0.7969 (t0) cc_final: 0.7717 (t0)
REVERT: A  164 PHE cc_start: 0.7966 (m-80) cc_final: 0.7688 (m-80)
REVERT: A  247 ASP cc_start: 0.7421 (t0) cc_final: 0.6825 (p0)
REVERT: A  292 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7046 (mptp)
REVERT: A  687 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7131 (mppt)
REVERT: A  914 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8072 (mmtm)
REVERT: A 1146 ASP cc_start: 0.8025 (t70) cc_final: 0.7816 (t0)
REVERT: A 1255 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.6218 (p0)
  outliers start: 20
  outliers final: 12
  residues processed: 94
  average time/residue: 1.2176
  time to fit residues: 123.8816
Evaluate side-chains
  94 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue 1255 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 26 optimal weight:    0.0370
   chunk 22 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 86 optimal weight:    0.1980
   chunk 92 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0030
   overall best weight:    0.3468

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

Flipped N/Q/H residues before XYZ refinement:
A 490 ASN
A 660 HIS
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.166945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.130580 restraints weight = 42972.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 7.18
r_work: 0.3100 rms_B_bonded: 6.46 restraints_weight: 2.0000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9774  Z= 0.095
  Angle     :  0.558   9.949  13331  Z= 0.283
  Chirality :  0.042   0.189   1446
  Planarity :  0.004   0.051   1761
  Dihedral  :  5.766  56.895   1326
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 19.01 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.23), residues: 1211
  helix: -0.05 (0.36), residues: 223
  sheet:  0.04 (0.40), residues: 155
  loop : -0.87 (0.21), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 418 
 HIS   0.001   0.000   HIS A 509 
 PHE   0.021   0.001   PHE A 126 
 TYR   0.006   0.001   TYR A 658 
 ARG   0.011   0.000   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02608 (  220)
  hydrogen bonds       : angle       5.30875 (  567)
  covalent geometry    : bond        0.00216 ( 9774)
  covalent geometry    : angle       0.55785 (13331)

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

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

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2422 Ramachandran restraints generated.
    1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A   65 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7480 (mmm160)
REVERT: A   98 LYS cc_start: 0.7912 (mppt) cc_final: 0.7351 (tptt)
REVERT: A  136 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7803 (ttm110)
REVERT: A  162 ASN cc_start: 0.7904 (t0) cc_final: 0.7688 (t0)
REVERT: A  164 PHE cc_start: 0.7954 (m-80) cc_final: 0.7667 (m-80)
REVERT: A  247 ASP cc_start: 0.7328 (t0) cc_final: 0.6616 (p0)
REVERT: A  292 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7145 (mmtt)
REVERT: A  490 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8456 (t0)
REVERT: A  776 GLN cc_start: 0.7352 (tp40) cc_final: 0.7091 (tp40)
REVERT: A  914 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8069 (mmtm)
REVERT: A 1255 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.5864 (p0)
REVERT: A 1259 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8269 (mtmt)
  outliers start: 13
  outliers final: 8
  residues processed: 91
  average time/residue: 1.6076
  time to fit residues: 158.1160
Evaluate side-chains
  88 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  490 ASN
Chi-restraints excluded: chain A residue  914 LYS
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1255 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0980
   chunk 8 optimal weight:    7.9990
   overall best weight:    2.2188

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 490 ASN
** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.162312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.127735 restraints weight = 46218.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 7.27
r_work: 0.2991 rms_B_bonded: 7.06 restraints_weight: 2.0000
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9774  Z= 0.187
  Angle     :  0.637  11.082  13331  Z= 0.323
  Chirality :  0.046   0.190   1446
  Planarity :  0.004   0.046   1761
  Dihedral  :  5.818  55.933   1319
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.81 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    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: -1.05 (0.23), residues: 1211
  helix: -0.21 (0.35), residues: 216
  sheet: -0.03 (0.39), residues: 155
  loop : -0.99 (0.20), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1098 
 HIS   0.003   0.001   HIS A 414 
 PHE   0.019   0.002   PHE A1115 
 TYR   0.011   0.002   TYR A 696 
 ARG   0.011   0.001   ARG A 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03657 (  220)
  hydrogen bonds       : angle       5.54259 (  567)
  covalent geometry    : bond        0.00448 ( 9774)
  covalent geometry    : angle       0.63720 (13331)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8086.20 seconds
wall clock time: 144 minutes 44.18 seconds (8684.18 seconds total)