Starting phenix.real_space_refine
on Sat Aug 23 00:09:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wyx_37940/08_2025/8wyx_37940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wyx_37940/08_2025/8wyx_37940.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wyx_37940/08_2025/8wyx_37940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wyx_37940/08_2025/8wyx_37940.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wyx_37940/08_2025/8wyx_37940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wyx_37940/08_2025/8wyx_37940.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      28      5.16       5
     C    5663      2.51       5
     N    1440      2.21       5
     O    1677      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8809
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1070, 8808
          Classifications: {'peptide': 1070}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 1043}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.96, per 1000 atoms: 0.22
  Number of scatterers: 8809
  At special positions: 0
  Unit cell: (96.264, 92.826, 91.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      28     16.00
     O    1677      8.00
     N    1440      7.00
     C    5663      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 270.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1201 "
        pdb="ZN    ZN A1201 " - pdb=" NE2 HIS A 129 "
        pdb="ZN    ZN A1201 " - pdb=" NE2 HIS A 133 "


  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2056

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 5 sheets defined
      57.4% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 64
      removed outlier: 4.295A  pdb=" N   GLU A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 135
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 177 through 194
    Processing helix  chain 'A' and resid 195 through 199
      removed outlier: 3.736A  pdb=" N   LEU A 198 " --> pdb=" O   PRO A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 208
      removed outlier: 3.869A  pdb=" N   PHE A 204 " --> pdb=" O   ASN A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 248
    Processing helix  chain 'A' and resid 250 through 264
    Processing helix  chain 'A' and resid 267 through 271
    Processing helix  chain 'A' and resid 276 through 281
      removed outlier: 4.025A  pdb=" N   THR A 281 " --> pdb=" O   PRO A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 296
    Processing helix  chain 'A' and resid 297 through 299
      No H-bonds generated for 'chain 'A' and resid 297 through 299'
    Processing helix  chain 'A' and resid 311 through 323
    Processing helix  chain 'A' and resid 324 through 325
      No H-bonds generated for 'chain 'A' and resid 324 through 325'
    Processing helix  chain 'A' and resid 326 through 330
      removed outlier: 4.036A  pdb=" N   LYS A 329 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 424
      removed outlier: 3.813A  pdb=" N   TYR A 413 " --> pdb=" O   ASN A 409 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE A 414 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 439
      removed outlier: 3.848A  pdb=" N   GLY A 439 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 497
      removed outlier: 3.501A  pdb=" N   GLU A 496 " --> pdb=" O   LYS A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 517
    Processing helix  chain 'A' and resid 523 through 536
    Processing helix  chain 'A' and resid 543 through 545
      No H-bonds generated for 'chain 'A' and resid 543 through 545'
    Processing helix  chain 'A' and resid 546 through 561
      removed outlier: 4.045A  pdb=" N   TYR A 550 " --> pdb=" O   GLU A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 573
    Processing helix  chain 'A' and resid 587 through 609
      removed outlier: 3.902A  pdb=" N   ALA A 591 " --> pdb=" O   ASP A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 629
    Processing helix  chain 'A' and resid 633 through 638
    Processing helix  chain 'A' and resid 644 through 648
    Processing helix  chain 'A' and resid 663 through 667
      removed outlier: 3.529A  pdb=" N   ASN A 667 " --> pdb=" O   ILE A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 679
      removed outlier: 3.923A  pdb=" N   THR A 679 " --> pdb=" O   ASN A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 696
    Processing helix  chain 'A' and resid 752 through 758
    Processing helix  chain 'A' and resid 758 through 768
      removed outlier: 4.178A  pdb=" N   LEU A 767 " --> pdb=" O   LYS A 763 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLU A 768 " --> pdb=" O   THR A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 787
    Processing helix  chain 'A' and resid 825 through 838
    Processing helix  chain 'A' and resid 844 through 875
      removed outlier: 3.584A  pdb=" N   GLY A 867 " --> pdb=" O   PHE A 863 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   TYR A 868 " --> pdb=" O   SER A 864 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   ALA A 869 " --> pdb=" O   GLU A 865 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   ILE A 870 " --> pdb=" O   LYS A 866 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LYS A 873 " --> pdb=" O   ALA A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 891
    Processing helix  chain 'A' and resid 891 through 908
    Processing helix  chain 'A' and resid 908 through 924
      removed outlier: 4.132A  pdb=" N   LEU A 912 " --> pdb=" O   ASP A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 927
      No H-bonds generated for 'chain 'A' and resid 925 through 927'
    Processing helix  chain 'A' and resid 936 through 947
      removed outlier: 3.557A  pdb=" N   LEU A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS A 941 " --> pdb=" O   TYR A 937 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   HIS A 942 " --> pdb=" O   GLY A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 947 through 962
    Processing helix  chain 'A' and resid 979 through 988
    Processing helix  chain 'A' and resid 1024 through 1037
      removed outlier: 3.827A  pdb=" N   VAL A1028 " --> pdb=" O   PRO A1024 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1042
    Processing helix  chain 'A' and resid 1071 through 1080
    Processing helix  chain 'A' and resid 1080 through 1092
    Processing helix  chain 'A' and resid 1093 through 1109
    Processing helix  chain 'A' and resid 1114 through 1128
    Processing helix  chain 'A' and resid 1130 through 1143
    Processing helix  chain 'A' and resid 1145 through 1159
    Processing helix  chain 'A' and resid 1160 through 1164
    Processing helix  chain 'A' and resid 1173 through 1183
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 79
      removed outlier: 5.619A  pdb=" N   ILE A  73 " --> pdb=" O   GLN A  90 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   GLN A  90 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLU A  75 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN A  97 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   SER A 307 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   THR A 103 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ARG A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   THR A 164 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   VAL A 170 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ALA A 162 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   MET A 172 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   LEU A 160 " --> pdb=" O   MET A 172 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   GLY A 174 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 215
    Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 354
      removed outlier: 6.060A  pdb=" N   PHE A 348 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   LEU A 583 " --> pdb=" O   PHE A 348 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ILE A 350 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   GLU A 585 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LYS A 352 " --> pdb=" O   GLU A 585 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   ASN A 363 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY A 464 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE A 457 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   LEU A 449 " --> pdb=" O   ILE A 457 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   SER A 459 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ARG A 447 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 658 through 662
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1050 through 1055
      removed outlier: 3.623A  pdb=" N   VAL A1009 " --> pdb=" O   SER A1065 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ASN A1166 " --> pdb=" O   SER A1012 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LYS A 997 " --> pdb=" O   LYS A1188 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   VAL A1190 " --> pdb=" O   LYS A 997 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   PHE A 999 " --> pdb=" O   VAL A1190 " (cutoff:3.500A)

    502 hydrogen bonds defined for protein.
    1446 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: 1.48

  Time building geometry restraints manager: 1.02 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: 2810
        1.34 -     1.45: 1198
        1.45 -     1.57: 4922
        1.57 -     1.69: 1
        1.69 -     1.80: 54
  Bond restraints: 8985
  Sorted by residual:
  bond pdb=" CB  ASN A 267 "
       pdb=" CG  ASN A 267 "
    ideal  model  delta    sigma   weight residual
    1.516  1.485  0.031 2.50e-02 1.60e+03 1.51e+00
  bond pdb=" CG  PRO A 347 "
       pdb=" CD  PRO A 347 "
    ideal  model  delta    sigma   weight residual
    1.512  1.479  0.033 2.70e-02 1.37e+03 1.51e+00
  bond pdb=" CG  GLU A 622 "
       pdb=" CD  GLU A 622 "
    ideal  model  delta    sigma   weight residual
    1.516  1.486  0.030 2.50e-02 1.60e+03 1.40e+00
  bond pdb=" SD  MET A 263 "
       pdb=" CE  MET A 263 "
    ideal  model  delta    sigma   weight residual
    1.791  1.762  0.029 2.50e-02 1.60e+03 1.38e+00
  bond pdb=" CA  ASN A 669 "
       pdb=" CB  ASN A 669 "
    ideal  model  delta    sigma   weight residual
    1.539  1.593 -0.054 4.88e-02 4.20e+02 1.21e+00
  ... (remaining 8980 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 11798
        1.53 -     3.05: 264
        3.05 -     4.58: 32
        4.58 -     6.11: 4
        6.11 -     7.64: 2
  Bond angle restraints: 12100
  Sorted by residual:
  angle pdb=" N   GLU A 622 "
        pdb=" CA  GLU A 622 "
        pdb=" CB  GLU A 622 "
      ideal   model   delta    sigma   weight residual
     110.16  114.31   -4.15 1.48e+00 4.57e-01 7.88e+00
  angle pdb=" C   PHE A 621 "
        pdb=" N   GLU A 622 "
        pdb=" CA  GLU A 622 "
      ideal   model   delta    sigma   weight residual
     120.29  116.87    3.42 1.42e+00 4.96e-01 5.79e+00
  angle pdb=" N   GLY A 154 "
        pdb=" CA  GLY A 154 "
        pdb=" C   GLY A 154 "
      ideal   model   delta    sigma   weight residual
     113.18  118.51   -5.33 2.37e+00 1.78e-01 5.06e+00
  angle pdb=" CA  LEU A1002 "
        pdb=" CB  LEU A1002 "
        pdb=" CG  LEU A1002 "
      ideal   model   delta    sigma   weight residual
     116.30  123.94   -7.64 3.50e+00 8.16e-02 4.76e+00
  angle pdb=" N   GLY A1114 "
        pdb=" CA  GLY A1114 "
        pdb=" C   GLY A1114 "
      ideal   model   delta    sigma   weight residual
     110.77  114.93   -4.16 1.93e+00 2.68e-01 4.64e+00
  ... (remaining 12095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.61: 4841
       16.61 -    33.21: 517
       33.21 -    49.82: 89
       49.82 -    66.42: 8
       66.42 -    83.03: 6
  Dihedral angle restraints: 5461
    sinusoidal: 2278
      harmonic: 3183
  Sorted by residual:
  dihedral pdb=" CA  HIS A 750 "
           pdb=" C   HIS A 750 "
           pdb=" N   LEU A 751 "
           pdb=" CA  LEU A 751 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.50   21.50     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  ILE A 424 "
           pdb=" C   ILE A 424 "
           pdb=" N   HIS A 425 "
           pdb=" CA  HIS A 425 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.49  -20.51     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  LEU A1002 "
           pdb=" C   LEU A1002 "
           pdb=" N   PRO A1003 "
           pdb=" CA  PRO A1003 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.84   18.16     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 5458 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 748
       0.032 -    0.064: 398
       0.064 -    0.096: 118
       0.096 -    0.128: 51
       0.128 -    0.159: 8
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" CA  GLU A 622 "
            pdb=" N   GLU A 622 "
            pdb=" C   GLU A 622 "
            pdb=" CB  GLU A 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  THR A 737 "
            pdb=" N   THR A 737 "
            pdb=" C   THR A 737 "
            pdb=" CB  THR A 737 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  ILE A 445 "
            pdb=" N   ILE A 445 "
            pdb=" C   ILE A 445 "
            pdb=" CB  ILE A 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.78e-01
  ... (remaining 1320 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1068 "   -0.029 5.00e-02 4.00e+02   4.34e-02 3.02e+00
        pdb=" N   PRO A1069 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A1069 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1069 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 297 "    0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 298 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 298 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 298 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 488 "   -0.007 2.00e-02 2.50e+03   1.36e-02 1.84e+00
        pdb=" C   ASN A 488 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ASN A 488 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ALA A 489 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 89
        2.60 -     3.18: 7753
        3.18 -     3.75: 13794
        3.75 -     4.33: 19973
        4.33 -     4.90: 32676
  Nonbonded interactions: 74285
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 243 "
            pdb="ZN    ZN A1201 "
     model   vdw
     2.029 2.230
  nonbonded pdb=" O   LEU A 151 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" OH  TYR A 413 "
            pdb=" OD2 ASP A 451 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OG  SER A 139 "
            pdb=" OD2 ASP A 190 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OH  TYR A 241 "
            pdb=" OE2 GLU A 598 "
     model   vdw
     2.206 3.040
  ... (remaining 74280 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6217
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      :  0.007   0.283   8987  Z= 0.267
  Angle     :  0.568   7.636  12100  Z= 0.322
  Chirality :  0.044   0.159   1323
  Planarity :  0.004   0.043   1544
  Dihedral  : 13.609  83.031   3405
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.30 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.25), residues: 1062
  helix:  0.90 (0.22), residues: 528
  sheet: -0.77 (0.35), residues: 197
  loop : -0.93 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 605 
 TYR   0.020   0.002   TYR A 660 
 PHE   0.018   0.002   PHE A 621 
 TRP   0.014   0.001   TRP A 369 
 HIS   0.006   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 8985)
  covalent geometry    : angle       0.56759 (12100)
  hydrogen bonds       : bond        0.13979 (  502)
  hydrogen bonds       : angle       6.51372 ( 1446)
  metal coordination   : bond        0.25504 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 250
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 GLU cc_start: 0.7411 (tt0) cc_final: 0.6875 (tp30)
REVERT: A  446 ASP cc_start: 0.8058 (p0) cc_final: 0.7649 (p0)
REVERT: A  695 TYR cc_start: 0.5042 (m-80) cc_final: 0.4153 (m-80)
REVERT: A  784 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8266 (mt-10)
REVERT: A  790 MET cc_start: 0.6218 (ttt) cc_final: 0.5763 (ttt)
REVERT: A  991 ASP cc_start: 0.4559 (m-30) cc_final: 0.3840 (t0)
REVERT: A 1012 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7673 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 252
  average time/residue: 0.0956
  time to fit residues: 32.4737
Evaluate side-chains
  154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1012 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    7.9990
   chunk 38 optimal weight:   20.0000
   overall best weight:    5.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  90 GLN
A  97 GLN
A 166 ASN
A 177 ASN
A 295 ASN
A 572 HIS
A 726 ASN
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 899 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.116225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.096157 restraints weight = 23132.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.099132 restraints weight = 12135.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.101135 restraints weight = 7870.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.102483 restraints weight = 5872.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.103306 restraints weight = 4765.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.3683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   8987  Z= 0.253
  Angle     :  0.730  12.713  12100  Z= 0.386
  Chirality :  0.046   0.167   1323
  Planarity :  0.005   0.058   1544
  Dihedral  :  5.123  48.446   1152
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.55 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.25), residues: 1062
  helix:  0.87 (0.21), residues: 540
  sheet: -0.78 (0.37), residues: 196
  loop : -0.82 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1112 
 TYR   0.026   0.003   TYR A1150 
 PHE   0.023   0.003   PHE A 165 
 TRP   0.016   0.003   TRP A 369 
 HIS   0.007   0.002   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 8985)
  covalent geometry    : angle       0.72994 (12100)
  hydrogen bonds       : bond        0.04923 (  502)
  hydrogen bonds       : angle       5.36146 ( 1446)
  metal coordination   : bond        0.01422 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 THR cc_start: 0.8486 (m) cc_final: 0.8226 (p)
REVERT: A  309 ASN cc_start: 0.7983 (m-40) cc_final: 0.7575 (m110)
REVERT: A  501 SER cc_start: 0.8649 (m) cc_final: 0.8414 (p)
REVERT: A  563 MET cc_start: 0.8603 (mmm) cc_final: 0.8379 (mmm)
REVERT: A  683 MET cc_start: 0.7998 (tpp) cc_final: 0.7760 (tpp)
REVERT: A  691 PHE cc_start: 0.8795 (t80) cc_final: 0.8379 (t80)
REVERT: A  872 MET cc_start: 0.8437 (tmm) cc_final: 0.7938 (tmm)
REVERT: A  920 ARG cc_start: 0.8602 (tmm-80) cc_final: 0.8368 (ttp-110)
REVERT: A  991 ASP cc_start: 0.6059 (m-30) cc_final: 0.5092 (t0)
REVERT: A 1011 MET cc_start: 0.6670 (ttp) cc_final: 0.6271 (ppp)
REVERT: A 1063 PHE cc_start: 0.8330 (m-80) cc_final: 0.8092 (m-80)
REVERT: A 1075 LEU cc_start: 0.7810 (tp) cc_final: 0.7567 (pp)
REVERT: A 1113 ARG cc_start: 0.5239 (OUTLIER) cc_final: 0.4927 (ptt-90)
  outliers start: 24
  outliers final: 16
  residues processed: 173
  average time/residue: 0.0887
  time to fit residues: 21.5419
Evaluate side-chains
  143 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  272 ASN
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  526 ASP
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  745 VAL
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  766 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1043 ARG
Chi-restraints excluded: chain A residue 1113 ARG
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain A residue 1172 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   chunk 95 optimal weight:    7.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 578 HIS
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.117553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.097381 restraints weight = 22692.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.100486 restraints weight = 11615.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.102539 restraints weight = 7484.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.103939 restraints weight = 5529.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.104766 restraints weight = 4472.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8987  Z= 0.150
  Angle     :  0.590   7.839  12100  Z= 0.316
  Chirality :  0.043   0.190   1323
  Planarity :  0.004   0.041   1544
  Dihedral  :  4.831  45.911   1152
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.98 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.26), residues: 1062
  helix:  1.15 (0.21), residues: 540
  sheet: -0.76 (0.37), residues: 196
  loop : -0.76 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1043 
 TYR   0.037   0.002   TYR A1150 
 PHE   0.022   0.002   PHE A 661 
 TRP   0.026   0.003   TRP A1039 
 HIS   0.021   0.001   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8985)
  covalent geometry    : angle       0.59011 (12100)
  hydrogen bonds       : bond        0.04033 (  502)
  hydrogen bonds       : angle       5.02314 ( 1446)
  metal coordination   : bond        0.00143 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ASN cc_start: 0.8052 (m-40) cc_final: 0.7691 (m110)
REVERT: A  314 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7081 (tp)
REVERT: A  369 TRP cc_start: 0.6978 (m-90) cc_final: 0.6273 (m-90)
REVERT: A  372 ASN cc_start: 0.6981 (p0) cc_final: 0.6707 (p0)
REVERT: A  432 TYR cc_start: 0.7774 (t80) cc_final: 0.7560 (t80)
REVERT: A  460 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8808 (mm)
REVERT: A  487 MET cc_start: 0.8442 (mmm) cc_final: 0.8082 (mmm)
REVERT: A  501 SER cc_start: 0.8603 (m) cc_final: 0.8354 (p)
REVERT: A  636 HIS cc_start: 0.8047 (t-170) cc_final: 0.7757 (t-170)
REVERT: A  683 MET cc_start: 0.7998 (tpp) cc_final: 0.7790 (tpp)
REVERT: A  685 LYS cc_start: 0.9355 (mttt) cc_final: 0.9127 (mtmm)
REVERT: A  872 MET cc_start: 0.8340 (tmm) cc_final: 0.7794 (tmm)
REVERT: A  961 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7452 (t0)
REVERT: A  991 ASP cc_start: 0.6337 (m-30) cc_final: 0.5353 (t0)
REVERT: A 1011 MET cc_start: 0.6521 (ttp) cc_final: 0.6220 (ppp)
REVERT: A 1029 ILE cc_start: 0.8492 (mt) cc_final: 0.8263 (mp)
REVERT: A 1063 PHE cc_start: 0.8302 (m-80) cc_final: 0.7995 (m-80)
  outliers start: 25
  outliers final: 12
  residues processed: 155
  average time/residue: 0.0776
  time to fit residues: 17.1834
Evaluate side-chains
  138 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  272 ASN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  961 ASN
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1071 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.116515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.096359 restraints weight = 23319.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.099458 restraints weight = 11869.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.101464 restraints weight = 7632.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.102814 restraints weight = 5649.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.103728 restraints weight = 4595.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6631
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8987  Z= 0.147
  Angle     :  0.589   9.099  12100  Z= 0.313
  Chirality :  0.043   0.179   1323
  Planarity :  0.004   0.040   1544
  Dihedral  :  4.648  38.841   1152
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.31 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.26), residues: 1062
  helix:  1.13 (0.21), residues: 544
  sheet: -0.80 (0.37), residues: 196
  loop : -0.74 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 920 
 TYR   0.032   0.002   TYR A1150 
 PHE   0.021   0.002   PHE A 691 
 TRP   0.014   0.002   TRP A1039 
 HIS   0.020   0.001   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8985)
  covalent geometry    : angle       0.58894 (12100)
  hydrogen bonds       : bond        0.03842 (  502)
  hydrogen bonds       : angle       4.90953 ( 1446)
  metal coordination   : bond        0.00118 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ASN cc_start: 0.8049 (m-40) cc_final: 0.7419 (m110)
REVERT: A  372 ASN cc_start: 0.7028 (p0) cc_final: 0.6798 (p0)
REVERT: A  432 TYR cc_start: 0.7873 (t80) cc_final: 0.7664 (t80)
REVERT: A  501 SER cc_start: 0.8589 (m) cc_final: 0.8316 (p)
REVERT: A  616 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8686 (tm-30)
REVERT: A  636 HIS cc_start: 0.8232 (t-170) cc_final: 0.8004 (t-170)
REVERT: A  674 TYR cc_start: 0.2981 (OUTLIER) cc_final: 0.2681 (t80)
REVERT: A  683 MET cc_start: 0.8075 (tpp) cc_final: 0.7841 (tpp)
REVERT: A  685 LYS cc_start: 0.9407 (mttt) cc_final: 0.9206 (mtmm)
REVERT: A  872 MET cc_start: 0.8359 (tmm) cc_final: 0.7777 (tmm)
REVERT: A  920 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (ptt90)
REVERT: A  961 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7128 (t0)
REVERT: A  991 ASP cc_start: 0.6492 (m-30) cc_final: 0.5580 (t0)
REVERT: A 1029 ILE cc_start: 0.8517 (mt) cc_final: 0.8227 (mp)
REVERT: A 1063 PHE cc_start: 0.8344 (m-80) cc_final: 0.7892 (m-80)
REVERT: A 1067 ARG cc_start: 0.7917 (mmp80) cc_final: 0.7642 (mmp80)
REVERT: A 1163 PHE cc_start: 0.7528 (m-80) cc_final: 0.7269 (m-80)
  outliers start: 22
  outliers final: 10
  residues processed: 159
  average time/residue: 0.0691
  time to fit residues: 15.7607
Evaluate side-chains
  136 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  272 ASN
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  674 TYR
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  961 ASN
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1071 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 0 optimal weight:   30.0000
   chunk 49 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 8 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 194 GLN
** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 925 ASN
A 928 ASN
A 961 ASN
A1103 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.114924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.095110 restraints weight = 22915.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.098129 restraints weight = 11975.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.100078 restraints weight = 7759.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.101447 restraints weight = 5770.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.102227 restraints weight = 4679.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6674
moved from start:          0.5073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8987  Z= 0.154
  Angle     :  0.619  13.991  12100  Z= 0.318
  Chirality :  0.043   0.269   1323
  Planarity :  0.004   0.040   1544
  Dihedral  :  4.496  14.822   1151
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.81 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.26), residues: 1062
  helix:  1.10 (0.21), residues: 545
  sheet: -0.96 (0.36), residues: 194
  loop : -0.82 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1112 
 TYR   0.028   0.002   TYR A1150 
 PHE   0.012   0.002   PHE A 909 
 TRP   0.030   0.002   TRP A1039 
 HIS   0.016   0.001   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8985)
  covalent geometry    : angle       0.61946 (12100)
  hydrogen bonds       : bond        0.03803 (  502)
  hydrogen bonds       : angle       4.92613 ( 1446)
  metal coordination   : bond        0.00127 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ASN cc_start: 0.8043 (m-40) cc_final: 0.7361 (m110)
REVERT: A  372 ASN cc_start: 0.7075 (p0) cc_final: 0.6797 (p0)
REVERT: A  487 MET cc_start: 0.8367 (mmm) cc_final: 0.8014 (mmm)
REVERT: A  501 SER cc_start: 0.8601 (m) cc_final: 0.8308 (p)
REVERT: A  588 GLU cc_start: 0.2834 (OUTLIER) cc_final: 0.2539 (pm20)
REVERT: A  616 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8790 (tm-30)
REVERT: A  636 HIS cc_start: 0.8265 (t-170) cc_final: 0.8030 (t-170)
REVERT: A  674 TYR cc_start: 0.2922 (OUTLIER) cc_final: 0.2619 (t80)
REVERT: A  683 MET cc_start: 0.8143 (tpp) cc_final: 0.7849 (tpp)
REVERT: A  685 LYS cc_start: 0.9382 (mttt) cc_final: 0.9175 (mtmm)
REVERT: A  872 MET cc_start: 0.8288 (tmm) cc_final: 0.7730 (tmm)
REVERT: A  961 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7301 (t0)
REVERT: A 1006 VAL cc_start: 0.4864 (OUTLIER) cc_final: 0.4550 (m)
REVERT: A 1029 ILE cc_start: 0.8478 (mt) cc_final: 0.8160 (mp)
REVERT: A 1067 ARG cc_start: 0.7902 (mmp80) cc_final: 0.7366 (mmp80)
REVERT: A 1088 MET cc_start: 0.8292 (ttt) cc_final: 0.8087 (ttt)
  outliers start: 31
  outliers final: 18
  residues processed: 151
  average time/residue: 0.0786
  time to fit residues: 16.8560
Evaluate side-chains
  139 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  272 ASN
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  588 GLU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  674 TYR
Chi-restraints excluded: chain A residue  745 VAL
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  863 PHE
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  961 ASN
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1071 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 9 optimal weight:    0.0270
   chunk 4 optimal weight:   20.0000
   chunk 18 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 78 optimal weight:   20.0000
   overall best weight:    2.3644

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.115405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.095572 restraints weight = 23173.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.098584 restraints weight = 11978.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.100568 restraints weight = 7744.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.101950 restraints weight = 5740.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.102846 restraints weight = 4637.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.5314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8987  Z= 0.135
  Angle     :  0.596  11.878  12100  Z= 0.306
  Chirality :  0.042   0.168   1323
  Planarity :  0.004   0.042   1544
  Dihedral  :  4.406  14.645   1151
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.33 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.26), residues: 1062
  helix:  1.19 (0.21), residues: 545
  sheet: -0.91 (0.37), residues: 184
  loop : -0.85 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1112 
 TYR   0.033   0.002   TYR A 674 
 PHE   0.016   0.001   PHE A1163 
 TRP   0.021   0.002   TRP A1039 
 HIS   0.017   0.001   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8985)
  covalent geometry    : angle       0.59615 (12100)
  hydrogen bonds       : bond        0.03625 (  502)
  hydrogen bonds       : angle       4.82482 ( 1446)
  metal coordination   : bond        0.00103 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LYS cc_start: 0.6761 (mttt) cc_final: 0.6415 (pttt)
REVERT: A  309 ASN cc_start: 0.8077 (m-40) cc_final: 0.7355 (m110)
REVERT: A  501 SER cc_start: 0.8605 (m) cc_final: 0.8322 (p)
REVERT: A  588 GLU cc_start: 0.3007 (OUTLIER) cc_final: 0.2617 (pm20)
REVERT: A  616 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8840 (tm-30)
REVERT: A  636 HIS cc_start: 0.8275 (t-170) cc_final: 0.8069 (t-170)
REVERT: A  683 MET cc_start: 0.8127 (tpp) cc_final: 0.7846 (tpp)
REVERT: A  872 MET cc_start: 0.8300 (tmm) cc_final: 0.7717 (tmm)
REVERT: A  961 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7293 (t0)
REVERT: A 1006 VAL cc_start: 0.4892 (OUTLIER) cc_final: 0.4600 (m)
REVERT: A 1029 ILE cc_start: 0.8497 (mt) cc_final: 0.8168 (mp)
REVERT: A 1067 ARG cc_start: 0.7854 (mmp80) cc_final: 0.7352 (mmp80)
  outliers start: 24
  outliers final: 17
  residues processed: 149
  average time/residue: 0.0779
  time to fit residues: 16.4599
Evaluate side-chains
  141 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  272 ASN
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  588 GLU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  745 VAL
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  863 PHE
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  961 ASN
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1071 LEU
Chi-restraints excluded: chain A residue 1103 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 94 optimal weight:    7.9990
   chunk 73 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    4.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.113574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.093822 restraints weight = 23342.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.096809 restraints weight = 12194.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.098783 restraints weight = 7896.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.100092 restraints weight = 5854.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.100895 restraints weight = 4759.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6727
moved from start:          0.5626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   8987  Z= 0.178
  Angle     :  0.646  12.931  12100  Z= 0.334
  Chirality :  0.044   0.171   1323
  Planarity :  0.004   0.041   1544
  Dihedral  :  4.522  15.290   1151
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.33 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.26), residues: 1062
  helix:  0.96 (0.21), residues: 550
  sheet: -0.98 (0.36), residues: 185
  loop : -0.92 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1112 
 TYR   0.036   0.002   TYR A1150 
 PHE   0.014   0.002   PHE A1163 
 TRP   0.018   0.002   TRP A1039 
 HIS   0.018   0.002   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 8985)
  covalent geometry    : angle       0.64590 (12100)
  hydrogen bonds       : bond        0.03877 (  502)
  hydrogen bonds       : angle       4.92955 ( 1446)
  metal coordination   : bond        0.00189 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.4480 (tpt) cc_final: 0.4259 (tpt)
REVERT: A  230 LYS cc_start: 0.6651 (mttt) cc_final: 0.6442 (pttt)
REVERT: A  501 SER cc_start: 0.8627 (m) cc_final: 0.8307 (p)
REVERT: A  616 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8884 (tm-30)
REVERT: A  636 HIS cc_start: 0.8349 (t-170) cc_final: 0.8125 (t-170)
REVERT: A  683 MET cc_start: 0.8087 (tpp) cc_final: 0.7819 (tpp)
REVERT: A  872 MET cc_start: 0.8302 (tmm) cc_final: 0.7883 (ppp)
REVERT: A  920 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8476 (ptt90)
REVERT: A  961 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7194 (t0)
REVERT: A 1006 VAL cc_start: 0.4980 (OUTLIER) cc_final: 0.4568 (m)
REVERT: A 1007 ASN cc_start: 0.7750 (m-40) cc_final: 0.7176 (t0)
REVERT: A 1029 ILE cc_start: 0.8466 (mt) cc_final: 0.8141 (mp)
REVERT: A 1067 ARG cc_start: 0.7834 (mmp80) cc_final: 0.7428 (mmp80)
  outliers start: 34
  outliers final: 21
  residues processed: 158
  average time/residue: 0.0747
  time to fit residues: 16.5206
Evaluate side-chains
  145 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  272 ASN
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  650 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  745 VAL
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  863 PHE
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  961 ASN
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1071 LEU
Chi-restraints excluded: chain A residue 1103 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 88 optimal weight:    0.2980
   chunk 61 optimal weight:    0.2980
   chunk 97 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.112670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.093278 restraints weight = 23252.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.096222 restraints weight = 12043.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.098149 restraints weight = 7755.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.099462 restraints weight = 5734.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.100221 restraints weight = 4639.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   8987  Z= 0.164
  Angle     :  0.640  11.676  12100  Z= 0.331
  Chirality :  0.044   0.247   1323
  Planarity :  0.004   0.044   1544
  Dihedral  :  4.535  15.230   1151
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.03 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.26), residues: 1062
  helix:  0.93 (0.21), residues: 550
  sheet: -1.02 (0.36), residues: 184
  loop : -0.91 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1112 
 TYR   0.032   0.002   TYR A 674 
 PHE   0.023   0.002   PHE A1187 
 TRP   0.018   0.002   TRP A1039 
 HIS   0.015   0.002   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8985)
  covalent geometry    : angle       0.64016 (12100)
  hydrogen bonds       : bond        0.03792 (  502)
  hydrogen bonds       : angle       4.92008 ( 1446)
  metal coordination   : bond        0.00134 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.4625 (tpt) cc_final: 0.4392 (tpt)
REVERT: A  230 LYS cc_start: 0.6709 (mttt) cc_final: 0.6484 (pttt)
REVERT: A  487 MET cc_start: 0.8344 (mmm) cc_final: 0.7961 (mmm)
REVERT: A  501 SER cc_start: 0.8638 (m) cc_final: 0.8308 (p)
REVERT: A  526 ASP cc_start: 0.8050 (m-30) cc_final: 0.7841 (m-30)
REVERT: A  616 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8869 (tm-30)
REVERT: A  683 MET cc_start: 0.8108 (tpp) cc_final: 0.7859 (tpp)
REVERT: A  872 MET cc_start: 0.8302 (tmm) cc_final: 0.7877 (ppp)
REVERT: A  920 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8493 (ptt90)
REVERT: A  936 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7250 (t70)
REVERT: A  961 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7243 (t0)
REVERT: A  978 MET cc_start: 0.4700 (ppp) cc_final: 0.4203 (ppp)
REVERT: A 1006 VAL cc_start: 0.5130 (OUTLIER) cc_final: 0.4800 (m)
REVERT: A 1029 ILE cc_start: 0.8468 (mt) cc_final: 0.8143 (mp)
REVERT: A 1067 ARG cc_start: 0.7741 (mmp80) cc_final: 0.7360 (mmp80)
REVERT: A 1088 MET cc_start: 0.8114 (ttt) cc_final: 0.7846 (ttt)
  outliers start: 33
  outliers final: 26
  residues processed: 152
  average time/residue: 0.0695
  time to fit residues: 15.0134
Evaluate side-chains
  149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  272 ASN
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  650 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  745 VAL
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  787 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  863 PHE
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  961 ASN
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1071 LEU
Chi-restraints excluded: chain A residue 1103 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 6 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 103 optimal weight:    4.9990
   chunk 43 optimal weight:   20.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.109255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.089841 restraints weight = 23631.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.092609 restraints weight = 12624.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.094493 restraints weight = 8324.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.095796 restraints weight = 6229.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.096610 restraints weight = 5070.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.6303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   8987  Z= 0.242
  Angle     :  0.722  14.316  12100  Z= 0.377
  Chirality :  0.046   0.257   1323
  Planarity :  0.004   0.045   1544
  Dihedral  :  4.889  15.822   1151
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.83 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.25), residues: 1062
  helix:  0.54 (0.21), residues: 553
  sheet: -1.12 (0.36), residues: 183
  loop : -1.19 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1112 
 TYR   0.038   0.003   TYR A 674 
 PHE   0.019   0.002   PHE A1187 
 TRP   0.020   0.002   TRP A1039 
 HIS   0.029   0.003   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 8985)
  covalent geometry    : angle       0.72241 (12100)
  hydrogen bonds       : bond        0.04361 (  502)
  hydrogen bonds       : angle       5.18818 ( 1446)
  metal coordination   : bond        0.00226 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6434 (mp0)
REVERT: A  230 LYS cc_start: 0.6934 (mttt) cc_final: 0.6605 (pttt)
REVERT: A  487 MET cc_start: 0.8315 (mmm) cc_final: 0.8043 (mmm)
REVERT: A  501 SER cc_start: 0.8731 (m) cc_final: 0.8363 (p)
REVERT: A  616 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8844 (tm-30)
REVERT: A  617 VAL cc_start: 0.9443 (t) cc_final: 0.9079 (t)
REVERT: A  683 MET cc_start: 0.8240 (tpp) cc_final: 0.7972 (tpp)
REVERT: A  684 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7897 (mp)
REVERT: A  872 MET cc_start: 0.8370 (tmm) cc_final: 0.8000 (ppp)
REVERT: A  920 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8440 (ptt90)
REVERT: A  978 MET cc_start: 0.4993 (ppp) cc_final: 0.4500 (ppp)
REVERT: A 1029 ILE cc_start: 0.8412 (mt) cc_final: 0.8122 (mp)
REVERT: A 1088 MET cc_start: 0.8179 (ttt) cc_final: 0.7963 (ttt)
  outliers start: 35
  outliers final: 26
  residues processed: 150
  average time/residue: 0.0771
  time to fit residues: 16.4673
Evaluate side-chains
  150 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 121
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  650 LYS
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  734 MET
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  745 VAL
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  787 ILE
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  863 PHE
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1071 LEU
Chi-restraints excluded: chain A residue 1103 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 104 optimal weight:    0.6980
   chunk 70 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0870
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.5564

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 750 HIS
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.113120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.093216 restraints weight = 23482.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.096163 restraints weight = 12328.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.098138 restraints weight = 8038.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.099466 restraints weight = 5978.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.100427 restraints weight = 4868.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.6307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.100   8987  Z= 0.136
  Angle     :  0.636   9.287  12100  Z= 0.328
  Chirality :  0.043   0.293   1323
  Planarity :  0.004   0.044   1544
  Dihedral  :  4.547  15.266   1151
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.95 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.26), residues: 1062
  helix:  0.94 (0.22), residues: 549
  sheet: -0.93 (0.36), residues: 179
  loop : -1.10 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1112 
 TYR   0.023   0.002   TYR A 343 
 PHE   0.018   0.002   PHE A1187 
 TRP   0.019   0.002   TRP A1039 
 HIS   0.022   0.002   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8985)
  covalent geometry    : angle       0.63607 (12100)
  hydrogen bonds       : bond        0.03631 (  502)
  hydrogen bonds       : angle       4.90145 ( 1446)
  metal coordination   : bond        0.00098 (    2)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6340 (mp0)
REVERT: A  230 LYS cc_start: 0.7078 (mttt) cc_final: 0.6837 (pttt)
REVERT: A  487 MET cc_start: 0.8400 (mmm) cc_final: 0.7976 (mmm)
REVERT: A  501 SER cc_start: 0.8572 (m) cc_final: 0.8245 (p)
REVERT: A  526 ASP cc_start: 0.7986 (m-30) cc_final: 0.7773 (m-30)
REVERT: A  616 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8932 (tm-30)
REVERT: A  617 VAL cc_start: 0.9438 (t) cc_final: 0.9071 (t)
REVERT: A  683 MET cc_start: 0.8181 (tpp) cc_final: 0.7916 (tpp)
REVERT: A  684 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7685 (mp)
REVERT: A  872 MET cc_start: 0.8319 (tmm) cc_final: 0.7935 (ppp)
REVERT: A  920 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8449 (ptt90)
REVERT: A  961 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7184 (t0)
REVERT: A  978 MET cc_start: 0.5220 (ppp) cc_final: 0.4640 (ppp)
REVERT: A 1029 ILE cc_start: 0.8443 (mt) cc_final: 0.8123 (mp)
REVERT: A 1088 MET cc_start: 0.8129 (ttt) cc_final: 0.7841 (ttt)
  outliers start: 23
  outliers final: 16
  residues processed: 148
  average time/residue: 0.0780
  time to fit residues: 16.3500
Evaluate side-chains
  143 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  650 LYS
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  750 HIS
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  863 PHE
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  961 ASN
Chi-restraints excluded: chain A residue 1014 ILE
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1071 LEU
Chi-restraints excluded: chain A residue 1103 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.111557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.092026 restraints weight = 23383.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.094927 restraints weight = 12302.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.096858 restraints weight = 8002.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.098223 restraints weight = 5945.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.099113 restraints weight = 4816.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.6417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   8987  Z= 0.173
  Angle     :  0.681  10.300  12100  Z= 0.352
  Chirality :  0.044   0.157   1323
  Planarity :  0.004   0.044   1544
  Dihedral  :  4.619  19.670   1151
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.66 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.26), residues: 1062
  helix:  0.83 (0.22), residues: 555
  sheet: -1.00 (0.36), residues: 179
  loop : -1.13 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1112 
 TYR   0.022   0.002   TYR A 343 
 PHE   0.018   0.002   PHE A 661 
 TRP   0.016   0.002   TRP A1039 
 HIS   0.015   0.002   HIS A 750 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 8985)
  covalent geometry    : angle       0.68062 (12100)
  hydrogen bonds       : bond        0.03830 (  502)
  hydrogen bonds       : angle       4.94007 ( 1446)
  metal coordination   : bond        0.00136 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1333.27 seconds
wall clock time: 23 minutes 54.59 seconds (1434.59 seconds total)