Starting phenix.real_space_refine
on Tue Mar  3 16:55:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v6z_31754/03_2026/7v6z_31754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v6z_31754/03_2026/7v6z_31754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v6z_31754/03_2026/7v6z_31754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v6z_31754/03_2026/7v6z_31754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v6z_31754/03_2026/7v6z_31754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v6z_31754/03_2026/7v6z_31754.cif"
  }
  resolution = 3.64
  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=   0.002 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4626      2.51       5
     N    1195      2.21       5
     O    1229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7082
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1008, 6984
          Classifications: {'peptide': 1008}
          Incomplete info: {'truncation_to_alanine': 260}
          Link IDs: {'PTRANS': 45, 'TRANS': 962}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1021
          Unresolved non-hydrogen angles: 1278
          Unresolved non-hydrogen dihedrals: 859
          Unresolved non-hydrogen chiralities: 49
          Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 18, 'TYR:plan': 12, 'ASP:plan': 36, 'GLU:plan': 42, 'GLN:plan1': 15, 'PHE:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 5}
          Unresolved non-hydrogen planarities: 660
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 70
          Unusual residues: {'CLR': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.50, per 1000 atoms: 0.21
  Number of scatterers: 7082
  At special positions: 0
  Unit cell: (88.56, 88.56, 132.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1229      8.00
     N    1195      7.00
     C    4626      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 212 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 313 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 290 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A1201 " - " ASN A 127 "
      " NAG A1202 " - " ASN A 335 "
      " NAG A1203 " - " ASN A 400 "
      " NAG B   1 " - " ASN A 986 "
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 283.4 milliseconds
  

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1892

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 4 sheets defined
      66.4% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 60 through 83
    Processing helix  chain 'A' and resid 83 through 99
      removed outlier: 3.831A  pdb=" N   LEU A  88 " --> pdb=" O   CYS A  84 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A  89 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA A  99 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 104
    Processing helix  chain 'A' and resid 110 through 114
    Processing helix  chain 'A' and resid 120 through 133
    Processing helix  chain 'A' and resid 157 through 173
    Processing helix  chain 'A' and resid 177 through 181
    Processing helix  chain 'A' and resid 184 through 188
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 222 through 228
      removed outlier: 4.124A  pdb=" N   LYS A 226 " --> pdb=" O   TRP A 222 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 222 through 228'
    Processing helix  chain 'A' and resid 241 through 245
    Processing helix  chain 'A' and resid 246 through 257
    Processing helix  chain 'A' and resid 261 through 271
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.561A  pdb=" N   ARG A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 310
    Processing helix  chain 'A' and resid 354 through 363
      removed outlier: 3.838A  pdb=" N   ARG A 363 " --> pdb=" O   TYR A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 397
      removed outlier: 3.586A  pdb=" N   ALA A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 422
      removed outlier: 3.649A  pdb=" N   LEU A 413 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 444
    Processing helix  chain 'A' and resid 452 through 478
    Processing helix  chain 'A' and resid 482 through 514
      removed outlier: 3.865A  pdb=" N   LEU A 489 " --> pdb=" O   THR A 485 " (cutoff:3.500A)
      Proline residue:  A 490  - end of helix
      removed outlier: 3.683A  pdb=" N   LEU A 494 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP A 500 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 549
      removed outlier: 4.354A  pdb=" N   ALA A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   SER A 533 " --> pdb=" O   ARG A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 591
      removed outlier: 3.891A  pdb=" N   PHE A 578 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
      Proline residue:  A 579  - end of helix
    Processing helix  chain 'A' and resid 717 through 732
      Proline residue:  A 728  - end of helix
    Processing helix  chain 'A' and resid 732 through 756
      removed outlier: 3.753A  pdb=" N   ILE A 740 " --> pdb=" O   LYS A 736 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   THR A 755 " --> pdb=" O   LEU A 751 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ARG A 756 " --> pdb=" O   TYR A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 767
      removed outlier: 4.142A  pdb=" N   ILE A 766 " --> pdb=" O   ASP A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 784
    Processing helix  chain 'A' and resid 802 through 815
      removed outlier: 3.963A  pdb=" N   TYR A 806 " --> pdb=" O   GLN A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 829 through 852
    Processing helix  chain 'A' and resid 863 through 874
    Processing helix  chain 'A' and resid 874 through 880
    Processing helix  chain 'A' and resid 904 through 915
    Processing helix  chain 'A' and resid 916 through 924
      removed outlier: 4.257A  pdb=" N   TYR A 920 " --> pdb=" O   ASP A 916 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLN A 924 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 990
    Processing helix  chain 'A' and resid 999 through 1034
      removed outlier: 3.571A  pdb=" N   PHE A1003 " --> pdb=" O   TYR A 999 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU A1005 " --> pdb=" O   PHE A1001 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   GLN A1006 " --> pdb=" O   LEU A1002 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   TYR A1007 " --> pdb=" O   PHE A1003 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A1008 " --> pdb=" O   TRP A1004 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER A1009 " --> pdb=" O   GLU A1005 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   ARG A1011 " --> pdb=" O   TYR A1007 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   HIS A1012 " --> pdb=" O   ILE A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1035 through 1061
    Processing helix  chain 'A' and resid 1065 through 1092
      removed outlier: 3.608A  pdb=" N   PHE A1082 " --> pdb=" O   ILE A1078 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE A1090 " --> pdb=" O   VAL A1086 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1127
      removed outlier: 3.520A  pdb=" N   MET A1102 " --> pdb=" O   ASN A1098 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   ALA A1110 " --> pdb=" O   GLU A1106 " (cutoff:3.500A)
      Proline residue:  A1111  - end of helix
      removed outlier: 3.555A  pdb=" N   GLY A1122 " --> pdb=" O   SER A1118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1152
      removed outlier: 3.742A  pdb=" N   VAL A1141 " --> pdb=" O   TYR A1137 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU A1142 " --> pdb=" O   PHE A1138 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE A1144 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1164
      Proline residue:  A1158  - end of helix
      removed outlier: 3.543A  pdb=" N   PHE A1163 " --> pdb=" O   VAL A1159 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215
    Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 215
    Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA4, first strand: chain 'A' and resid 957 through 965

    485 hydrogen bonds defined for protein.
    1410 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: 1.19

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1118
        1.31 -     1.44: 2015
        1.44 -     1.57: 4064
        1.57 -     1.70: 1
        1.70 -     1.83: 50
  Bond restraints: 7248
  Sorted by residual:
  bond pdb=" CA  ALA A 171 "
       pdb=" C   ALA A 171 "
    ideal  model  delta    sigma   weight residual
    1.524  1.439  0.085 1.26e-02 6.30e+03 4.50e+01
  bond pdb=" C   VAL A 393 "
       pdb=" O   VAL A 393 "
    ideal  model  delta    sigma   weight residual
    1.237  1.313 -0.076 1.17e-02 7.31e+03 4.24e+01
  bond pdb=" CA  TYR A 774 "
       pdb=" C   TYR A 774 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.082 1.29e-02 6.01e+03 4.01e+01
  bond pdb=" N   SER A 172 "
       pdb=" CA  SER A 172 "
    ideal  model  delta    sigma   weight residual
    1.459  1.386  0.073 1.21e-02 6.83e+03 3.64e+01
  bond pdb=" CA  ALA A 921 "
       pdb=" C   ALA A 921 "
    ideal  model  delta    sigma   weight residual
    1.523  1.449  0.074 1.30e-02 5.92e+03 3.27e+01
  ... (remaining 7243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 8964
        2.46 -     4.92: 773
        4.92 -     7.38: 173
        7.38 -     9.84: 50
        9.84 -    12.30: 12
  Bond angle restraints: 9972
  Sorted by residual:
  angle pdb=" N   LYS A 297 "
        pdb=" CA  LYS A 297 "
        pdb=" C   LYS A 297 "
      ideal   model   delta    sigma   weight residual
     111.28   99.40   11.88 1.09e+00 8.42e-01 1.19e+02
  angle pdb=" N   LEU A 594 "
        pdb=" CA  LEU A 594 "
        pdb=" C   LEU A 594 "
      ideal   model   delta    sigma   weight residual
     111.28  122.43  -11.15 1.09e+00 8.42e-01 1.05e+02
  angle pdb=" N   TYR A 210 "
        pdb=" CA  TYR A 210 "
        pdb=" C   TYR A 210 "
      ideal   model   delta    sigma   weight residual
     109.72   98.10   11.62 1.25e+00 6.40e-01 8.65e+01
  angle pdb=" N   SER A  40 "
        pdb=" CA  SER A  40 "
        pdb=" C   SER A  40 "
      ideal   model   delta    sigma   weight residual
     111.74   99.44   12.30 1.35e+00 5.49e-01 8.30e+01
  angle pdb=" N   PHE A 729 "
        pdb=" CA  PHE A 729 "
        pdb=" C   PHE A 729 "
      ideal   model   delta    sigma   weight residual
     111.07  102.04    9.03 1.07e+00 8.73e-01 7.12e+01
  ... (remaining 9967 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3939
       17.94 -    35.89: 263
       35.89 -    53.83: 91
       53.83 -    71.77: 17
       71.77 -    89.71: 3
  Dihedral angle restraints: 4313
    sinusoidal: 1386
      harmonic: 2927
  Sorted by residual:
  dihedral pdb=" CB  CYS A 282 "
           pdb=" SG  CYS A 282 "
           pdb=" SG  CYS A 290 "
           pdb=" CB  CYS A 290 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.29  -89.71     1      1.00e+01 1.00e-02 9.55e+01
  dihedral pdb=" CB  CYS A 189 "
           pdb=" SG  CYS A 189 "
           pdb=" SG  CYS A 212 "
           pdb=" CB  CYS A 212 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -36.82  -49.18     1      1.00e+01 1.00e-02 3.32e+01
  dihedral pdb=" C   ILE A 777 "
           pdb=" N   ILE A 777 "
           pdb=" CA  ILE A 777 "
           pdb=" CB  ILE A 777 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.26   14.26     0      2.50e+00 1.60e-01 3.25e+01
  ... (remaining 4310 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 975
       0.120 -    0.239: 206
       0.239 -    0.359: 49
       0.359 -    0.479: 13
       0.479 -    0.598: 4
  Chirality restraints: 1247
  Sorted by residual:
  chirality pdb=" CA  TRP A1004 "
            pdb=" N   TRP A1004 "
            pdb=" C   TRP A1004 "
            pdb=" CB  TRP A1004 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.94e+00
  chirality pdb=" CA  ILE A 777 "
            pdb=" N   ILE A 777 "
            pdb=" C   ILE A 777 "
            pdb=" CB  ILE A 777 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.90    0.53 2.00e-01 2.50e+01 7.08e+00
  chirality pdb=" CA  LEU A 594 "
            pdb=" N   LEU A 594 "
            pdb=" C   LEU A 594 "
            pdb=" CB  LEU A 594 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.84e+00
  ... (remaining 1244 not shown)

  Planarity restraints: 1255
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1157 "   -0.098 5.00e-02 4.00e+02   1.47e-01 3.47e+01
        pdb=" N   PRO A1158 "    0.255 5.00e-02 4.00e+02
        pdb=" CA  PRO A1158 "   -0.079 5.00e-02 4.00e+02
        pdb=" CD  PRO A1158 "   -0.078 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A1153 "    0.023 2.00e-02 2.50e+03   4.59e-02 2.11e+01
        pdb=" C   GLY A1153 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   GLY A1153 "    0.029 2.00e-02 2.50e+03
        pdb=" N   LEU A1154 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 294 "    0.069 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO A 295 "   -0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO A 295 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 295 "    0.060 5.00e-02 4.00e+02
  ... (remaining 1252 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2308
        2.81 -     3.33: 7578
        3.33 -     3.85: 11798
        3.85 -     4.38: 13600
        4.38 -     4.90: 21272
  Nonbonded interactions: 56556
  Sorted by model distance:
  nonbonded pdb=" O   GLY A1115 "
            pdb=" OG  SER A1118 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" CG2 ILE A1071 "
            pdb=" CD1 ILE A1071 "
     model   vdw
     2.314 3.104
  nonbonded pdb=" N   SER A1065 "
            pdb=" O   SER A1065 "
     model   vdw
     2.354 2.496
  nonbonded pdb=" N   ASP A 591 "
            pdb=" O   ASP A 591 "
     model   vdw
     2.410 2.496
  nonbonded pdb=" N   ARG A 772 "
            pdb=" N   GLU A 773 "
     model   vdw
     2.436 2.560
  ... (remaining 56551 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.960
  Find NCS groups from input model:        0.040
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
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      :  0.012   0.085   7256  Z= 0.880
  Angle     :  1.670  12.301   9993  Z= 1.164
  Chirality :  0.114   0.598   1247
  Planarity :  0.010   0.147   1251
  Dihedral  : 14.342  88.724   2412
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.20 %
    Favored  : 96.50 %
  Rotamer:
    Outliers : 10.76 %
    Allowed  :  8.91 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.63 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.27), residues: 1000
  helix:  2.51 (0.22), residues: 581
  sheet:  0.56 (0.75), residues: 47
  loop : -1.15 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 280 
 TYR   0.035   0.003   TYR A 774 
 PHE   0.023   0.002   PHE A1131 
 TRP   0.019   0.002   TRP A 837 
 HIS   0.007   0.002   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.01177 ( 7248)
  covalent geometry    : angle       1.66642 ( 9972)
  SS BOND              : bond        0.01264 (    3)
  SS BOND              : angle       1.93037 (    6)
  hydrogen bonds       : bond        0.17478 (  483)
  hydrogen bonds       : angle       6.92692 ( 1410)
  link_BETA1-4         : bond        0.00463 (    1)
  link_BETA1-4         : angle       1.29096 (    3)
  link_NAG-ASN         : bond        0.01855 (    4)
  link_NAG-ASN         : angle       3.63763 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 204
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 PHE cc_start: 0.7940 (t80) cc_final: 0.7585 (t80)
REVERT: A  771 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7236 (m)
REVERT: A  829 MET cc_start: 0.7569 (ptp) cc_final: 0.7362 (ptp)
REVERT: A  984 CYS cc_start: 0.7857 (m) cc_final: 0.7548 (t)
REVERT: A 1099 HIS cc_start: 0.6329 (OUTLIER) cc_final: 0.5892 (t70)
  outliers start: 64
  outliers final: 22
  residues processed: 243
  average time/residue: 0.0653
  time to fit residues: 22.3623
Evaluate side-chains
  162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  569 PHE
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  771 THR
Chi-restraints excluded: chain A residue  777 ILE
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1099 HIS
Chi-restraints excluded: chain A residue 1133 PHE
Chi-restraints excluded: chain A residue 1150 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 131 GLN
A 154 ASN
A 175 HIS
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 296 ASN
A 386 GLN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 794 GLN
A1006 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.161969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.126486 restraints weight = 11905.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.131002 restraints weight = 5944.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.134036 restraints weight = 3869.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.135669 restraints weight = 2994.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.136650 restraints weight = 2588.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7256  Z= 0.188
  Angle     :  0.729   7.486   9993  Z= 0.385
  Chirality :  0.046   0.240   1247
  Planarity :  0.006   0.065   1251
  Dihedral  :  8.027  55.859   1266
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.80 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  8.40 %
    Allowed  : 16.30 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1000
  helix:  1.73 (0.21), residues: 594
  sheet: -0.30 (0.69), residues: 49
  loop : -1.12 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 756 
 TYR   0.025   0.002   TYR A 179 
 PHE   0.019   0.002   PHE A 786 
 TRP   0.020   0.002   TRP A 837 
 HIS   0.011   0.001   HIS A 809 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 7248)
  covalent geometry    : angle       0.72444 ( 9972)
  SS BOND              : bond        0.00309 (    3)
  SS BOND              : angle       0.20758 (    6)
  hydrogen bonds       : bond        0.06187 (  483)
  hydrogen bonds       : angle       5.11867 ( 1410)
  link_BETA1-4         : bond        0.00753 (    1)
  link_BETA1-4         : angle       1.29784 (    3)
  link_NAG-ASN         : bond        0.00367 (    4)
  link_NAG-ASN         : angle       2.41702 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 153
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7079 (pt0)
REVERT: A  316 LEU cc_start: 0.7664 (mt) cc_final: 0.7458 (mp)
REVERT: A  403 GLN cc_start: 0.6552 (mp10) cc_final: 0.6142 (tm-30)
REVERT: A  526 CYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6030 (t)
REVERT: A  573 MET cc_start: 0.8195 (tmm) cc_final: 0.7852 (tmm)
REVERT: A  832 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7527 (m170)
REVERT: A  972 ASP cc_start: 0.8127 (m-30) cc_final: 0.7727 (t0)
REVERT: A  984 CYS cc_start: 0.7775 (m) cc_final: 0.7241 (t)
REVERT: A 1099 HIS cc_start: 0.6023 (OUTLIER) cc_final: 0.5482 (t70)
  outliers start: 50
  outliers final: 31
  residues processed: 187
  average time/residue: 0.0541
  time to fit residues: 15.5965
Evaluate side-chains
  167 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  344 HIS
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  546 PHE
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  777 ILE
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  832 HIS
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1099 HIS
Chi-restraints excluded: chain A residue 1133 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1145 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 98 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.159904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.124791 restraints weight = 11981.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.129229 restraints weight = 5936.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.132129 restraints weight = 3858.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.133696 restraints weight = 2970.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.134861 restraints weight = 2569.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7256  Z= 0.177
  Angle     :  0.696   9.942   9993  Z= 0.358
  Chirality :  0.044   0.214   1247
  Planarity :  0.006   0.054   1251
  Dihedral  :  6.919  52.608   1250
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.20 %
    Favored  : 96.70 %
  Rotamer:
    Outliers : 10.25 %
    Allowed  : 18.15 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.27), residues: 1000
  helix:  1.63 (0.21), residues: 594
  sheet: -0.51 (0.70), residues: 49
  loop : -1.10 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 318 
 TYR   0.023   0.002   TYR A 179 
 PHE   0.016   0.002   PHE A1133 
 TRP   0.016   0.002   TRP A 837 
 HIS   0.008   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 7248)
  covalent geometry    : angle       0.69110 ( 9972)
  SS BOND              : bond        0.00728 (    3)
  SS BOND              : angle       0.63366 (    6)
  hydrogen bonds       : bond        0.05251 (  483)
  hydrogen bonds       : angle       4.87135 ( 1410)
  link_BETA1-4         : bond        0.00339 (    1)
  link_BETA1-4         : angle       1.22731 (    3)
  link_NAG-ASN         : bond        0.00242 (    4)
  link_NAG-ASN         : angle       2.34507 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 138
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7083 (pt0)
REVERT: A  473 LEU cc_start: 0.8522 (tp) cc_final: 0.8251 (tt)
REVERT: A  504 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8524 (tt)
REVERT: A  526 CYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6128 (t)
REVERT: A  573 MET cc_start: 0.8272 (tmm) cc_final: 0.8005 (tmm)
REVERT: A  984 CYS cc_start: 0.7851 (m) cc_final: 0.7204 (t)
REVERT: A 1072 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5393 (mp)
REVERT: A 1099 HIS cc_start: 0.5925 (OUTLIER) cc_final: 0.5401 (t70)
  outliers start: 61
  outliers final: 36
  residues processed: 176
  average time/residue: 0.0548
  time to fit residues: 14.7505
Evaluate side-chains
  170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 129
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  344 HIS
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  546 PHE
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  775 ASP
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1009 SER
Chi-restraints excluded: chain A residue 1013 TRP
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1099 HIS
Chi-restraints excluded: chain A residue 1133 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1147 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 64 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 163 GLN
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.160227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.125099 restraints weight = 12093.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.129591 restraints weight = 5997.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.132131 restraints weight = 3902.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.134272 restraints weight = 3064.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.135112 restraints weight = 2601.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7256  Z= 0.149
  Angle     :  0.665  10.534   9993  Z= 0.338
  Chirality :  0.043   0.205   1247
  Planarity :  0.005   0.049   1251
  Dihedral  :  6.555  52.445   1248
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.90 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  7.90 %
    Allowed  : 19.66 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.27), residues: 1000
  helix:  1.65 (0.21), residues: 594
  sheet: -0.36 (0.77), residues: 44
  loop : -1.07 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 756 
 TYR   0.020   0.002   TYR A 179 
 PHE   0.025   0.002   PHE A 408 
 TRP   0.015   0.001   TRP A 837 
 HIS   0.005   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7248)
  covalent geometry    : angle       0.66062 ( 9972)
  SS BOND              : bond        0.00630 (    3)
  SS BOND              : angle       0.50516 (    6)
  hydrogen bonds       : bond        0.04765 (  483)
  hydrogen bonds       : angle       4.72106 ( 1410)
  link_BETA1-4         : bond        0.00475 (    1)
  link_BETA1-4         : angle       1.23733 (    3)
  link_NAG-ASN         : bond        0.00211 (    4)
  link_NAG-ASN         : angle       2.24852 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 140
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 GLN cc_start: 0.6666 (tm-30) cc_final: 0.6175 (mp10)
REVERT: A  408 PHE cc_start: 0.7746 (t80) cc_final: 0.7439 (t80)
REVERT: A  422 ASP cc_start: 0.7809 (m-30) cc_final: 0.7455 (m-30)
REVERT: A  475 SER cc_start: 0.8257 (m) cc_final: 0.7928 (p)
REVERT: A  526 CYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6248 (t)
REVERT: A  573 MET cc_start: 0.8267 (tmm) cc_final: 0.8058 (tmm)
REVERT: A  783 TYR cc_start: 0.7061 (m-80) cc_final: 0.6838 (m-80)
REVERT: A  972 ASP cc_start: 0.8104 (m-30) cc_final: 0.7814 (t0)
REVERT: A  984 CYS cc_start: 0.7818 (m) cc_final: 0.7177 (t)
REVERT: A 1099 HIS cc_start: 0.5919 (OUTLIER) cc_final: 0.5372 (t70)
  outliers start: 47
  outliers final: 36
  residues processed: 169
  average time/residue: 0.0542
  time to fit residues: 14.1109
Evaluate side-chains
  171 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 133
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  344 HIS
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  546 PHE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  788 ASN
Chi-restraints excluded: chain A residue  789 MET
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1009 SER
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1032 PHE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1099 HIS
Chi-restraints excluded: chain A residue 1133 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    0.1980
   chunk 56 optimal weight:   20.0000
   chunk 22 optimal weight:    0.3980
   chunk 7 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.161636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.126562 restraints weight = 12038.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.131120 restraints weight = 5900.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.134119 restraints weight = 3816.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.135781 restraints weight = 2929.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.137196 restraints weight = 2526.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7256  Z= 0.135
  Angle     :  0.665  11.306   9993  Z= 0.328
  Chirality :  0.042   0.218   1247
  Planarity :  0.005   0.048   1251
  Dihedral  :  6.208  51.768   1245
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.10 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  7.90 %
    Allowed  : 21.85 %
    Favored  : 70.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.27), residues: 1000
  helix:  1.72 (0.21), residues: 594
  sheet: -0.36 (0.80), residues: 44
  loop : -1.11 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 756 
 TYR   0.019   0.002   TYR A 190 
 PHE   0.020   0.001   PHE A 786 
 TRP   0.021   0.001   TRP A1037 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7248)
  covalent geometry    : angle       0.66053 ( 9972)
  SS BOND              : bond        0.00078 (    3)
  SS BOND              : angle       1.49857 (    6)
  hydrogen bonds       : bond        0.04412 (  483)
  hydrogen bonds       : angle       4.65328 ( 1410)
  link_BETA1-4         : bond        0.00283 (    1)
  link_BETA1-4         : angle       1.22048 (    3)
  link_NAG-ASN         : bond        0.00254 (    4)
  link_NAG-ASN         : angle       2.14251 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 138
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 GLN cc_start: 0.6636 (tm-30) cc_final: 0.6106 (mp10)
REVERT: A  408 PHE cc_start: 0.7698 (t80) cc_final: 0.7458 (t80)
REVERT: A  475 SER cc_start: 0.8225 (m) cc_final: 0.7882 (p)
REVERT: A  526 CYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5869 (t)
REVERT: A  774 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6785 (t80)
REVERT: A  972 ASP cc_start: 0.8133 (m-30) cc_final: 0.7855 (t0)
REVERT: A  984 CYS cc_start: 0.7865 (m) cc_final: 0.7291 (t)
REVERT: A 1099 HIS cc_start: 0.5867 (OUTLIER) cc_final: 0.5380 (t70)
REVERT: A 1144 ILE cc_start: 0.8309 (tt) cc_final: 0.8022 (pt)
  outliers start: 47
  outliers final: 34
  residues processed: 163
  average time/residue: 0.0525
  time to fit residues: 13.2074
Evaluate side-chains
  165 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 128
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  526 CYS
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  789 MET
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1009 SER
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1032 PHE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1099 HIS
Chi-restraints excluded: chain A residue 1133 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    0.0050
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0670
   chunk 53 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0970
   chunk 67 optimal weight:    1.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    0.3932

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

Flipped N/Q/H residues before XYZ refinement:
A 344 HIS
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1152 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.163941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.129533 restraints weight = 12122.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.134160 restraints weight = 5845.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.137177 restraints weight = 3730.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.138166 restraints weight = 2852.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.139422 restraints weight = 2540.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7256  Z= 0.122
  Angle     :  0.640  11.662   9993  Z= 0.315
  Chirality :  0.042   0.228   1247
  Planarity :  0.005   0.046   1251
  Dihedral  :  5.897  50.639   1244
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.90 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  8.07 %
    Allowed  : 21.34 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.27), residues: 1000
  helix:  1.68 (0.21), residues: 606
  sheet: -0.39 (0.78), residues: 44
  loop : -1.12 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 280 
 TYR   0.019   0.001   TYR A 190 
 PHE   0.017   0.001   PHE A 408 
 TRP   0.022   0.001   TRP A1037 
 HIS   0.012   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7248)
  covalent geometry    : angle       0.63588 ( 9972)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       1.34643 (    6)
  hydrogen bonds       : bond        0.03942 (  483)
  hydrogen bonds       : angle       4.52606 ( 1410)
  link_BETA1-4         : bond        0.00590 (    1)
  link_BETA1-4         : angle       1.23750 (    3)
  link_NAG-ASN         : bond        0.00295 (    4)
  link_NAG-ASN         : angle       1.96672 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 146
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 ILE cc_start: 0.8753 (mt) cc_final: 0.8541 (mp)
REVERT: A  403 GLN cc_start: 0.6681 (tm-30) cc_final: 0.6274 (mp10)
REVERT: A  475 SER cc_start: 0.8138 (m) cc_final: 0.7842 (p)
REVERT: A  774 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6735 (t80)
REVERT: A  972 ASP cc_start: 0.8119 (m-30) cc_final: 0.7867 (t0)
REVERT: A  984 CYS cc_start: 0.7856 (m) cc_final: 0.7517 (t)
REVERT: A 1099 HIS cc_start: 0.5812 (OUTLIER) cc_final: 0.5442 (t70)
  outliers start: 48
  outliers final: 36
  residues processed: 174
  average time/residue: 0.0569
  time to fit residues: 15.0018
Evaluate side-chains
  171 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 133
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  506 HIS
Chi-restraints excluded: chain A residue  546 PHE
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  789 MET
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1032 PHE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1099 HIS
Chi-restraints excluded: chain A residue 1133 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1145 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 88 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.162277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.127526 restraints weight = 12064.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.131963 restraints weight = 5960.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.135012 restraints weight = 3865.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.136486 restraints weight = 2943.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.136486 restraints weight = 2551.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.4398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7256  Z= 0.133
  Angle     :  0.656  10.702   9993  Z= 0.322
  Chirality :  0.042   0.266   1247
  Planarity :  0.005   0.044   1251
  Dihedral  :  5.641  50.241   1241
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.40 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  7.56 %
    Allowed  : 24.71 %
    Favored  : 67.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.27), residues: 1000
  helix:  1.70 (0.21), residues: 606
  sheet: -0.35 (0.78), residues: 44
  loop : -1.13 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 318 
 TYR   0.018   0.001   TYR A 190 
 PHE   0.043   0.002   PHE A 408 
 TRP   0.015   0.001   TRP A 837 
 HIS   0.016   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7248)
  covalent geometry    : angle       0.65195 ( 9972)
  SS BOND              : bond        0.00137 (    3)
  SS BOND              : angle       1.19260 (    6)
  hydrogen bonds       : bond        0.04017 (  483)
  hydrogen bonds       : angle       4.53359 ( 1410)
  link_BETA1-4         : bond        0.00550 (    1)
  link_BETA1-4         : angle       1.19062 (    3)
  link_NAG-ASN         : bond        0.00231 (    4)
  link_NAG-ASN         : angle       2.06608 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 140
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6282 (mp10)
REVERT: A  561 LEU cc_start: 0.8779 (mt) cc_final: 0.8524 (mt)
REVERT: A  569 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7650 (m-10)
REVERT: A  774 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6674 (t80)
REVERT: A  972 ASP cc_start: 0.8119 (m-30) cc_final: 0.7853 (t0)
REVERT: A  984 CYS cc_start: 0.8066 (m) cc_final: 0.7612 (t)
  outliers start: 45
  outliers final: 37
  residues processed: 166
  average time/residue: 0.0566
  time to fit residues: 14.3797
Evaluate side-chains
  169 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 130
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  506 HIS
Chi-restraints excluded: chain A residue  546 PHE
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  569 PHE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  789 MET
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1032 PHE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1133 PHE
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1145 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:   30.0000
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 9 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 44 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 68 optimal weight:   10.0000
   chunk 47 optimal weight:    7.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.159167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.123642 restraints weight = 12266.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.127858 restraints weight = 6220.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.130712 restraints weight = 4093.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.131988 restraints weight = 3175.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.133308 restraints weight = 2779.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.4595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7256  Z= 0.153
  Angle     :  0.666   9.002   9993  Z= 0.330
  Chirality :  0.042   0.252   1247
  Planarity :  0.005   0.044   1251
  Dihedral  :  5.556  49.517   1239
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.40 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  7.73 %
    Allowed  : 25.04 %
    Favored  : 67.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.27), residues: 1000
  helix:  1.52 (0.21), residues: 606
  sheet: -0.38 (0.78), residues: 44
  loop : -1.13 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 387 
 TYR   0.018   0.001   TYR A 190 
 PHE   0.042   0.002   PHE A 408 
 TRP   0.014   0.001   TRP A1037 
 HIS   0.011   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7248)
  covalent geometry    : angle       0.66273 ( 9972)
  SS BOND              : bond        0.00115 (    3)
  SS BOND              : angle       0.97620 (    6)
  hydrogen bonds       : bond        0.04342 (  483)
  hydrogen bonds       : angle       4.59344 ( 1410)
  link_BETA1-4         : bond        0.00522 (    1)
  link_BETA1-4         : angle       1.29417 (    3)
  link_NAG-ASN         : bond        0.00204 (    4)
  link_NAG-ASN         : angle       2.00092 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 135
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6354 (t80)
REVERT: A  403 GLN cc_start: 0.6677 (tm-30) cc_final: 0.6337 (mp10)
REVERT: A  569 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7709 (m-10)
REVERT: A  573 MET cc_start: 0.8239 (tmm) cc_final: 0.7903 (tmm)
REVERT: A  774 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.6638 (t80)
REVERT: A  905 PHE cc_start: 0.8105 (t80) cc_final: 0.7703 (t80)
REVERT: A  949 ILE cc_start: 0.5100 (mm) cc_final: 0.4870 (mm)
REVERT: A  984 CYS cc_start: 0.8091 (m) cc_final: 0.7729 (t)
  outliers start: 46
  outliers final: 37
  residues processed: 163
  average time/residue: 0.0600
  time to fit residues: 14.7518
Evaluate side-chains
  167 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  546 PHE
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  569 PHE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  789 MET
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  990 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue  994 SER
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1032 PHE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1072 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   chunk 73 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 92 optimal weight:    6.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.153401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.117376 restraints weight = 12271.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.121314 restraints weight = 6509.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.123903 restraints weight = 4378.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.125224 restraints weight = 3454.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.126517 restraints weight = 3026.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.4701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   7256  Z= 0.251
  Angle     :  0.756   8.797   9993  Z= 0.386
  Chirality :  0.045   0.273   1247
  Planarity :  0.005   0.043   1251
  Dihedral  :  5.832  53.944   1237
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.20 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  8.24 %
    Allowed  : 25.71 %
    Favored  : 66.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.26), residues: 1000
  helix:  1.13 (0.21), residues: 604
  sheet: -0.59 (0.77), residues: 44
  loop : -1.26 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 981 
 TYR   0.021   0.002   TYR A 957 
 PHE   0.051   0.003   PHE A 408 
 TRP   0.015   0.002   TRP A1037 
 HIS   0.009   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 7248)
  covalent geometry    : angle       0.75131 ( 9972)
  SS BOND              : bond        0.00194 (    3)
  SS BOND              : angle       1.60805 (    6)
  hydrogen bonds       : bond        0.05214 (  483)
  hydrogen bonds       : angle       4.89884 ( 1410)
  link_BETA1-4         : bond        0.00553 (    1)
  link_BETA1-4         : angle       1.07886 (    3)
  link_NAG-ASN         : bond        0.00094 (    4)
  link_NAG-ASN         : angle       2.23030 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 127
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6494 (t80)
REVERT: A  403 GLN cc_start: 0.6634 (tm-30) cc_final: 0.6350 (mp-120)
REVERT: A  504 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8527 (tt)
REVERT: A  569 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7844 (m-10)
REVERT: A  573 MET cc_start: 0.8235 (tmm) cc_final: 0.7950 (tmm)
REVERT: A  774 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6674 (t80)
REVERT: A  972 ASP cc_start: 0.8009 (m-30) cc_final: 0.7787 (t0)
REVERT: A  984 CYS cc_start: 0.8200 (m) cc_final: 0.7975 (m)
REVERT: A 1071 ILE cc_start: 0.5263 (OUTLIER) cc_final: 0.4983 (tp)
  outliers start: 49
  outliers final: 35
  residues processed: 156
  average time/residue: 0.0531
  time to fit residues: 12.7453
Evaluate side-chains
  167 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  546 PHE
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  569 PHE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  788 ASN
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue  994 SER
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1009 SER
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1032 PHE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1144 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 67 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 GLN
** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.158411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.122921 restraints weight = 12272.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.127073 restraints weight = 6233.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.129932 restraints weight = 4125.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.131320 restraints weight = 3191.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.132769 restraints weight = 2780.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7256  Z= 0.140
  Angle     :  0.692  10.380   9993  Z= 0.341
  Chirality :  0.043   0.297   1247
  Planarity :  0.005   0.044   1251
  Dihedral  :  5.605  50.194   1237
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.30 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 29.41 %
    Favored  : 65.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.27), residues: 1000
  helix:  1.48 (0.21), residues: 602
  sheet: -0.66 (0.74), residues: 44
  loop : -1.26 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 427 
 TYR   0.018   0.002   TYR A 190 
 PHE   0.038   0.002   PHE A 408 
 TRP   0.015   0.001   TRP A1037 
 HIS   0.010   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7248)
  covalent geometry    : angle       0.68823 ( 9972)
  SS BOND              : bond        0.00162 (    3)
  SS BOND              : angle       1.25519 (    6)
  hydrogen bonds       : bond        0.04357 (  483)
  hydrogen bonds       : angle       4.65091 ( 1410)
  link_BETA1-4         : bond        0.00457 (    1)
  link_BETA1-4         : angle       1.16702 (    3)
  link_NAG-ASN         : bond        0.00268 (    4)
  link_NAG-ASN         : angle       1.97612 (   12)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  362 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6331 (t80)
REVERT: A  569 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7669 (m-10)
REVERT: A  573 MET cc_start: 0.8270 (tmm) cc_final: 0.7979 (tmm)
REVERT: A  774 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6548 (t80)
REVERT: A  984 CYS cc_start: 0.8138 (m) cc_final: 0.7866 (m)
  outliers start: 32
  outliers final: 26
  residues processed: 152
  average time/residue: 0.0540
  time to fit residues: 12.6315
Evaluate side-chains
  156 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  190 TYR
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  373 TRP
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  546 PHE
Chi-restraints excluded: chain A residue  569 PHE
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  764 THR
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1018 ILE
Chi-restraints excluded: chain A residue 1032 PHE
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1072 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 24 optimal weight:    0.2980
   chunk 46 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 91 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.161322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.126471 restraints weight = 12134.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.130767 restraints weight = 6112.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.133686 restraints weight = 4021.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.135229 restraints weight = 3114.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.136022 restraints weight = 2697.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.5119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7256  Z= 0.131
  Angle     :  0.677   9.692   9993  Z= 0.332
  Chirality :  0.042   0.296   1247
  Planarity :  0.005   0.044   1251
  Dihedral  :  5.364  49.078   1237
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.30 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 29.75 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.27), residues: 1000
  helix:  1.54 (0.21), residues: 604
  sheet: -0.52 (0.74), residues: 44
  loop : -1.19 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 756 
 TYR   0.020   0.001   TYR A 190 
 PHE   0.036   0.002   PHE A 408 
 TRP   0.014   0.001   TRP A 837 
 HIS   0.008   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7248)
  covalent geometry    : angle       0.67458 ( 9972)
  SS BOND              : bond        0.00106 (    3)
  SS BOND              : angle       0.97483 (    6)
  hydrogen bonds       : bond        0.04109 (  483)
  hydrogen bonds       : angle       4.59133 ( 1410)
  link_BETA1-4         : bond        0.00569 (    1)
  link_BETA1-4         : angle       1.39539 (    3)
  link_NAG-ASN         : bond        0.00384 (    4)
  link_NAG-ASN         : angle       1.71779 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1406.36 seconds
wall clock time: 24 minutes 50.87 seconds (1490.87 seconds total)