Starting phenix.real_space_refine
on Wed Mar 12 20:21:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlc_36392/03_2025/8jlc_36392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlc_36392/03_2025/8jlc_36392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlc_36392/03_2025/8jlc_36392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlc_36392/03_2025/8jlc_36392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlc_36392/03_2025/8jlc_36392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlc_36392/03_2025/8jlc_36392.cif"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    5291      2.51       5
     N    1362      2.21       5
     O    1489      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8189
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4674
          Classifications: {'peptide': 592}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 576}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3437
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411}
    Chain: "F"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 40
          Unusual residues: {'NAG': 2, 'UKX': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.59, per 1000 atoms: 0.68
  Number of scatterers: 8189
  At special positions: 0
  Unit cell: (87.98, 85.49, 147.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1489      8.00
     N    1362      7.00
     C    5291      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
    BETA1-6
      " NAG F   1 " - " FUC F   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 801 " - " ASN A 498 "
      " NAG A 802 " - " ASN A 548 "
      " NAG F   1 " - " ASN A 573 "
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 880.5 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 7 sheets defined
      44.9% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 137 through 160
    Processing helix  chain 'A' and resid 162 through 183
      removed outlier: 4.099A  pdb=" N   ASP A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   VAL A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 197
      Proline residue:  A 191  - end of helix
      removed outlier: 4.316A  pdb=" N   LYS A 195 " --> pdb=" O   PRO A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 209
    Processing helix  chain 'A' and resid 209 through 230
      removed outlier: 3.965A  pdb=" N   LEU A 213 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET A 215 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE A 220 " --> pdb=" O   MET A 216 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ASP A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ARG A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 252
      removed outlier: 3.911A  pdb=" N   PHE A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 271
      removed outlier: 4.319A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 281
      removed outlier: 3.525A  pdb=" N   ILE A 275 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 284
      No H-bonds generated for 'chain 'A' and resid 282 through 284'
    Processing helix  chain 'A' and resid 285 through 288
      removed outlier: 3.766A  pdb=" N   LYS A 288 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 285 through 288'
    Processing helix  chain 'A' and resid 289 through 295
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.802A  pdb=" N   MET A 301 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.754A  pdb=" N   VAL A 335 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 3.577A  pdb=" N   PHE A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 386
    Processing helix  chain 'A' and resid 419 through 439
    Processing helix  chain 'A' and resid 444 through 483
      Proline residue:  A 469  - end of helix
    Processing helix  chain 'A' and resid 562 through 564
      No H-bonds generated for 'chain 'A' and resid 562 through 564'
    Processing helix  chain 'A' and resid 593 through 623
      Proline residue:  A 610  - end of helix
      removed outlier: 5.245A  pdb=" N   ASP A 620 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   LYS A 621 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 641
      removed outlier: 3.678A  pdb=" N   MET A 634 " --> pdb=" O   GLY A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 644
      No H-bonds generated for 'chain 'A' and resid 642 through 644'
    Processing helix  chain 'A' and resid 647 through 676
      removed outlier: 3.720A  pdb=" N   ILE A 663 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   ALA A 664 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   SER A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 707
      removed outlier: 3.567A  pdb=" N   PHE A 707 " --> pdb=" O   ILE A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 731
    Processing helix  chain 'B' and resid 929 through 933
      removed outlier: 3.760A  pdb=" N   VAL B 933 " --> pdb=" O   ASN B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 958
    Processing helix  chain 'B' and resid 1080 through 1092
    Processing helix  chain 'B' and resid 1210 through 1215
      removed outlier: 4.235A  pdb=" N   VAL B1214 " --> pdb=" O   ILE B1211 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   GLY B1215 " --> pdb=" O   PRO B1212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1265 through 1273
    Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 485 through 492
    current: chain 'A' and resid 515 through 527
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 515 through 527
    current: chain 'B' and resid 1142 through 1144
    Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884
      removed outlier: 3.590A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 887 through 890
    current: chain 'B' and resid 914 through 916
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 914 through 916
    current: chain 'B' and resid 1015 through 1021
      removed outlier: 4.000A  pdb=" N   ASP B1037 " --> pdb=" O   ILE B1029 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ILE B1031 " --> pdb=" O   LEU B1035 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   LEU B1035 " --> pdb=" O   ILE B1031 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 897 through 900
    Processing sheet with id=AA4, first strand: chain 'B' and resid 962 through 966
      removed outlier: 6.724A  pdb=" N   VAL B 976 " --> pdb=" O   ILE B 964 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ASN B 966 " --> pdb=" O   TRP B 974 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   TRP B 974 " --> pdb=" O   ASN B 966 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1112 through 1115
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1122 through 1124
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1159 through 1164
      removed outlier: 4.119A  pdb=" N   LYS B1159 " --> pdb=" O   VAL B1185 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE B1182 " --> pdb=" O   LEU B1193 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1189 through 1194
    current: chain 'B' and resid 1232 through 1240
      removed outlier: 27.387A  pdb=" N   ASN B1233 " --> pdb=" O   LEU B1254 " (cutoff:3.500A)
      removed outlier: 23.558A  pdb=" N   LEU B1254 " --> pdb=" O   ASN B1233 " (cutoff:3.500A)
      removed outlier: 15.950A  pdb=" N   CYS B1235 " --> pdb=" O   PHE B1252 " (cutoff:3.500A)
      removed outlier: 11.246A  pdb=" N   PHE B1252 " --> pdb=" O   CYS B1235 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   MET B1237 " --> pdb=" O   ILE B1250 " (cutoff:3.500A)

    374 hydrogen bonds defined for protein.
    1077 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.37

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 1771
        1.33 -     1.47: 3037
        1.47 -     1.61: 3497
        1.61 -     1.75: 3
        1.75 -     1.89: 75
  Bond restraints: 8383
  Sorted by residual:
  bond pdb=" C   GLY A 591 "
       pdb=" N   GLU A 592 "
    ideal  model  delta    sigma   weight residual
    1.335  1.458 -0.123 1.35e-02 5.49e+03 8.37e+01
  bond pdb=" C5  UKX A 803 "
       pdb=" C6  UKX A 803 "
    ideal  model  delta    sigma   weight residual
    1.533  1.709 -0.176 2.00e-02 2.50e+03 7.78e+01
  bond pdb=" C   GLY A 604 "
       pdb=" O   GLY A 604 "
    ideal  model  delta    sigma   weight residual
    1.233  1.290 -0.057 1.17e-02 7.31e+03 2.40e+01
  bond pdb=" N   GLU A 592 "
       pdb=" CA  GLU A 592 "
    ideal  model  delta    sigma   weight residual
    1.458  1.517 -0.059 1.30e-02 5.92e+03 2.07e+01
  bond pdb=" C   VAL A 171 "
       pdb=" O   VAL A 171 "
    ideal  model  delta    sigma   weight residual
    1.237  1.285 -0.048 1.13e-02 7.83e+03 1.82e+01
  ... (remaining 8378 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 11091
        3.17 -     6.35: 231
        6.35 -     9.52: 11
        9.52 -    12.69: 1
       12.69 -    15.87: 1
  Bond angle restraints: 11335
  Sorted by residual:
  angle pdb=" C   GLY A 591 "
        pdb=" N   GLU A 592 "
        pdb=" CA  GLU A 592 "
      ideal   model   delta    sigma   weight residual
     120.60  136.47  -15.87 1.60e+00 3.91e-01 9.84e+01
  angle pdb=" OD1 ASN A 498 "
        pdb=" CG  ASN A 498 "
        pdb=" ND2 ASN A 498 "
      ideal   model   delta    sigma   weight residual
     122.60  116.64    5.96 1.00e+00 1.00e+00 3.55e+01
  angle pdb=" N   VAL A 671 "
        pdb=" CA  VAL A 671 "
        pdb=" C   VAL A 671 "
      ideal   model   delta    sigma   weight residual
     110.62  115.27   -4.65 1.02e+00 9.61e-01 2.08e+01
  angle pdb=" CA  ASP B1256 "
        pdb=" CB  ASP B1256 "
        pdb=" CG  ASP B1256 "
      ideal   model   delta    sigma   weight residual
     112.60  117.08   -4.48 1.00e+00 1.00e+00 2.01e+01
  angle pdb=" N   ILE B1148 "
        pdb=" CA  ILE B1148 "
        pdb=" C   ILE B1148 "
      ideal   model   delta    sigma   weight residual
     111.62  108.13    3.49 7.90e-01 1.60e+00 1.95e+01
  ... (remaining 11330 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.69: 4439
       15.69 -    31.38: 423
       31.38 -    47.07: 75
       47.07 -    62.76: 15
       62.76 -    78.45: 12
  Dihedral angle restraints: 4964
    sinusoidal: 2041
      harmonic: 2923
  Sorted by residual:
  dihedral pdb=" CA  ILE B1053 "
           pdb=" C   ILE B1053 "
           pdb=" N   MET B1054 "
           pdb=" CA  MET B1054 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.88  -28.12     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  GLU B1210 "
           pdb=" C   GLU B1210 "
           pdb=" N   ILE B1211 "
           pdb=" CA  ILE B1211 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.43  -20.57     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  PHE A 497 "
           pdb=" C   PHE A 497 "
           pdb=" N   ASN A 498 "
           pdb=" CA  ASN A 498 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.23   19.77     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 4961 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.252: 1237
       0.252 -    0.504: 6
       0.504 -    0.755: 0
       0.755 -    1.007: 0
       1.007 -    1.259: 1
  Chirality restraints: 1244
  Sorted by residual:
  chirality pdb=" C1  FUC F   3 "
            pdb=" O6  NAG F   1 "
            pdb=" C2  FUC F   3 "
            pdb=" O5  FUC F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-02 2.50e+03 5.32e+01
  chirality pdb=" C1  NAG A 801 "
            pdb=" ND2 ASN A 498 "
            pdb=" C2  NAG A 801 "
            pdb=" O5  NAG A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.14   -1.26 2.00e-01 2.50e+01 3.96e+01
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.67e+01
  ... (remaining 1241 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 467 "    0.067 2.00e-02 2.50e+03   5.61e-02 7.88e+01
        pdb=" CG  TRP A 467 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 467 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 467 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 467 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 467 "    0.076 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 467 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 467 "    0.085 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 467 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 467 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 548 "    0.066 2.00e-02 2.50e+03   7.39e-02 6.82e+01
        pdb=" CG  ASN A 548 "   -0.019 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 548 "   -0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 548 "   -0.124 2.00e-02 2.50e+03
        pdb=" C1  NAG A 802 "    0.085 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 802 "   -0.073 2.00e-02 2.50e+03   6.05e-02 4.57e+01
        pdb=" C7  NAG A 802 "    0.019 2.00e-02 2.50e+03
        pdb=" C8  NAG A 802 "   -0.055 2.00e-02 2.50e+03
        pdb=" N2  NAG A 802 "    0.098 2.00e-02 2.50e+03
        pdb=" O7  NAG A 802 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 613
        2.74 -     3.28: 8249
        3.28 -     3.82: 13731
        3.82 -     4.36: 16864
        4.36 -     4.90: 28701
  Nonbonded interactions: 68158
  Sorted by model distance:
  nonbonded pdb=" O   TRP B1266 "
            pdb=" NE2 GLN B1270 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" OG1 THR B1195 "
            pdb=" O   ILE B1205 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" O   PRO A 355 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NE2 GLN A 323 "
            pdb=" O   GLY A 325 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OD1 ASP A 470 "
            pdb=" NH2 ARG A 473 "
     model   vdw
     2.288 3.120
  ... (remaining 68153 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.110
  Process input model:                     22.530
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
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      :  0.011   0.176   8383  Z= 0.703
  Angle     :  1.185  15.868  11335  Z= 0.775
  Chirality :  0.086   1.259   1244
  Planarity :  0.011   0.149   1428
  Dihedral  : 13.035  78.450   3098
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1006
  helix:  1.06 (0.25), residues: 405
  sheet: -0.08 (0.33), residues: 241
  loop : -1.33 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.085   0.012   TRP A 467 
 HIS   0.013   0.004   HIS A 161 
 PHE   0.068   0.011   PHE A 299 
 TYR   0.053   0.009   TYR A 169 
 ARG   0.024   0.003   ARG B1140 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ARG cc_start: 0.6366 (tpp80) cc_final: 0.5741 (mtp85)
REVERT: A  197 MET cc_start: 0.6566 (mtm) cc_final: 0.5263 (tpt)
REVERT: A  227 ASP cc_start: 0.8194 (m-30) cc_final: 0.7946 (m-30)
REVERT: A  366 LYS cc_start: 0.6546 (mtmt) cc_final: 0.6283 (mttm)
REVERT: A  372 MET cc_start: 0.7261 (mtm) cc_final: 0.7027 (mmm)
REVERT: A  444 ARG cc_start: 0.6477 (ttp-110) cc_final: 0.6245 (ttt180)
REVERT: A  491 ARG cc_start: 0.7519 (tmt170) cc_final: 0.7252 (tmt170)
REVERT: A  520 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7509 (tmm-80)
REVERT: A  542 SER cc_start: 0.8059 (t) cc_final: 0.7844 (t)
REVERT: A  563 GLU cc_start: 0.8138 (pt0) cc_final: 0.7196 (tp30)
REVERT: A  567 VAL cc_start: 0.7421 (t) cc_final: 0.7180 (t)
REVERT: A  568 ASN cc_start: 0.8211 (t0) cc_final: 0.7877 (p0)
REVERT: A  581 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7273 (mm-30)
REVERT: B  910 ASP cc_start: 0.5165 (t0) cc_final: 0.4352 (t0)
REVERT: B  925 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7527 (mm-30)
REVERT: B 1097 LEU cc_start: 0.6800 (mm) cc_final: 0.6475 (tt)
REVERT: B 1127 ASN cc_start: 0.8545 (m-40) cc_final: 0.8332 (p0)
REVERT: B 1203 GLU cc_start: 0.5470 (mt-10) cc_final: 0.4936 (mm-30)
REVERT: B 1219 GLN cc_start: 0.7566 (pt0) cc_final: 0.6767 (pt0)
REVERT: B 1246 ASP cc_start: 0.7038 (p0) cc_final: 0.6682 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 1.7037
  time to fit residues: 318.7238
Evaluate side-chains
  131 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0050
   chunk 91 optimal weight:    0.2980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 434 ASN
A 513 ASN
B1073 ASN
B1115 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.223967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.145376 restraints weight = 8791.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.58
r_work: 0.3464 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8383  Z= 0.189
  Angle     :  0.577   8.180  11335  Z= 0.306
  Chirality :  0.046   0.473   1244
  Planarity :  0.003   0.034   1428
  Dihedral  :  6.235  56.778   1221
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  9.33 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 1006
  helix:  1.95 (0.25), residues: 408
  sheet:  0.12 (0.34), residues: 231
  loop : -1.17 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 300 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.017   0.001   PHE A 512 
 TYR   0.013   0.001   TYR A 306 
 ARG   0.005   0.001   ARG B 903 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7801 (tm-30)
REVERT: A  197 MET cc_start: 0.6778 (mtm) cc_final: 0.6168 (ttm)
REVERT: A  366 LYS cc_start: 0.7351 (mtmt) cc_final: 0.6742 (mttm)
REVERT: A  372 MET cc_start: 0.7592 (mtm) cc_final: 0.6990 (mmm)
REVERT: A  379 ASP cc_start: 0.6238 (m-30) cc_final: 0.5962 (m-30)
REVERT: A  382 MET cc_start: 0.6827 (mmt) cc_final: 0.6602 (mmt)
REVERT: A  444 ARG cc_start: 0.6943 (ttp-110) cc_final: 0.6669 (ttt180)
REVERT: A  491 ARG cc_start: 0.7537 (tmt170) cc_final: 0.7244 (tpt-90)
REVERT: A  497 PHE cc_start: 0.7996 (m-80) cc_final: 0.7766 (m-10)
REVERT: A  522 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7468 (tppt)
REVERT: A  563 GLU cc_start: 0.8126 (pt0) cc_final: 0.7491 (tp30)
REVERT: A  567 VAL cc_start: 0.8562 (t) cc_final: 0.8185 (m)
REVERT: A  568 ASN cc_start: 0.8321 (t0) cc_final: 0.7982 (p0)
REVERT: A  581 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7117 (mm-30)
REVERT: B  903 ARG cc_start: 0.6153 (mmm-85) cc_final: 0.5826 (mmm-85)
REVERT: B  910 ASP cc_start: 0.5409 (t0) cc_final: 0.4778 (t0)
REVERT: B  913 GLN cc_start: 0.5785 (pt0) cc_final: 0.5496 (pt0)
REVERT: B  925 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7587 (mm-30)
REVERT: B  955 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7671 (ptmt)
REVERT: B 1064 ARG cc_start: 0.6132 (mtm-85) cc_final: 0.5931 (mtm-85)
REVERT: B 1175 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.6145 (mtm-85)
REVERT: B 1219 GLN cc_start: 0.7709 (pt0) cc_final: 0.7257 (pt0)
REVERT: B 1226 LYS cc_start: 0.7332 (pttm) cc_final: 0.6815 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7499 (p0) cc_final: 0.7158 (p0)
  outliers start: 20
  outliers final: 6
  residues processed: 153
  average time/residue: 1.1977
  time to fit residues: 194.5916
Evaluate side-chains
  136 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  522 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  955 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1175 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 93 optimal weight:   10.0000
   chunk 64 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 96 optimal weight:    0.6980
   chunk 88 optimal weight:    9.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN
A 387 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.218194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137447 restraints weight = 8956.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.64
r_work: 0.3436 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8383  Z= 0.278
  Angle     :  0.586   7.670  11335  Z= 0.308
  Chirality :  0.047   0.444   1244
  Planarity :  0.003   0.027   1428
  Dihedral  :  5.911  55.243   1221
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.74 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.26), residues: 1006
  helix:  1.87 (0.25), residues: 412
  sheet:  0.30 (0.33), residues: 228
  loop : -1.10 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B1266 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.017   0.002   PHE A 516 
 TYR   0.018   0.001   TYR A 306 
 ARG   0.004   0.000   ARG B 903 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7743 (tm-30)
REVERT: A  197 MET cc_start: 0.6532 (mtm) cc_final: 0.5052 (tpt)
REVERT: A  366 LYS cc_start: 0.7242 (mtmt) cc_final: 0.6599 (mttm)
REVERT: A  371 TRP cc_start: 0.7753 (t60) cc_final: 0.7507 (t60)
REVERT: A  372 MET cc_start: 0.7384 (mtm) cc_final: 0.6872 (mmm)
REVERT: A  379 ASP cc_start: 0.6202 (m-30) cc_final: 0.5900 (m-30)
REVERT: A  444 ARG cc_start: 0.6913 (ttp-110) cc_final: 0.6445 (ttt180)
REVERT: A  491 ARG cc_start: 0.7545 (tmt170) cc_final: 0.7095 (tpt-90)
REVERT: A  497 PHE cc_start: 0.7972 (m-80) cc_final: 0.7588 (m-10)
REVERT: A  522 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7436 (tppt)
REVERT: A  563 GLU cc_start: 0.8102 (pt0) cc_final: 0.7467 (tp30)
REVERT: A  567 VAL cc_start: 0.8500 (t) cc_final: 0.8046 (m)
REVERT: A  568 ASN cc_start: 0.8244 (t0) cc_final: 0.7837 (p0)
REVERT: A  581 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7097 (mm-30)
REVERT: A  742 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6703 (tm-30)
REVERT: B  903 ARG cc_start: 0.6221 (mmm-85) cc_final: 0.6009 (mmm-85)
REVERT: B  910 ASP cc_start: 0.5458 (t0) cc_final: 0.4676 (t0)
REVERT: B  913 GLN cc_start: 0.5562 (pt0) cc_final: 0.5201 (pt0)
REVERT: B  925 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7637 (mm-30)
REVERT: B  947 ILE cc_start: 0.7985 (tt) cc_final: 0.7645 (tp)
REVERT: B  996 ARG cc_start: 0.6027 (mtp85) cc_final: 0.5700 (mtt180)
REVERT: B 1061 ARG cc_start: 0.6675 (mtm-85) cc_final: 0.5982 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6107 (mtm-85) cc_final: 0.5820 (mtm-85)
REVERT: B 1097 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5993 (tt)
REVERT: B 1175 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6038 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5857 (tm)
REVERT: B 1226 LYS cc_start: 0.7406 (pttm) cc_final: 0.6893 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7586 (p0) cc_final: 0.7093 (p0)
  outliers start: 26
  outliers final: 11
  residues processed: 155
  average time/residue: 1.2519
  time to fit residues: 205.5943
Evaluate side-chains
  143 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1097 LEU
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0170
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.1822

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

Flipped N/Q/H residues before XYZ refinement:
A 378 HIS
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.218590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.140016 restraints weight = 8889.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.87
r_work: 0.3436 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8383  Z= 0.248
  Angle     :  0.572   8.109  11335  Z= 0.299
  Chirality :  0.047   0.413   1244
  Planarity :  0.003   0.062   1428
  Dihedral  :  5.753  55.527   1221
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.02 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1006
  helix:  1.90 (0.25), residues: 412
  sheet:  0.39 (0.35), residues: 217
  loop : -1.06 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 985 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.017   0.001   PHE A 512 
 TYR   0.016   0.001   TYR A 306 
 ARG   0.007   0.001   ARG A 145 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6538 (mtm) cc_final: 0.5079 (tpt)
REVERT: A  366 LYS cc_start: 0.7220 (mtmt) cc_final: 0.6593 (mttm)
REVERT: A  371 TRP cc_start: 0.7746 (t60) cc_final: 0.7500 (t60)
REVERT: A  372 MET cc_start: 0.7359 (mtm) cc_final: 0.6906 (mmp)
REVERT: A  379 ASP cc_start: 0.6195 (m-30) cc_final: 0.5966 (m-30)
REVERT: A  444 ARG cc_start: 0.6895 (ttp-110) cc_final: 0.6332 (ttt180)
REVERT: A  491 ARG cc_start: 0.7539 (tmt170) cc_final: 0.7034 (tpt-90)
REVERT: A  497 PHE cc_start: 0.7942 (m-80) cc_final: 0.7562 (m-10)
REVERT: A  522 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7439 (tppt)
REVERT: A  563 GLU cc_start: 0.8159 (pt0) cc_final: 0.7526 (tp30)
REVERT: A  567 VAL cc_start: 0.8487 (t) cc_final: 0.8240 (m)
REVERT: A  581 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7196 (mm-30)
REVERT: A  742 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6760 (tm-30)
REVERT: B  903 ARG cc_start: 0.6192 (mmm-85) cc_final: 0.5978 (mmm-85)
REVERT: B  910 ASP cc_start: 0.5365 (t0) cc_final: 0.5000 (t0)
REVERT: B  925 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7702 (mm-30)
REVERT: B  996 ARG cc_start: 0.6036 (mtp85) cc_final: 0.5696 (mtt180)
REVERT: B 1061 ARG cc_start: 0.6725 (mtm-85) cc_final: 0.5994 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6178 (mtm-85) cc_final: 0.5857 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6295 (mp10)
REVERT: B 1175 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.6022 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5549 (pp)
REVERT: B 1219 GLN cc_start: 0.7171 (pt0) cc_final: 0.6873 (pt0)
REVERT: B 1226 LYS cc_start: 0.7451 (pttm) cc_final: 0.6842 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7645 (p0) cc_final: 0.7193 (p0)
REVERT: B 1265 ASN cc_start: 0.7795 (m-40) cc_final: 0.7547 (m110)
  outliers start: 25
  outliers final: 15
  residues processed: 148
  average time/residue: 1.2233
  time to fit residues: 192.5637
Evaluate side-chains
  144 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 988 GLN
B1199 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.217077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.136262 restraints weight = 8840.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.61
r_work: 0.3420 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8383  Z= 0.273
  Angle     :  0.576   9.155  11335  Z= 0.302
  Chirality :  0.046   0.349   1244
  Planarity :  0.003   0.029   1428
  Dihedral  :  5.647  56.661   1221
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 16.04 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1006
  helix:  1.79 (0.25), residues: 412
  sheet:  0.27 (0.34), residues: 229
  loop : -1.08 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 985 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.015   0.001   PHE A 516 
 TYR   0.017   0.002   TYR A 306 
 ARG   0.007   0.000   ARG A 141 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6368 (mtm) cc_final: 0.4924 (tpt)
REVERT: A  366 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6512 (mttm)
REVERT: A  372 MET cc_start: 0.7327 (mtm) cc_final: 0.6879 (mmp)
REVERT: A  444 ARG cc_start: 0.6794 (ttp-110) cc_final: 0.6280 (ttt180)
REVERT: A  491 ARG cc_start: 0.7540 (tmt170) cc_final: 0.6983 (tpt-90)
REVERT: A  515 LYS cc_start: 0.7572 (ptpp) cc_final: 0.7343 (ptpp)
REVERT: A  522 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7451 (tppt)
REVERT: A  563 GLU cc_start: 0.8144 (pt0) cc_final: 0.7575 (tp30)
REVERT: A  567 VAL cc_start: 0.8530 (t) cc_final: 0.8282 (m)
REVERT: A  581 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7324 (mm-30)
REVERT: A  742 GLN cc_start: 0.6926 (tm-30) cc_final: 0.6720 (tm-30)
REVERT: B  910 ASP cc_start: 0.5300 (t0) cc_final: 0.4969 (t0)
REVERT: B  996 ARG cc_start: 0.6088 (mtp85) cc_final: 0.5772 (mtt180)
REVERT: B 1061 ARG cc_start: 0.6719 (mtm-85) cc_final: 0.5991 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6185 (mtm-85) cc_final: 0.5856 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6162 (mp10)
REVERT: B 1115 ASN cc_start: 0.7309 (m110) cc_final: 0.6887 (t0)
REVERT: B 1175 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6078 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5556 (pp)
REVERT: B 1226 LYS cc_start: 0.7432 (pttm) cc_final: 0.6876 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7577 (p0) cc_final: 0.7123 (p0)
REVERT: B 1265 ASN cc_start: 0.7835 (m-40) cc_final: 0.7595 (m110)
  outliers start: 30
  outliers final: 13
  residues processed: 148
  average time/residue: 1.2446
  time to fit residues: 195.3047
Evaluate side-chains
  140 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  465 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 91 optimal weight:    8.9990
   chunk 61 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 76 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 46 optimal weight:    0.2980
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 513 ASN
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.219371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.138941 restraints weight = 8905.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.64
r_work: 0.3454 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8383  Z= 0.198
  Angle     :  0.554  10.706  11335  Z= 0.286
  Chirality :  0.044   0.309   1244
  Planarity :  0.003   0.035   1428
  Dihedral  :  5.429  56.858   1221
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.61 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.27), residues: 1006
  helix:  2.04 (0.25), residues: 412
  sheet:  0.28 (0.34), residues: 229
  loop : -1.06 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B1266 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.017   0.001   PHE A 512 
 TYR   0.013   0.001   TYR A 306 
 ARG   0.008   0.000   ARG A 141 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6371 (mtm) cc_final: 0.4916 (tpt)
REVERT: A  366 LYS cc_start: 0.7039 (mtmt) cc_final: 0.6441 (mttm)
REVERT: A  372 MET cc_start: 0.7366 (mtm) cc_final: 0.6869 (mmp)
REVERT: A  444 ARG cc_start: 0.6647 (ttp-110) cc_final: 0.6113 (ttt180)
REVERT: A  491 ARG cc_start: 0.7403 (tmt170) cc_final: 0.6979 (tpt-90)
REVERT: A  522 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7478 (tppt)
REVERT: A  535 TYR cc_start: 0.8494 (t80) cc_final: 0.8225 (t80)
REVERT: A  563 GLU cc_start: 0.8134 (pt0) cc_final: 0.7629 (tp30)
REVERT: A  567 VAL cc_start: 0.8533 (t) cc_final: 0.8300 (m)
REVERT: A  581 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7269 (mm-30)
REVERT: A  742 GLN cc_start: 0.6789 (tm-30) cc_final: 0.6575 (tm-30)
REVERT: B  910 ASP cc_start: 0.5338 (t0) cc_final: 0.4977 (t0)
REVERT: B  925 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7575 (mm-30)
REVERT: B  975 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7727 (ptmm)
REVERT: B  996 ARG cc_start: 0.6093 (mtp85) cc_final: 0.5815 (mtt180)
REVERT: B 1000 LYS cc_start: 0.7730 (tptp) cc_final: 0.7491 (tppp)
REVERT: B 1061 ARG cc_start: 0.6620 (mtm-85) cc_final: 0.5889 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6188 (mtm-85) cc_final: 0.5846 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6281 (mp10)
REVERT: B 1133 TYR cc_start: 0.5662 (p90) cc_final: 0.5296 (p90)
REVERT: B 1175 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.6102 (mtm-85)
REVERT: B 1192 ARG cc_start: 0.4563 (mmm160) cc_final: 0.4034 (mmm160)
REVERT: B 1193 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5654 (mm)
REVERT: B 1209 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5586 (pp)
REVERT: B 1246 ASP cc_start: 0.7461 (p0) cc_final: 0.7025 (p0)
REVERT: B 1265 ASN cc_start: 0.7838 (m-40) cc_final: 0.7620 (m110)
REVERT: B 1282 TRP cc_start: 0.7192 (m100) cc_final: 0.6853 (m100)
  outliers start: 27
  outliers final: 13
  residues processed: 147
  average time/residue: 1.2970
  time to fit residues: 202.0483
Evaluate side-chains
  145 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  522 LYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1193 LEU
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 93 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 64 optimal weight:    9.9990
   chunk 90 optimal weight:    7.9990
   chunk 88 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN
A 513 ASN
A 742 GLN
** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.217368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.137143 restraints weight = 8892.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.54
r_work: 0.3434 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8383  Z= 0.316
  Angle     :  0.604  11.197  11335  Z= 0.315
  Chirality :  0.046   0.315   1244
  Planarity :  0.003   0.028   1428
  Dihedral  :  5.531  59.184   1221
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.84 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.26), residues: 1006
  helix:  1.82 (0.25), residues: 411
  sheet:  0.17 (0.35), residues: 224
  loop : -1.11 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 985 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.014   0.002   PHE A 299 
 TYR   0.019   0.002   TYR A 306 
 ARG   0.007   0.000   ARG B 903 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.6552 (mtm) cc_final: 0.4968 (tmm)
REVERT: A  366 LYS cc_start: 0.7386 (mtmt) cc_final: 0.6722 (mttm)
REVERT: A  372 MET cc_start: 0.7580 (mtm) cc_final: 0.7102 (mmp)
REVERT: A  444 ARG cc_start: 0.7134 (ttp-110) cc_final: 0.6625 (ttt180)
REVERT: A  491 ARG cc_start: 0.7492 (tmt170) cc_final: 0.7063 (tpt-90)
REVERT: A  522 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7545 (tppt)
REVERT: A  563 GLU cc_start: 0.8201 (pt0) cc_final: 0.7795 (tp30)
REVERT: A  567 VAL cc_start: 0.8763 (t) cc_final: 0.8517 (m)
REVERT: A  570 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7011 (mtm110)
REVERT: A  581 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7438 (mm-30)
REVERT: B  910 ASP cc_start: 0.5475 (t0) cc_final: 0.5239 (t0)
REVERT: B  975 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7754 (ptmm)
REVERT: B 1000 LYS cc_start: 0.7845 (tptp) cc_final: 0.7560 (tppp)
REVERT: B 1061 ARG cc_start: 0.6648 (mtm-85) cc_final: 0.5888 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6408 (mtm-85) cc_final: 0.6045 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6517 (mp10)
REVERT: B 1175 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6263 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5762 (pp)
REVERT: B 1226 LYS cc_start: 0.7432 (pttm) cc_final: 0.6920 (ptmm)
REVERT: B 1246 ASP cc_start: 0.7532 (p0) cc_final: 0.7079 (p0)
REVERT: B 1265 ASN cc_start: 0.7913 (m-40) cc_final: 0.7661 (m110)
REVERT: B 1282 TRP cc_start: 0.7568 (m100) cc_final: 0.7172 (m100)
  outliers start: 31
  outliers final: 16
  residues processed: 151
  average time/residue: 1.3756
  time to fit residues: 220.6708
Evaluate side-chains
  151 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  522 LYS
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  944 SER
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 91 optimal weight:    9.9990
   chunk 96 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 513 ASN
B 988 GLN
** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.219604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.140070 restraints weight = 8990.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.57
r_work: 0.3470 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8383  Z= 0.205
  Angle     :  0.574  12.200  11335  Z= 0.298
  Chirality :  0.044   0.296   1244
  Planarity :  0.003   0.051   1428
  Dihedral  :  5.385  55.613   1221
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.43 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1006
  helix:  1.99 (0.25), residues: 412
  sheet:  0.20 (0.34), residues: 224
  loop : -1.05 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B1266 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.021   0.001   PHE A 512 
 TYR   0.023   0.001   TYR B1111 
 ARG   0.008   0.000   ARG A 157 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.7262 (mtm110)
REVERT: A  197 MET cc_start: 0.6563 (mtm) cc_final: 0.4970 (tmm)
REVERT: A  366 LYS cc_start: 0.7315 (mtmt) cc_final: 0.6685 (mttm)
REVERT: A  372 MET cc_start: 0.7570 (mtm) cc_final: 0.7079 (mmp)
REVERT: A  444 ARG cc_start: 0.7154 (ttp-110) cc_final: 0.6636 (ttt180)
REVERT: A  491 ARG cc_start: 0.7488 (tmt170) cc_final: 0.7062 (tpt-90)
REVERT: A  522 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7592 (tppt)
REVERT: A  535 TYR cc_start: 0.8631 (t80) cc_final: 0.8397 (t80)
REVERT: A  563 GLU cc_start: 0.8194 (pt0) cc_final: 0.7806 (tp30)
REVERT: A  567 VAL cc_start: 0.8788 (t) cc_final: 0.8561 (m)
REVERT: A  581 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7406 (mm-30)
REVERT: B  910 ASP cc_start: 0.5461 (t0) cc_final: 0.5249 (t0)
REVERT: B  975 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7818 (ptmm)
REVERT: B  982 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7167 (mt-10)
REVERT: B 1000 LYS cc_start: 0.7847 (tptp) cc_final: 0.7605 (tppp)
REVERT: B 1061 ARG cc_start: 0.6668 (mtm-85) cc_final: 0.5888 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6399 (mtm-85) cc_final: 0.6037 (mtm-85)
REVERT: B 1106 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6753 (mp10)
REVERT: B 1175 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6374 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5775 (pp)
REVERT: B 1246 ASP cc_start: 0.7550 (p0) cc_final: 0.7120 (p0)
REVERT: B 1265 ASN cc_start: 0.7917 (m-40) cc_final: 0.7663 (m110)
REVERT: B 1282 TRP cc_start: 0.7480 (m100) cc_final: 0.7038 (m100)
  outliers start: 29
  outliers final: 14
  residues processed: 148
  average time/residue: 1.5678
  time to fit residues: 245.0113
Evaluate side-chains
  149 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  522 LYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1106 GLN
Chi-restraints excluded: chain B residue 1175 ARG
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 98 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.219508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.139815 restraints weight = 9049.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.59
r_work: 0.3458 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8383  Z= 0.220
  Angle     :  0.587  11.739  11335  Z= 0.303
  Chirality :  0.044   0.289   1244
  Planarity :  0.003   0.044   1428
  Dihedral  :  5.258  49.101   1221
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.77 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1006
  helix:  2.06 (0.25), residues: 411
  sheet:  0.17 (0.34), residues: 224
  loop : -1.10 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B1266 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.012   0.001   PHE A 516 
 TYR   0.026   0.001   TYR B1133 
 ARG   0.006   0.000   ARG A 157 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ARG cc_start: 0.7476 (ttp-110) cc_final: 0.7255 (mtm110)
REVERT: A  197 MET cc_start: 0.6463 (mtm) cc_final: 0.4876 (tmm)
REVERT: A  366 LYS cc_start: 0.7315 (mtmt) cc_final: 0.6680 (mttm)
REVERT: A  372 MET cc_start: 0.7561 (mtm) cc_final: 0.7067 (mmp)
REVERT: A  379 ASP cc_start: 0.6792 (m-30) cc_final: 0.6026 (p0)
REVERT: A  382 MET cc_start: 0.6914 (mmt) cc_final: 0.6552 (mpt)
REVERT: A  444 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6617 (ttt180)
REVERT: A  491 ARG cc_start: 0.7487 (tmt170) cc_final: 0.7042 (tpt-90)
REVERT: A  522 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7572 (tppt)
REVERT: A  535 TYR cc_start: 0.8634 (t80) cc_final: 0.8402 (t80)
REVERT: A  563 GLU cc_start: 0.8221 (pt0) cc_final: 0.7767 (tp30)
REVERT: A  567 VAL cc_start: 0.8784 (t) cc_final: 0.8556 (m)
REVERT: A  581 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7410 (mm-30)
REVERT: B  910 ASP cc_start: 0.5406 (t0) cc_final: 0.5175 (t0)
REVERT: B  975 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7800 (ptmm)
REVERT: B  982 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7167 (mt-10)
REVERT: B 1000 LYS cc_start: 0.7818 (tptp) cc_final: 0.7579 (tppp)
REVERT: B 1061 ARG cc_start: 0.6635 (mtm-85) cc_final: 0.5849 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6389 (mtm-85) cc_final: 0.6021 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.5732 (pp)
REVERT: B 1246 ASP cc_start: 0.7547 (p0) cc_final: 0.7159 (p0)
REVERT: B 1265 ASN cc_start: 0.7887 (m-40) cc_final: 0.7658 (m110)
REVERT: B 1282 TRP cc_start: 0.7385 (m100) cc_final: 0.6939 (m100)
  outliers start: 26
  outliers final: 15
  residues processed: 146
  average time/residue: 1.3148
  time to fit residues: 204.1055
Evaluate side-chains
  146 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  522 LYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  615 SER
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 80 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 69 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0670
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
A 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.220523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.141639 restraints weight = 8814.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.55
r_work: 0.3488 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8383  Z= 0.198
  Angle     :  0.583  12.566  11335  Z= 0.299
  Chirality :  0.043   0.276   1244
  Planarity :  0.003   0.044   1428
  Dihedral  :  4.990  44.713   1221
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 19.80 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.26), residues: 1006
  helix:  2.09 (0.25), residues: 414
  sheet:  0.18 (0.34), residues: 224
  loop : -1.16 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B1266 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.019   0.001   PHE A 512 
 TYR   0.022   0.001   TYR B1133 
 ARG   0.006   0.000   ARG B 903 

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

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.7252 (mtm110)
REVERT: A  197 MET cc_start: 0.6474 (mtm) cc_final: 0.4915 (tmm)
REVERT: A  366 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6673 (mttm)
REVERT: A  372 MET cc_start: 0.7563 (mtm) cc_final: 0.7065 (mmp)
REVERT: A  382 MET cc_start: 0.6944 (mmt) cc_final: 0.6555 (mpt)
REVERT: A  444 ARG cc_start: 0.7024 (ttp-110) cc_final: 0.6532 (ttt180)
REVERT: A  491 ARG cc_start: 0.7483 (tmt170) cc_final: 0.7044 (tpt-90)
REVERT: A  535 TYR cc_start: 0.8644 (t80) cc_final: 0.8423 (t80)
REVERT: A  563 GLU cc_start: 0.8211 (pt0) cc_final: 0.7792 (tp30)
REVERT: B  975 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7820 (ptmm)
REVERT: B  982 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6871 (mm-30)
REVERT: B 1061 ARG cc_start: 0.6656 (mtm-85) cc_final: 0.5851 (ptp-170)
REVERT: B 1064 ARG cc_start: 0.6435 (mtm-85) cc_final: 0.6082 (mtm-85)
REVERT: B 1209 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.5794 (pp)
REVERT: B 1219 GLN cc_start: 0.7289 (pt0) cc_final: 0.5954 (pp30)
REVERT: B 1246 ASP cc_start: 0.7583 (p0) cc_final: 0.7238 (p0)
REVERT: B 1265 ASN cc_start: 0.7874 (m-40) cc_final: 0.7657 (m110)
  outliers start: 22
  outliers final: 15
  residues processed: 135
  average time/residue: 1.2460
  time to fit residues: 178.4311
Evaluate side-chains
  139 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  975 LYS
Chi-restraints excluded: chain B residue 1019 ILE
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1289 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 93 optimal weight:   20.0000
   chunk 69 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 513 ASN
B 913 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.220389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.140963 restraints weight = 8995.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.57
r_work: 0.3476 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8383  Z= 0.207
  Angle     :  0.578  11.691  11335  Z= 0.298
  Chirality :  0.043   0.265   1244
  Planarity :  0.003   0.040   1428
  Dihedral  :  4.781  42.949   1221
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.14 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.26), residues: 1006
  helix:  2.09 (0.25), residues: 414
  sheet:  0.18 (0.34), residues: 224
  loop : -1.12 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B1266 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.012   0.001   PHE A 516 
 TYR   0.019   0.001   TYR B1133 
 ARG   0.007   0.000   ARG B 903 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8816.75 seconds
wall clock time: 152 minutes 59.55 seconds (9179.55 seconds total)