Starting phenix.real_space_refine
on Thu Jul 31 02:13:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z4g_14496/07_2025/7z4g_14496.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z4g_14496/07_2025/7z4g_14496.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2025/7z4g_14496.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2025/7z4g_14496.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2025/7z4g_14496.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z4g_14496/07_2025/7z4g_14496.cif"
  }
  resolution = 3.64
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     140      5.49       5
     S      19      5.16       5
     C    7585      2.51       5
     N    2223      2.21       5
     O    2747      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12714
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1932
          Classifications: {'DNA': 1, 'RNA': 90}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 12, 'rna3p': 78}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  A%5*END:plan2': 1, '  A%5*END:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 9711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1188, 9711
          Classifications: {'peptide': 1188}
          Link IDs: {'PTRANS': 32, 'TRANS': 1155}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 625
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
    Chain: "D"
      Number of atoms: 446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 446
          Inner-chain residues flagged as termini: ['pdbres=" DA D  -2 "']
          Classifications: {'DNA': 22}
          Modifications used: {'5*END': 2}
          Link IDs: {'rna3p': 21}
  Time building chain proxies: 7.94, per 1000 atoms: 0.62
  Number of scatterers: 12714
  At special positions: 0
  Unit cell: (86.45, 130, 122.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     140     15.00
     O    2747      8.00
     N    2223      7.00
     C    7585      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.99
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 10 sheets defined
      55.3% alpha, 9.1% beta
      53 base pairs and 85 stacking pairs defined.
    Time for finding SS restraints: 4.60
  Creating SS restraints...
    Processing helix  chain 'B' and resid 22 through 26
      removed outlier: 3.569A  pdb=" N   LYS B  26 " --> pdb=" O   ASP B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 86
    Processing helix  chain 'B' and resid 86 through 94
    Processing helix  chain 'B' and resid 96 through 103
    Processing helix  chain 'B' and resid 104 through 106
      No H-bonds generated for 'chain 'B' and resid 104 through 106'
    Processing helix  chain 'B' and resid 121 through 132
    Processing helix  chain 'B' and resid 134 through 145
      removed outlier: 3.553A  pdb=" N   LEU B 138 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 164
    Processing helix  chain 'B' and resid 182 through 196
    Processing helix  chain 'B' and resid 207 through 213
    Processing helix  chain 'B' and resid 217 through 228
    Processing helix  chain 'B' and resid 236 through 247
    Processing helix  chain 'B' and resid 251 through 256
      removed outlier: 4.332A  pdb=" N   ASN B 255 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 279
    Processing helix  chain 'B' and resid 283 through 285
      No H-bonds generated for 'chain 'B' and resid 283 through 285'
    Processing helix  chain 'B' and resid 286 through 306
      removed outlier: 3.983A  pdb=" N   ASP B 304 " --> pdb=" O   ILE B 300 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ILE B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 343
    Processing helix  chain 'B' and resid 343 through 352
      removed outlier: 3.585A  pdb=" N   TYR B 347 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LYS B 348 " --> pdb=" O   PRO B 344 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLU B 349 " --> pdb=" O   GLU B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 364
    Processing helix  chain 'B' and resid 368 through 383
      Proline residue:  B 378  - end of helix
    Processing helix  chain 'B' and resid 387 through 395
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 3.869A  pdb=" N   ASN B 407 " --> pdb=" O   THR B 404 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLY B 408 " --> pdb=" O   PHE B 405 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   SER B 409 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 427
      removed outlier: 4.117A  pdb=" N   HIS B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 436
    Processing helix  chain 'B' and resid 436 through 446
    Processing helix  chain 'B' and resid 477 through 482
    Processing helix  chain 'B' and resid 483 through 494
      removed outlier: 3.556A  pdb=" N   ILE B 492 " --> pdb=" O   ALA B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 526
      removed outlier: 4.146A  pdb=" N   LYS B 526 " --> pdb=" O   ASN B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 552
    Processing helix  chain 'B' and resid 560 through 568
      removed outlier: 3.567A  pdb=" N   TYR B 568 " --> pdb=" O   LEU B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 602
    Processing helix  chain 'B' and resid 603 through 609
    Processing helix  chain 'B' and resid 612 through 626
      removed outlier: 3.520A  pdb=" N   THR B 622 " --> pdb=" O   ASP B 618 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   PHE B 626 " --> pdb=" O   THR B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 637
    Processing helix  chain 'B' and resid 638 through 640
      No H-bonds generated for 'chain 'B' and resid 638 through 640'
    Processing helix  chain 'B' and resid 644 through 654
    Processing helix  chain 'B' and resid 664 through 669
    Processing helix  chain 'B' and resid 678 through 685
    Processing helix  chain 'B' and resid 692 through 698
    Processing helix  chain 'B' and resid 702 through 712
      removed outlier: 4.241A  pdb=" N   GLU B 706 " --> pdb=" O   LEU B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 720 through 726
    Processing helix  chain 'B' and resid 730 through 751
    Processing helix  chain 'B' and resid 911 through 922
    Processing helix  chain 'B' and resid 925 through 940
      removed outlier: 3.796A  pdb=" N   LYS B 929 " --> pdb=" O   ARG B 925 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 959 through 970
      removed outlier: 3.879A  pdb=" N   VAL B 963 " --> pdb=" O   LYS B 959 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 980 through 1001
      removed outlier: 4.112A  pdb=" N   ALA B 984 " --> pdb=" O   ASN B 980 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1004 through 1009
    Processing helix  chain 'B' and resid 1043 through 1047
    Processing helix  chain 'B' and resid 1076 through 1088
      removed outlier: 3.905A  pdb=" N   PHE B1080 " --> pdb=" O   LYS B1076 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   ALA B1081 " --> pdb=" O   GLY B1077 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1127 through 1132
    Processing helix  chain 'B' and resid 1170 through 1177
    Processing helix  chain 'B' and resid 1177 through 1185
      removed outlier: 3.561A  pdb=" N   LYS B1185 " --> pdb=" O   PHE B1181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1229 through 1241
      removed outlier: 3.570A  pdb=" N   HIS B1241 " --> pdb=" O   TYR B1237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1249 through 1264
    Processing helix  chain 'B' and resid 1265 through 1280
      removed outlier: 3.652A  pdb=" N   ILE B1269 " --> pdb=" O   TYR B1265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1283 through 1297
    Processing helix  chain 'B' and resid 1298 through 1300
      No H-bonds generated for 'chain 'B' and resid 1298 through 1300'
    Processing helix  chain 'B' and resid 1301 through 1313
    Processing helix  chain 'B' and resid 1340 through 1344
    Processing helix  chain 'B' and resid 1363 through 1365
      No H-bonds generated for 'chain 'B' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 958
      removed outlier: 6.296A  pdb=" N   ILE B 759 " --> pdb=" O   ILE B 956 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   LEU B 958 " --> pdb=" O   ILE B 759 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ILE B 761 " --> pdb=" O   LEU B 958 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 32
    Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509
      removed outlier: 5.485A  pdb=" N   LEU B 508 " --> pdb=" O   GLY B 660 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539
      removed outlier: 3.847A  pdb=" N   ALA B 538 " --> pdb=" O   TYR B 529 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS B 528 " --> pdb=" O   SER B 581 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER B 581 " --> pdb=" O   LYS B 528 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1049 through 1051
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1063 through 1065
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1107 through 1111
      removed outlier: 6.909A  pdb=" N   SER B1109 " --> pdb=" O   ASP B1135 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ASP B1135 " --> pdb=" O   SER B1109 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1156 through 1167
      removed outlier: 3.557A  pdb=" N   LYS B1158 " --> pdb=" O   VAL B1149 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL B1149 " --> pdb=" O   LYS B1158 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU B1162 " --> pdb=" O   VAL B1145 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL B1145 " --> pdb=" O   GLU B1162 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TYR B1141 " --> pdb=" O   ILE B1166 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE B1196 " --> pdb=" O   LEU B1144 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1219 through 1222
      removed outlier: 6.249A  pdb=" N   GLU B1219 " --> pdb=" O   ALA B1215 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   SER B1202 " --> pdb=" O   LEU B1214 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LEU B1203 " --> pdb=" O   ILE B1348 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326

    457 hydrogen bonds defined for protein.
    1326 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      133 hydrogen bonds
      262 hydrogen bond angles
      0 basepair planarities
      53 basepair parallelities
      85 stacking parallelities
  Total time for adding SS restraints: 6.70

  Time building geometry restraints manager: 3.58 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2820
        1.33 -     1.45: 3374
        1.45 -     1.57: 6738
        1.57 -     1.69: 281
        1.69 -     1.81: 36
  Bond restraints: 13249
  Sorted by residual:
  bond pdb=" O3'  DT C  12 "
       pdb=" P    DA C  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.633 -0.026 1.50e-02 4.44e+03 3.10e+00
  bond pdb=" CG  LEU B1266 "
       pdb=" CD2 LEU B1266 "
    ideal  model  delta    sigma   weight residual
    1.521  1.574 -0.053 3.30e-02 9.18e+02 2.59e+00
  bond pdb=" N   ARG B 655 "
       pdb=" CA  ARG B 655 "
    ideal  model  delta    sigma   weight residual
    1.462  1.484 -0.021 1.32e-02 5.74e+03 2.55e+00
  bond pdb=" CA  ARG B 655 "
       pdb=" C   ARG B 655 "
    ideal  model  delta    sigma   weight residual
    1.529  1.515  0.014 1.04e-02 9.25e+03 1.89e+00
  bond pdb=" C   GLY B 752 "
       pdb=" N   ARG B 753 "
    ideal  model  delta    sigma   weight residual
    1.333  1.314  0.019 1.39e-02 5.18e+03 1.80e+00
  ... (remaining 13244 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 18153
        1.43 -     2.86: 304
        2.86 -     4.28: 42
        4.28 -     5.71: 5
        5.71 -     7.14: 1
  Bond angle restraints: 18505
  Sorted by residual:
  angle pdb=" N   ARG B 655 "
        pdb=" CA  ARG B 655 "
        pdb=" C   ARG B 655 "
      ideal   model   delta    sigma   weight residual
     107.20  114.34   -7.14 1.70e+00 3.46e-01 1.76e+01
  angle pdb=" O3'  DT C  11 "
        pdb=" C3'  DT C  11 "
        pdb=" C2'  DT C  11 "
      ideal   model   delta    sigma   weight residual
     111.50  106.48    5.02 1.50e+00 4.44e-01 1.12e+01
  angle pdb=" C2'  DC C  10 "
        pdb=" C1'  DC C  10 "
        pdb=" N1   DC C  10 "
      ideal   model   delta    sigma   weight residual
     113.50  118.22   -4.72 1.50e+00 4.44e-01 9.91e+00
  angle pdb=" C3'  DT C  11 "
        pdb=" C2'  DT C  11 "
        pdb=" C1'  DT C  11 "
      ideal   model   delta    sigma   weight residual
     101.60  105.26   -3.66 1.50e+00 4.44e-01 5.96e+00
  angle pdb=" C2'   C A  83 "
        pdb=" C1'   C A  83 "
        pdb=" N1    C A  83 "
      ideal   model   delta    sigma   weight residual
     112.00  108.35    3.65 1.50e+00 4.44e-01 5.91e+00
  ... (remaining 18500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 7067
       17.09 -    34.18: 503
       34.18 -    51.27: 233
       51.27 -    68.35: 165
       68.35 -    85.44: 20
  Dihedral angle restraints: 7988
    sinusoidal: 4495
      harmonic: 3493
  Sorted by residual:
  dihedral pdb=" CA  LYS B1263 "
           pdb=" C   LYS B1263 "
           pdb=" N   HIS B1264 "
           pdb=" CA  HIS B1264 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.68   17.32     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CG  ARG B 753 "
           pdb=" CD  ARG B 753 "
           pdb=" NE  ARG B 753 "
           pdb=" CZ  ARG B 753 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.51   44.49     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" O5'   U A  44 "
           pdb=" C5'   U A  44 "
           pdb=" C4'   U A  44 "
           pdb=" C3'   U A  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -65.00   -5.23  -59.77     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 7985 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1797
       0.046 -    0.092: 275
       0.092 -    0.137: 53
       0.137 -    0.183: 2
       0.183 -    0.229: 1
  Chirality restraints: 2128
  Sorted by residual:
  chirality pdb=" CA  ARG B 753 "
            pdb=" N   ARG B 753 "
            pdb=" C   ARG B 753 "
            pdb=" CB  ARG B 753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  ILE B 956 "
            pdb=" N   ILE B 956 "
            pdb=" C   ILE B 956 "
            pdb=" CB  ILE B 956 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" C1'   A A  42 "
            pdb=" O4'   A A  42 "
            pdb=" C2'   A A  42 "
            pdb=" N9    A A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.15 2.00e-01 2.50e+01 5.34e-01
  ... (remaining 2125 not shown)

  Planarity restraints: 1842
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 993 "   -0.012 2.00e-02 2.50e+03   2.40e-02 5.78e+00
        pdb=" C   VAL B 993 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL B 993 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLY B 994 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 991 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.11e+00
        pdb=" C   ALA B 991 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA B 991 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B 992 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A  83 "   -0.025 2.00e-02 2.50e+03   1.39e-02 4.36e+00
        pdb=" N1    C A  83 "    0.031 2.00e-02 2.50e+03
        pdb=" C2    C A  83 "    0.008 2.00e-02 2.50e+03
        pdb=" O2    C A  83 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    C A  83 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    C A  83 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C A  83 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    C A  83 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    C A  83 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1839 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1550
        2.75 -     3.29: 12666
        3.29 -     3.82: 23604
        3.82 -     4.36: 27947
        4.36 -     4.90: 42620
  Nonbonded interactions: 108387
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 209 "
            pdb=" OG  SER B 213 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O2'   G A  58 "
            pdb=" O   LEU B 455 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NZ  LYS B 140 "
            pdb=" OD2 ASP B 144 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" NZ  LYS B1161 "
            pdb=" OD1 ASP B1344 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   GLU B1304 "
            pdb=" ND2 ASN B1308 "
     model   vdw
     2.219 3.120
  ... (remaining 108382 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             66.380
  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:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     35.300
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  105.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
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      :  0.003   0.053  13249  Z= 0.155
  Angle     :  0.478   7.138  18505  Z= 0.269
  Chirality :  0.034   0.229   2128
  Planarity :  0.004   0.034   1842
  Dihedral  : 16.648  85.443   5724
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  4.89 %
    Favored  : 94.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1178
  helix:  1.99 (0.23), residues: 590
  sheet: -0.09 (0.61), residues: 78
  loop : -0.29 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 464 
 HIS   0.008   0.001   HIS B 328 
 PHE   0.012   0.001   PHE B 462 
 TYR   0.015   0.001   TYR B1001 
 ARG   0.004   0.000   ARG B 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12206 (  590)
  hydrogen bonds       : angle       5.78352 ( 1588)
  covalent geometry    : bond        0.00308 (13249)
  covalent geometry    : angle       0.47792 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 216
  time to evaluate  : 1.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8969 (tptt)
REVERT: B   80 CYS cc_start: 0.8333 (m) cc_final: 0.8092 (m)
REVERT: B   90 MET cc_start: 0.7978 (tpp) cc_final: 0.7647 (tpt)
REVERT: B  100 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.7821 (mtm-85)
REVERT: B  151 LEU cc_start: 0.8537 (tp) cc_final: 0.8083 (pt)
REVERT: B  534 MET cc_start: 0.8219 (mtp) cc_final: 0.6923 (ppp)
REVERT: B  569 PHE cc_start: 0.9358 (m-80) cc_final: 0.9112 (m-80)
REVERT: B  593 THR cc_start: 0.8038 (m) cc_final: 0.7803 (p)
REVERT: B  625 LEU cc_start: 0.8289 (mt) cc_final: 0.8085 (mt)
REVERT: B  723 HIS cc_start: 0.9258 (t70) cc_final: 0.8924 (m90)
REVERT: B 1043 MET cc_start: 0.6177 (ttp) cc_final: 0.5707 (tmm)
REVERT: B 1170 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8550 (mm-30)
REVERT: B 1242 TYR cc_start: 0.7596 (t80) cc_final: 0.7010 (t80)
REVERT: B 1268 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8713 (mp0)
  outliers start: 11
  outliers final: 2
  residues processed: 222
  average time/residue: 0.3262
  time to fit residues: 97.2427
Evaluate side-chains
  115 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue 1042 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.1980
   chunk 100 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    0.2980
   chunk 53 optimal weight:    4.9990
   chunk 103 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0270
   chunk 77 optimal weight:    6.9990
   chunk 119 optimal weight:    9.9990
   overall best weight:    1.1042

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

Flipped N/Q/H residues before XYZ refinement:
B 277 ASN
B 459 ASN
B 497 ASN
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 721 HIS
B 726 ASN
B 920 GLN
B1101 GLN
B1311 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.075450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.060890 restraints weight = 75918.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.062712 restraints weight = 40154.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.063896 restraints weight = 26212.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13249  Z= 0.132
  Angle     :  0.546   9.331  18505  Z= 0.287
  Chirality :  0.036   0.189   2128
  Planarity :  0.003   0.036   1842
  Dihedral  : 19.404  87.664   3219
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.09 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1178
  helix:  1.99 (0.22), residues: 596
  sheet:  0.41 (0.63), residues: 80
  loop : -0.14 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 464 
 HIS   0.007   0.001   HIS B 328 
 PHE   0.014   0.001   PHE B1046 
 TYR   0.018   0.001   TYR B1265 
 ARG   0.007   0.001   ARG B 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  590)
  hydrogen bonds       : angle       4.74397 ( 1588)
  covalent geometry    : bond        0.00278 (13249)
  covalent geometry    : angle       0.54618 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8887 (tptt)
REVERT: B   80 CYS cc_start: 0.8292 (m) cc_final: 0.8039 (m)
REVERT: B  271 TYR cc_start: 0.8689 (t80) cc_final: 0.8373 (t80)
REVERT: B  487 SER cc_start: 0.8324 (m) cc_final: 0.8093 (p)
REVERT: B  569 PHE cc_start: 0.9354 (m-80) cc_final: 0.9150 (m-80)
REVERT: B  682 PHE cc_start: 0.8534 (m-80) cc_final: 0.8231 (m-80)
REVERT: B  722 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9043 (pp20)
REVERT: B 1043 MET cc_start: 0.6115 (ttp) cc_final: 0.5676 (tmm)
REVERT: B 1089 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8530 (mtt)
REVERT: B 1170 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8641 (mt-10)
REVERT: B 1253 GLU cc_start: 0.9487 (tp30) cc_final: 0.8982 (mm-30)
  outliers start: 28
  outliers final: 15
  residues processed: 148
  average time/residue: 0.3027
  time to fit residues: 62.3478
Evaluate side-chains
  118 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  630 GLU
Chi-restraints excluded: chain B residue  744 VAL
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  976 ARG
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1042 ILE
Chi-restraints excluded: chain B residue 1089 MET
Chi-restraints excluded: chain B residue 1190 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 111 optimal weight:    7.9990
   chunk 100 optimal weight:    0.1980
   chunk 43 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   chunk 128 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 90 optimal weight:    8.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 329 HIS
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 698 HIS
** B 979 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 = 0.3832 r_free = 0.3832 target = 0.073835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.059099 restraints weight = 76842.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.060898 restraints weight = 41039.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.061997 restraints weight = 26706.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13249  Z= 0.170
  Angle     :  0.563  12.024  18505  Z= 0.292
  Chirality :  0.036   0.145   2128
  Planarity :  0.004   0.065   1842
  Dihedral  : 19.394  88.490   3219
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.88 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.25), residues: 1178
  helix:  1.87 (0.22), residues: 591
  sheet:  0.47 (0.62), residues: 78
  loop : -0.13 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 464 
 HIS   0.007   0.001   HIS B 328 
 PHE   0.017   0.001   PHE B1046 
 TYR   0.024   0.001   TYR B1001 
 ARG   0.012   0.001   ARG B 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  590)
  hydrogen bonds       : angle       4.64284 ( 1588)
  covalent geometry    : bond        0.00362 (13249)
  covalent geometry    : angle       0.56337 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8908 (tptt)
REVERT: B   80 CYS cc_start: 0.8343 (m) cc_final: 0.8101 (m)
REVERT: B  271 TYR cc_start: 0.8847 (t80) cc_final: 0.8646 (t80)
REVERT: B  483 ASP cc_start: 0.7928 (t0) cc_final: 0.7682 (t0)
REVERT: B  534 MET cc_start: 0.8032 (mtp) cc_final: 0.4527 (ptm)
REVERT: B  569 PHE cc_start: 0.9393 (m-80) cc_final: 0.9180 (m-80)
REVERT: B  679 ILE cc_start: 0.9066 (mm) cc_final: 0.8742 (mp)
REVERT: B  682 PHE cc_start: 0.8578 (m-80) cc_final: 0.8276 (m-80)
REVERT: B  933 GLN cc_start: 0.9552 (tp-100) cc_final: 0.9166 (tp-100)
REVERT: B 1043 MET cc_start: 0.5952 (ttp) cc_final: 0.5475 (tmm)
REVERT: B 1089 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8423 (mtt)
REVERT: B 1253 GLU cc_start: 0.9522 (tp30) cc_final: 0.8987 (mm-30)
REVERT: B 1357 GLU cc_start: 0.8244 (mp0) cc_final: 0.8002 (mp0)
  outliers start: 32
  outliers final: 23
  residues processed: 127
  average time/residue: 0.2794
  time to fit residues: 50.9365
Evaluate side-chains
  121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  694 MET
Chi-restraints excluded: chain B residue  724 ILE
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  744 VAL
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  953 VAL
Chi-restraints excluded: chain B residue  974 LYS
Chi-restraints excluded: chain B residue  976 ARG
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1042 ILE
Chi-restraints excluded: chain B residue 1089 MET
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1221 GLN
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 GLN
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 985 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.072404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.057815 restraints weight = 74850.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.059580 restraints weight = 39358.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.060729 restraints weight = 25718.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13249  Z= 0.158
  Angle     :  0.541  11.759  18505  Z= 0.281
  Chirality :  0.035   0.141   2128
  Planarity :  0.004   0.076   1842
  Dihedral  : 19.402  90.345   3219
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 12.59 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.25), residues: 1178
  helix:  1.87 (0.22), residues: 591
  sheet:  0.38 (0.60), residues: 78
  loop : -0.16 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 464 
 HIS   0.007   0.001   HIS B 328 
 PHE   0.020   0.001   PHE B1046 
 TYR   0.018   0.001   TYR B1265 
 ARG   0.008   0.001   ARG B 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  590)
  hydrogen bonds       : angle       4.55121 ( 1588)
  covalent geometry    : bond        0.00333 (13249)
  covalent geometry    : angle       0.54141 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 101
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9191 (mmtt) cc_final: 0.8935 (tptt)
REVERT: B   80 CYS cc_start: 0.8370 (m) cc_final: 0.8113 (m)
REVERT: B  271 TYR cc_start: 0.8934 (t80) cc_final: 0.8726 (t80)
REVERT: B  483 ASP cc_start: 0.8087 (t0) cc_final: 0.7847 (t0)
REVERT: B  525 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8451 (t)
REVERT: B  569 PHE cc_start: 0.9411 (m-80) cc_final: 0.9191 (m-80)
REVERT: B  755 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8204 (ptmm)
REVERT: B  933 GLN cc_start: 0.9576 (tp-100) cc_final: 0.9184 (tp-100)
REVERT: B 1043 MET cc_start: 0.5676 (ttp) cc_final: 0.5155 (tmm)
REVERT: B 1253 GLU cc_start: 0.9520 (tp30) cc_final: 0.8986 (mm-30)
REVERT: B 1357 GLU cc_start: 0.8399 (mp0) cc_final: 0.8093 (mp0)
  outliers start: 40
  outliers final: 28
  residues processed: 123
  average time/residue: 0.2488
  time to fit residues: 45.2457
Evaluate side-chains
  123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 93
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain B residue  228 GLN
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  525 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  694 MET
Chi-restraints excluded: chain B residue  724 ILE
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  744 VAL
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  755 LYS
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  974 LYS
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1166 ILE
Chi-restraints excluded: chain B residue 1167 THR
Chi-restraints excluded: chain B residue 1172 SER
Chi-restraints excluded: chain B residue 1221 GLN
Chi-restraints excluded: chain B residue 1265 TYR
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 126 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 92 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.071109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.056561 restraints weight = 76505.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.058263 restraints weight = 39929.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.059371 restraints weight = 26044.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13249  Z= 0.180
  Angle     :  0.552  11.035  18505  Z= 0.289
  Chirality :  0.036   0.200   2128
  Planarity :  0.004   0.045   1842
  Dihedral  : 19.441  91.218   3217
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.91 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.25), residues: 1178
  helix:  1.72 (0.22), residues: 598
  sheet:  0.40 (0.63), residues: 73
  loop : -0.16 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 464 
 HIS   0.007   0.001   HIS B 328 
 PHE   0.015   0.001   PHE B1235 
 TYR   0.014   0.001   TYR B1265 
 ARG   0.005   0.000   ARG B 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  590)
  hydrogen bonds       : angle       4.61268 ( 1588)
  covalent geometry    : bond        0.00378 (13249)
  covalent geometry    : angle       0.55230 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 98
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8949 (tptt)
REVERT: B   80 CYS cc_start: 0.8365 (m) cc_final: 0.8087 (m)
REVERT: B  271 TYR cc_start: 0.8974 (t80) cc_final: 0.8736 (t80)
REVERT: B  483 ASP cc_start: 0.8124 (t0) cc_final: 0.7879 (t0)
REVERT: B  525 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8522 (t)
REVERT: B  569 PHE cc_start: 0.9428 (m-80) cc_final: 0.9202 (m-80)
REVERT: B  666 LEU cc_start: 0.8594 (tp) cc_final: 0.8384 (tt)
REVERT: B  755 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8429 (ptmm)
REVERT: B  933 GLN cc_start: 0.9585 (tp-100) cc_final: 0.9124 (tp-100)
REVERT: B 1043 MET cc_start: 0.5490 (ttp) cc_final: 0.5113 (tmm)
REVERT: B 1357 GLU cc_start: 0.8495 (mp0) cc_final: 0.8222 (mp0)
  outliers start: 34
  outliers final: 26
  residues processed: 118
  average time/residue: 0.2432
  time to fit residues: 42.8858
Evaluate side-chains
  118 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  525 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  694 MET
Chi-restraints excluded: chain B residue  724 ILE
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  755 LYS
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  974 LYS
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1087 LEU
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1172 SER
Chi-restraints excluded: chain B residue 1221 GLN
Chi-restraints excluded: chain B residue 1265 TYR
Chi-restraints excluded: chain B residue 1302 ILE
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 7 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 125 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 104 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1101 GLN
B1261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.068251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.053831 restraints weight = 79428.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.055434 restraints weight = 42469.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.056495 restraints weight = 28287.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  13249  Z= 0.273
  Angle     :  0.647  11.018  18505  Z= 0.342
  Chirality :  0.039   0.161   2128
  Planarity :  0.004   0.047   1842
  Dihedral  : 19.686  93.321   3217
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 20.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 14.94 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1178
  helix:  1.26 (0.21), residues: 598
  sheet:  0.17 (0.62), residues: 75
  loop : -0.34 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 464 
 HIS   0.008   0.002   HIS B 930 
 PHE   0.023   0.002   PHE B1235 
 TYR   0.021   0.002   TYR B  25 
 ARG   0.007   0.001   ARG B 557 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05403 (  590)
  hydrogen bonds       : angle       4.97441 ( 1588)
  covalent geometry    : bond        0.00563 (13249)
  covalent geometry    : angle       0.64699 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 87
  time to evaluate  : 1.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8984 (tptt)
REVERT: B   80 CYS cc_start: 0.8425 (m) cc_final: 0.8148 (m)
REVERT: B  101 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8605 (mp)
REVERT: B  271 TYR cc_start: 0.9003 (t80) cc_final: 0.8792 (t80)
REVERT: B  383 MET cc_start: 0.8855 (tpp) cc_final: 0.8520 (tpp)
REVERT: B  569 PHE cc_start: 0.9464 (m-80) cc_final: 0.8920 (m-10)
REVERT: B  666 LEU cc_start: 0.8787 (tp) cc_final: 0.8574 (tt)
REVERT: B  755 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8246 (ptmm)
REVERT: B  933 GLN cc_start: 0.9586 (tp-100) cc_final: 0.9128 (tp-100)
REVERT: B 1043 MET cc_start: 0.5454 (ttp) cc_final: 0.5068 (tmm)
REVERT: B 1357 GLU cc_start: 0.8642 (mp0) cc_final: 0.8217 (mp0)
  outliers start: 41
  outliers final: 31
  residues processed: 117
  average time/residue: 0.2456
  time to fit residues: 42.2663
Evaluate side-chains
  109 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 76
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  624 THR
Chi-restraints excluded: chain B residue  694 MET
Chi-restraints excluded: chain B residue  724 ILE
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  755 LYS
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1087 LEU
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1172 SER
Chi-restraints excluded: chain B residue 1221 GLN
Chi-restraints excluded: chain B residue 1233 VAL
Chi-restraints excluded: chain B residue 1265 TYR
Chi-restraints excluded: chain B residue 1286 ASN
Chi-restraints excluded: chain B residue 1302 ILE
Chi-restraints excluded: chain B residue 1331 ILE
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 105 optimal weight:   10.0000
   chunk 73 optimal weight:    0.0870
   chunk 125 optimal weight:    0.6980
   chunk 4 optimal weight:   10.0000
   chunk 129 optimal weight:    8.9990
   chunk 100 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    2.9564

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

Flipped N/Q/H residues before XYZ refinement:
** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 511 HIS
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1091 GLN ** 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 = 0.3767 r_free = 0.3767 target = 0.069561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.054988 restraints weight = 78186.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.056664 restraints weight = 40950.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.057724 restraints weight = 27022.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.4452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13249  Z= 0.173
  Angle     :  0.580  12.687  18505  Z= 0.304
  Chirality :  0.037   0.174   2128
  Planarity :  0.005   0.130   1842
  Dihedral  : 19.668  92.181   3217
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.64 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.86 (0.25), residues: 1178
  helix:  1.34 (0.21), residues: 598
  sheet:  0.25 (0.58), residues: 79
  loop : -0.23 (0.29), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 464 
 HIS   0.006   0.001   HIS B 328 
 PHE   0.012   0.001   PHE B1235 
 TYR   0.039   0.002   TYR B 656 
 ARG   0.007   0.001   ARG B 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04275 (  590)
  hydrogen bonds       : angle       4.78841 ( 1588)
  covalent geometry    : bond        0.00367 (13249)
  covalent geometry    : angle       0.58001 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 85
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9226 (mmtt) cc_final: 0.8916 (tptt)
REVERT: B   80 CYS cc_start: 0.8376 (m) cc_final: 0.8079 (m)
REVERT: B  101 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8650 (mp)
REVERT: B  161 MET cc_start: 0.7963 (ptp) cc_final: 0.7721 (ptm)
REVERT: B  383 MET cc_start: 0.8883 (tpp) cc_final: 0.8667 (tpp)
REVERT: B  419 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9119 (mm)
REVERT: B  534 MET cc_start: 0.3185 (ptt) cc_final: 0.2983 (ptt)
REVERT: B  569 PHE cc_start: 0.9454 (m-80) cc_final: 0.8887 (m-10)
REVERT: B  645 ASP cc_start: 0.9380 (p0) cc_final: 0.8726 (t0)
REVERT: B  722 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9057 (pm20)
REVERT: B  755 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8145 (ptmm)
REVERT: B 1043 MET cc_start: 0.5400 (ttp) cc_final: 0.5036 (tmm)
REVERT: B 1108 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8823 (mp0)
  outliers start: 35
  outliers final: 26
  residues processed: 110
  average time/residue: 0.2714
  time to fit residues: 43.4980
Evaluate side-chains
  106 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  653 ARG
Chi-restraints excluded: chain B residue  654 ARG
Chi-restraints excluded: chain B residue  694 MET
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  755 LYS
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1087 LEU
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1172 SER
Chi-restraints excluded: chain B residue 1265 TYR
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0980
   chunk 68 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 125 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   overall best weight:    3.8188

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

Flipped N/Q/H residues before XYZ refinement:
** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.068576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.054052 restraints weight = 79339.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.055699 restraints weight = 41137.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.056770 restraints weight = 27038.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.4847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13249  Z= 0.214
  Angle     :  0.609  12.295  18505  Z= 0.322
  Chirality :  0.038   0.230   2128
  Planarity :  0.004   0.051   1842
  Dihedral  : 19.726  89.373   3217
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 19.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.17 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1178
  helix:  1.28 (0.22), residues: 597
  sheet: -0.27 (0.54), residues: 88
  loop : -0.23 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 464 
 HIS   0.010   0.002   HIS B1262 
 PHE   0.012   0.001   PHE B 462 
 TYR   0.027   0.002   TYR B 656 
 ARG   0.005   0.001   ARG B 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04847 (  590)
  hydrogen bonds       : angle       4.85597 ( 1588)
  covalent geometry    : bond        0.00452 (13249)
  covalent geometry    : angle       0.60925 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 78
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8870 (tptt)
REVERT: B   80 CYS cc_start: 0.8408 (m) cc_final: 0.8110 (m)
REVERT: B  101 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8647 (mp)
REVERT: B  161 MET cc_start: 0.8081 (ptp) cc_final: 0.7879 (ptm)
REVERT: B  271 TYR cc_start: 0.8945 (t80) cc_final: 0.8703 (t80)
REVERT: B  383 MET cc_start: 0.8895 (tpp) cc_final: 0.8466 (tpp)
REVERT: B  534 MET cc_start: 0.3488 (ptt) cc_final: 0.3131 (ptt)
REVERT: B  569 PHE cc_start: 0.9489 (m-80) cc_final: 0.8941 (m-10)
REVERT: B  645 ASP cc_start: 0.9332 (p0) cc_final: 0.8436 (t0)
REVERT: B  648 MET cc_start: 0.9127 (tmm) cc_final: 0.8503 (ppp)
REVERT: B  722 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9078 (pm20)
REVERT: B  755 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8171 (ptmm)
REVERT: B 1043 MET cc_start: 0.5425 (ttp) cc_final: 0.5054 (tmm)
  outliers start: 33
  outliers final: 28
  residues processed: 100
  average time/residue: 0.2132
  time to fit residues: 33.5560
Evaluate side-chains
  106 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 76
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  694 MET
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  755 LYS
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1087 LEU
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1166 ILE
Chi-restraints excluded: chain B residue 1172 SER
Chi-restraints excluded: chain B residue 1265 TYR
Chi-restraints excluded: chain B residue 1286 ASN
Chi-restraints excluded: chain B residue 1314 THR
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 107 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 89 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B 129 HIS
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 426 GLN
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1091 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.070603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.056196 restraints weight = 76953.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.057894 restraints weight = 39620.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.059009 restraints weight = 25800.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13249  Z= 0.119
  Angle     :  0.555  13.840  18505  Z= 0.289
  Chirality :  0.036   0.228   2128
  Planarity :  0.003   0.049   1842
  Dihedral  : 19.581  89.249   3217
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.92 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.25), residues: 1178
  helix:  1.47 (0.22), residues: 603
  sheet: -0.17 (0.56), residues: 89
  loop : -0.04 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 476 
 HIS   0.007   0.001   HIS B 328 
 PHE   0.033   0.001   PHE B1008 
 TYR   0.019   0.001   TYR B 271 
 ARG   0.005   0.000   ARG B 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  590)
  hydrogen bonds       : angle       4.55925 ( 1588)
  covalent geometry    : bond        0.00259 (13249)
  covalent geometry    : angle       0.55526 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 1.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8802 (tptt)
REVERT: B   80 CYS cc_start: 0.8300 (m) cc_final: 0.8030 (m)
REVERT: B  101 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8652 (mp)
REVERT: B  161 MET cc_start: 0.8010 (ptp) cc_final: 0.7783 (ptm)
REVERT: B  271 TYR cc_start: 0.8952 (t80) cc_final: 0.8742 (t80)
REVERT: B  383 MET cc_start: 0.8879 (tpp) cc_final: 0.8617 (tpp)
REVERT: B  483 ASP cc_start: 0.8137 (t0) cc_final: 0.7577 (p0)
REVERT: B  534 MET cc_start: 0.3464 (ptt) cc_final: 0.3117 (ptt)
REVERT: B  569 PHE cc_start: 0.9449 (m-80) cc_final: 0.9233 (m-80)
REVERT: B  645 ASP cc_start: 0.9314 (p0) cc_final: 0.8987 (t0)
REVERT: B  722 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9048 (pm20)
REVERT: B  755 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8241 (ptmm)
REVERT: B 1043 MET cc_start: 0.5454 (ttp) cc_final: 0.5077 (tmm)
REVERT: B 1089 MET cc_start: 0.8903 (mmm) cc_final: 0.8694 (mmm)
REVERT: B 1271 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8444 (pp20)
  outliers start: 27
  outliers final: 23
  residues processed: 106
  average time/residue: 0.2088
  time to fit residues: 34.2984
Evaluate side-chains
  105 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  755 LYS
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1166 ILE
Chi-restraints excluded: chain B residue 1182 LEU
Chi-restraints excluded: chain B residue 1265 TYR
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 9 optimal weight:   20.0000
   chunk 101 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 116 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 128 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 130 optimal weight:   20.0000
   chunk 64 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1262 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.068172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.053944 restraints weight = 77929.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.055549 restraints weight = 40801.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.056581 restraints weight = 26864.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.5170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13249  Z= 0.215
  Angle     :  0.627  13.610  18505  Z= 0.328
  Chirality :  0.038   0.228   2128
  Planarity :  0.004   0.048   1842
  Dihedral  : 19.694  88.571   3217
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.58 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1178
  helix:  1.23 (0.22), residues: 604
  sheet: -0.35 (0.57), residues: 92
  loop : -0.16 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 464 
 HIS   0.008   0.002   HIS B1264 
 PHE   0.052   0.002   PHE B1008 
 TYR   0.022   0.002   TYR B 136 
 ARG   0.007   0.001   ARG B 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04762 (  590)
  hydrogen bonds       : angle       4.81107 ( 1588)
  covalent geometry    : bond        0.00452 (13249)
  covalent geometry    : angle       0.62748 (18505)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8852 (tptt)
REVERT: B   80 CYS cc_start: 0.8363 (m) cc_final: 0.8086 (m)
REVERT: B  101 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8649 (mp)
REVERT: B  161 MET cc_start: 0.8086 (ptp) cc_final: 0.7850 (ptm)
REVERT: B  483 ASP cc_start: 0.8227 (t0) cc_final: 0.7538 (p0)
REVERT: B  534 MET cc_start: 0.3695 (ptt) cc_final: 0.3278 (ptt)
REVERT: B  569 PHE cc_start: 0.9475 (m-80) cc_final: 0.9251 (m-80)
REVERT: B  645 ASP cc_start: 0.9279 (p0) cc_final: 0.8413 (t0)
REVERT: B  722 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9064 (pm20)
REVERT: B  755 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8296 (ptmm)
REVERT: B 1043 MET cc_start: 0.5505 (ttp) cc_final: 0.5174 (tmm)
REVERT: B 1089 MET cc_start: 0.8976 (mmm) cc_final: 0.8756 (mmm)
  outliers start: 26
  outliers final: 24
  residues processed: 96
  average time/residue: 0.2020
  time to fit residues: 31.3026
Evaluate side-chains
  99 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  167 HIS
Chi-restraints excluded: chain B residue  175 ASN
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  713 VAL
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  755 LYS
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  946 ASN
Chi-restraints excluded: chain B residue  960 SER
Chi-restraints excluded: chain B residue  980 ASN
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1166 ILE
Chi-restraints excluded: chain B residue 1182 LEU
Chi-restraints excluded: chain B residue 1265 TYR
Chi-restraints excluded: chain B residue 1286 ASN
Chi-restraints excluded: chain B residue 1314 THR
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 115 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 101 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 121 optimal weight:    0.0070
   chunk 40 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9980
   chunk 87 optimal weight:   10.0000
   chunk 129 optimal weight:   10.0000
   overall best weight:    2.8004

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

Flipped N/Q/H residues before XYZ refinement:
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.068823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.054475 restraints weight = 77355.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.056107 restraints weight = 39949.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.057165 restraints weight = 26172.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.5315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  13249  Z= 0.167
  Angle     :  0.590  13.064  18505  Z= 0.309
  Chirality :  0.037   0.210   2128
  Planarity :  0.004   0.049   1842
  Dihedral  : 19.697  89.124   3217
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.58 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.82 (0.25), residues: 1178
  helix:  1.27 (0.22), residues: 605
  sheet: -0.10 (0.61), residues: 85
  loop : -0.16 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 476 
 HIS   0.006   0.001   HIS B 723 
 PHE   0.051   0.001   PHE B1008 
 TYR   0.020   0.002   TYR B 271 
 ARG   0.006   0.000   ARG B 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  590)
  hydrogen bonds       : angle       4.73421 ( 1588)
  covalent geometry    : bond        0.00361 (13249)
  covalent geometry    : angle       0.59041 (18505)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4389.90 seconds
wall clock time: 78 minutes 2.23 seconds (4682.23 seconds total)