Starting phenix.real_space_refine on Thu Feb 5 03:27:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6u_44288/02_2026/9b6u_44288.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6u_44288/02_2026/9b6u_44288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6u_44288/02_2026/9b6u_44288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6u_44288/02_2026/9b6u_44288.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6u_44288/02_2026/9b6u_44288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6u_44288/02_2026/9b6u_44288.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9054 2.51 5 N 2448 2.21 5 O 2793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14385 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3004 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 377} Chain: "B" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3004 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 377} Chain: "C" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3004 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 377} Chain: "D" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "E" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 845 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "G" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 845 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 845 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.17, per 1000 atoms: 0.22 Number of scatterers: 14385 At special positions: 0 Unit cell: (121.92, 202.56, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2793 8.00 N 2448 7.00 C 9054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 151 " " NAG B 401 " - " ASN B 151 " " NAG C 401 " - " ASN C 151 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 663.2 milliseconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 32 sheets defined 10.3% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.547A pdb=" N ASN A 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.795A pdb=" N LEU A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 380 through 384 removed outlier: 4.197A pdb=" N SER A 383 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.948A pdb=" N GLY B 5 " --> pdb=" O HIS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.604A pdb=" N ILE B 135 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 227 through 230 removed outlier: 3.855A pdb=" N HIS B 230 " --> pdb=" O GLU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.772A pdb=" N LEU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 227 through 230 removed outlier: 4.000A pdb=" N HIS C 230 " --> pdb=" O GLU C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.903A pdb=" N MET I 83 " --> pdb=" O TYR I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.852A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 50 current: chain 'A' and resid 112 through 129 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 112 through 129 current: chain 'A' and resid 157 through 162 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 162 current: chain 'A' and resid 202 through 206 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 202 through 206 current: chain 'A' and resid 274 through 276 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 311 removed outlier: 3.972A pdb=" N PHE A 305 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 323 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLN A 321 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN A 309 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 319 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 337 Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.329A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N MET B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 12 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA B 35 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE B 43 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN B 142 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU B 45 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG B 140 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 47 " --> pdb=" O VAL B 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 157 through 161 current: chain 'B' and resid 273 through 276 Processing sheet with id=AA8, first strand: chain 'B' and resid 21 through 26 removed outlier: 3.715A pdb=" N THR B 179 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 202 through 206 removed outlier: 3.599A pdb=" N ARG B 57 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU B 129 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU B 55 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 63 through 73 removed outlier: 4.905A pdb=" N VAL B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS B 116 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 114 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER B 112 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AB3, first strand: chain 'B' and resid 298 through 299 removed outlier: 6.870A pdb=" N LYS B 298 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 304 through 311 removed outlier: 6.704A pdb=" N GLN B 321 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B 309 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 319 " --> pdb=" O ASN B 309 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 348 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 334 through 337 removed outlier: 3.582A pdb=" N ILE B 335 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 376 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 387 " --> pdb=" O ILE B 376 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 8 through 13 removed outlier: 4.016A pdb=" N CYS C 30 " --> pdb=" O ASP C 8 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS C 29 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU C 45 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 31 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA C 35 " --> pdb=" O PRO C 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 50 current: chain 'C' and resid 109 through 129 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 109 through 129 current: chain 'C' and resid 157 through 161 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 161 current: chain 'C' and resid 202 through 206 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 202 through 206 current: chain 'C' and resid 274 through 276 Processing sheet with id=AB7, first strand: chain 'C' and resid 21 through 26 removed outlier: 3.573A pdb=" N VAL C 21 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.841A pdb=" N GLN C 321 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASN C 309 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 319 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 330 through 331 Processing sheet with id=AC2, first strand: chain 'C' and resid 334 through 337 Processing sheet with id=AC3, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.606A pdb=" N ILE D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 58 current: chain 'D' and resid 110 through 111 Processing sheet with id=AC5, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.896A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 33 through 38 removed outlier: 5.388A pdb=" N GLN E 37 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 53 through 54 current: chain 'E' and resid 97 through 98 Processing sheet with id=AC7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.964A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 13 current: chain 'G' and resid 45 through 50 removed outlier: 4.048A pdb=" N ARG G 50 " --> pdb=" O ARG G 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 53 through 54 current: chain 'G' and resid 97 through 98 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.524A pdb=" N ILE H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 removed outlier: 3.624A pdb=" N SER H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 58 current: chain 'H' and resid 110 through 111 Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.813A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4488 1.34 - 1.46: 2653 1.46 - 1.58: 7418 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 14691 Sorted by residual: bond pdb=" CA LEU B 247 " pdb=" C LEU B 247 " ideal model delta sigma weight residual 1.523 1.481 0.043 1.80e-02 3.09e+03 5.63e+00 bond pdb=" CB TRP C 389 " pdb=" CG TRP C 389 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.71e+00 bond pdb=" CB PHE B 305 " pdb=" CG PHE B 305 " ideal model delta sigma weight residual 1.502 1.551 -0.049 2.30e-02 1.89e+03 4.56e+00 bond pdb=" CB PHE C 161 " pdb=" CG PHE C 161 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.24e+00 bond pdb=" CA LEU A 65 " pdb=" CB LEU A 65 " ideal model delta sigma weight residual 1.539 1.441 0.099 4.88e-02 4.20e+02 4.07e+00 ... (remaining 14686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18556 2.09 - 4.17: 1259 4.17 - 6.26: 76 6.26 - 8.35: 7 8.35 - 10.44: 4 Bond angle restraints: 19902 Sorted by residual: angle pdb=" C VAL H 5 " pdb=" N GLU H 6 " pdb=" CA GLU H 6 " ideal model delta sigma weight residual 121.32 129.87 -8.55 2.10e+00 2.27e-01 1.66e+01 angle pdb=" C ASP H 99 " pdb=" N TYR H 100 " pdb=" CA TYR H 100 " ideal model delta sigma weight residual 120.38 125.60 -5.22 1.46e+00 4.69e-01 1.28e+01 angle pdb=" CA TYR H 100 " pdb=" CB TYR H 100 " pdb=" CG TYR H 100 " ideal model delta sigma weight residual 113.90 120.27 -6.37 1.80e+00 3.09e-01 1.25e+01 angle pdb=" N SER E 31 " pdb=" CA SER E 31 " pdb=" C SER E 31 " ideal model delta sigma weight residual 113.72 118.94 -5.22 1.52e+00 4.33e-01 1.18e+01 angle pdb=" C LYS B 73 " pdb=" N CYS B 74 " pdb=" CA CYS B 74 " ideal model delta sigma weight residual 121.03 126.50 -5.47 1.60e+00 3.91e-01 1.17e+01 ... (remaining 19897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.21: 8119 18.21 - 36.43: 536 36.43 - 54.64: 65 54.64 - 72.85: 21 72.85 - 91.06: 7 Dihedral angle restraints: 8748 sinusoidal: 3444 harmonic: 5304 Sorted by residual: dihedral pdb=" CA SER C 76 " pdb=" C SER C 76 " pdb=" N THR C 77 " pdb=" CA THR C 77 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA VAL F 5 " pdb=" C VAL F 5 " pdb=" N GLU F 6 " pdb=" CA GLU F 6 " ideal model delta harmonic sigma weight residual -180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA SER H 53 " pdb=" C SER H 53 " pdb=" N GLY H 54 " pdb=" CA GLY H 54 " ideal model delta harmonic sigma weight residual 180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 8745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1399 0.054 - 0.107: 632 0.107 - 0.161: 160 0.161 - 0.214: 23 0.214 - 0.268: 3 Chirality restraints: 2217 Sorted by residual: chirality pdb=" CA PHE H 67 " pdb=" N PHE H 67 " pdb=" C PHE H 67 " pdb=" CB PHE H 67 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 151 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA HIS C 230 " pdb=" N HIS C 230 " pdb=" C HIS C 230 " pdb=" CB HIS C 230 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2214 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 32 " -0.026 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR G 32 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR G 32 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR G 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 32 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR G 32 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G 32 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR G 32 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 119 " -0.031 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE B 119 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE B 119 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 119 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 119 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 101 " -0.027 2.00e-02 2.50e+03 1.96e-02 9.65e+00 pdb=" CG TRP C 101 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 101 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 101 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 101 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 101 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 101 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 101 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 101 " -0.001 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2185 2.77 - 3.30: 14131 3.30 - 3.83: 20837 3.83 - 4.37: 23407 4.37 - 4.90: 40740 Nonbonded interactions: 101300 Sorted by model distance: nonbonded pdb=" OE2 GLU B 46 " pdb=" NH1 ARG B 140 " model vdw 2.236 3.120 nonbonded pdb=" NZ LYS C 323 " pdb=" O ASN C 359 " model vdw 2.333 3.120 nonbonded pdb=" OE1 GLU B 84 " pdb=" OH TYR G 32 " model vdw 2.334 3.040 nonbonded pdb=" NZ LYS C 38 " pdb=" O SER C 288 " model vdw 2.340 3.120 nonbonded pdb=" NH1 ARG G 61 " pdb=" OD2 ASP G 82 " model vdw 2.345 3.120 ... (remaining 101295 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 4.000 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.090 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.009 0.099 14694 Z= 0.400 Angle : 1.067 10.435 19911 Z= 0.619 Chirality : 0.062 0.268 2217 Planarity : 0.009 0.109 2544 Dihedral : 12.747 91.063 5364 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.06 % Allowed : 0.32 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 1836 helix: -3.10 (0.49), residues: 58 sheet: -0.31 (0.18), residues: 673 loop : -0.81 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG A 94 TYR 0.041 0.007 TYR G 32 PHE 0.058 0.005 PHE B 119 TRP 0.054 0.004 TRP C 101 HIS 0.016 0.003 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00887 (14691) covalent geometry : angle 1.06420 (19902) hydrogen bonds : bond 0.22103 ( 354) hydrogen bonds : angle 8.68996 ( 828) link_NAG-ASN : bond 0.00556 ( 3) link_NAG-ASN : angle 3.91053 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 672 time to evaluate : 0.504 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: A 40 SER cc_start: 0.8549 (p) cc_final: 0.8347 (t) REVERT: A 61 TYR cc_start: 0.8258 (p90) cc_final: 0.7548 (p90) REVERT: A 148 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8354 (ptpp) REVERT: A 155 ASP cc_start: 0.8486 (t0) cc_final: 0.8130 (t0) REVERT: A 181 GLU cc_start: 0.8223 (tt0) cc_final: 0.7991 (tt0) REVERT: A 199 GLU cc_start: 0.8274 (tt0) cc_final: 0.7925 (tm-30) REVERT: A 217 TRP cc_start: 0.8181 (p-90) cc_final: 0.7744 (p-90) REVERT: A 228 MET cc_start: 0.8891 (mpp) cc_final: 0.8609 (mpp) REVERT: A 235 GLU cc_start: 0.8023 (pt0) cc_final: 0.7613 (pt0) REVERT: A 251 GLU cc_start: 0.9128 (tt0) cc_final: 0.8814 (tt0) REVERT: A 276 LEU cc_start: 0.9017 (tt) cc_final: 0.8761 (tt) REVERT: A 303 LYS cc_start: 0.8810 (mttm) cc_final: 0.8561 (pptt) REVERT: A 317 THR cc_start: 0.9816 (p) cc_final: 0.9422 (t) REVERT: A 318 VAL cc_start: 0.9686 (m) cc_final: 0.9471 (p) REVERT: A 320 MET cc_start: 0.8039 (ptt) cc_final: 0.7817 (ptt) REVERT: B 123 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8511 (mtmt) REVERT: B 131 ASP cc_start: 0.7636 (m-30) cc_final: 0.7293 (p0) REVERT: B 137 TYR cc_start: 0.8123 (m-80) cc_final: 0.7890 (m-10) REVERT: B 169 GLU cc_start: 0.7376 (tt0) cc_final: 0.6688 (tt0) REVERT: B 177 LYS cc_start: 0.8375 (pttt) cc_final: 0.7947 (ptmt) REVERT: B 198 MET cc_start: 0.8058 (mtt) cc_final: 0.7750 (mtp) REVERT: B 227 GLU cc_start: 0.9052 (tp30) cc_final: 0.8838 (tt0) REVERT: B 245 LEU cc_start: 0.8732 (mt) cc_final: 0.8478 (mt) REVERT: B 303 LYS cc_start: 0.6267 (tttt) cc_final: 0.6028 (mtpt) REVERT: B 323 LYS cc_start: 0.8412 (tttt) cc_final: 0.7723 (ttpt) REVERT: B 332 ILE cc_start: 0.9607 (mm) cc_final: 0.9304 (tt) REVERT: B 348 ILE cc_start: 0.9227 (pt) cc_final: 0.8971 (mp) REVERT: B 361 ASP cc_start: 0.8582 (t0) cc_final: 0.8380 (m-30) REVERT: B 362 GLU cc_start: 0.7965 (tt0) cc_final: 0.7379 (tt0) REVERT: B 368 ASN cc_start: 0.9359 (t0) cc_final: 0.8402 (p0) REVERT: C 38 LYS cc_start: 0.8616 (mttt) cc_final: 0.8231 (ttmt) REVERT: C 89 ASP cc_start: 0.9259 (m-30) cc_final: 0.9020 (m-30) REVERT: C 92 CYS cc_start: 0.7983 (m) cc_final: 0.7403 (m) REVERT: C 116 CYS cc_start: 0.7827 (m) cc_final: 0.7286 (m) REVERT: C 160 LYS cc_start: 0.8499 (pttm) cc_final: 0.8234 (mtpp) REVERT: C 230 HIS cc_start: 0.7597 (m90) cc_final: 0.7269 (m-70) REVERT: C 251 GLU cc_start: 0.8947 (tt0) cc_final: 0.8576 (tt0) REVERT: C 267 ASP cc_start: 0.7427 (t0) cc_final: 0.7221 (t0) REVERT: C 297 TYR cc_start: 0.8122 (m-10) cc_final: 0.7915 (m-80) REVERT: C 320 MET cc_start: 0.8121 (ptt) cc_final: 0.7549 (ptp) REVERT: C 346 LYS cc_start: 0.8758 (tptt) cc_final: 0.8377 (tppp) REVERT: D 18 LEU cc_start: 0.6434 (mt) cc_final: 0.5917 (mt) REVERT: D 35 SER cc_start: 0.8788 (m) cc_final: 0.8527 (m) REVERT: D 43 LYS cc_start: 0.8277 (mttt) cc_final: 0.8006 (tppt) REVERT: D 44 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7518 (ppt170) REVERT: D 45 LEU cc_start: 0.7135 (mt) cc_final: 0.6889 (mt) REVERT: D 95 CYS cc_start: 0.8016 (p) cc_final: 0.7805 (p) REVERT: E 23 CYS cc_start: 0.8515 (m) cc_final: 0.8211 (m) REVERT: E 35 TRP cc_start: 0.9287 (m100) cc_final: 0.8613 (m100) REVERT: E 69 GLN cc_start: 0.8339 (mt0) cc_final: 0.7718 (mt0) REVERT: E 87 TYR cc_start: 0.8360 (m-80) cc_final: 0.7819 (m-80) REVERT: E 92 ASP cc_start: 0.8718 (t70) cc_final: 0.7999 (t70) REVERT: E 98 PHE cc_start: 0.7242 (m-80) cc_final: 0.6973 (m-10) REVERT: E 104 LEU cc_start: 0.8253 (tp) cc_final: 0.8007 (tp) REVERT: F 4 LEU cc_start: 0.8332 (mt) cc_final: 0.8016 (mt) REVERT: F 36 TRP cc_start: 0.8802 (m100) cc_final: 0.8581 (m100) REVERT: F 46 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7429 (mt-10) REVERT: F 47 TRP cc_start: 0.8894 (t60) cc_final: 0.8476 (t60) REVERT: F 59 TYR cc_start: 0.8812 (m-80) cc_final: 0.8396 (m-80) REVERT: F 72 ASP cc_start: 0.8252 (t0) cc_final: 0.7882 (t0) REVERT: F 75 ARG cc_start: 0.8985 (mtp180) cc_final: 0.8672 (mtm110) REVERT: F 94 TYR cc_start: 0.8184 (m-80) cc_final: 0.6787 (m-80) REVERT: F 99 ASP cc_start: 0.8723 (p0) cc_final: 0.8521 (p0) REVERT: F 113 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8098 (tp40) REVERT: G 61 ARG cc_start: 0.7324 (ptp90) cc_final: 0.6858 (ptp-170) REVERT: G 62 PHE cc_start: 0.9164 (m-80) cc_final: 0.8951 (m-80) REVERT: G 70 ASP cc_start: 0.8500 (p0) cc_final: 0.8263 (p0) REVERT: G 87 TYR cc_start: 0.8502 (m-80) cc_final: 0.8187 (m-80) REVERT: H 36 TRP cc_start: 0.8903 (m100) cc_final: 0.8179 (m100) REVERT: H 77 ILE cc_start: 0.9028 (mm) cc_final: 0.8789 (mm) REVERT: I 85 ILE cc_start: 0.8539 (mm) cc_final: 0.8136 (tp) REVERT: I 90 GLN cc_start: 0.9373 (pp30) cc_final: 0.8962 (pp30) REVERT: I 91 TYR cc_start: 0.9031 (p90) cc_final: 0.8489 (p90) REVERT: I 92 ASP cc_start: 0.8383 (t0) cc_final: 0.8011 (t0) REVERT: I 96 PHE cc_start: 0.9229 (m-80) cc_final: 0.8734 (m-80) outliers start: 1 outliers final: 1 residues processed: 673 average time/residue: 0.1036 time to fit residues: 101.9572 Evaluate side-chains 499 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 498 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 280 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 218 GLN A 388 GLN B 67 HIS G 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109334 restraints weight = 27899.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.113333 restraints weight = 13697.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116009 restraints weight = 8485.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117780 restraints weight = 6033.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119013 restraints weight = 4725.108| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14694 Z= 0.138 Angle : 0.732 11.434 19911 Z= 0.391 Chirality : 0.048 0.239 2217 Planarity : 0.005 0.050 2544 Dihedral : 7.041 59.233 2066 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.63 % Allowed : 13.38 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 1836 helix: -1.71 (0.63), residues: 67 sheet: -0.19 (0.18), residues: 709 loop : -0.42 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 61 TYR 0.032 0.002 TYR B 194 PHE 0.036 0.002 PHE H 67 TRP 0.019 0.002 TRP A 20 HIS 0.005 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00299 (14691) covalent geometry : angle 0.72870 (19902) hydrogen bonds : bond 0.04117 ( 354) hydrogen bonds : angle 6.49070 ( 828) link_NAG-ASN : bond 0.00469 ( 3) link_NAG-ASN : angle 3.35013 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 576 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8441 (mmtp) cc_final: 0.8186 (mmtp) REVERT: A 46 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: A 61 TYR cc_start: 0.8203 (p90) cc_final: 0.7407 (p90) REVERT: A 148 LYS cc_start: 0.8795 (ptpt) cc_final: 0.8557 (ptpp) REVERT: A 152 TRP cc_start: 0.8990 (m-10) cc_final: 0.8592 (m-10) REVERT: A 155 ASP cc_start: 0.8311 (t0) cc_final: 0.7850 (t0) REVERT: A 198 MET cc_start: 0.7449 (ptp) cc_final: 0.6977 (ptp) REVERT: A 201 GLU cc_start: 0.7364 (mp0) cc_final: 0.6860 (mp0) REVERT: A 217 TRP cc_start: 0.8246 (p-90) cc_final: 0.7623 (p-90) REVERT: A 235 GLU cc_start: 0.8205 (pt0) cc_final: 0.7847 (pt0) REVERT: A 276 LEU cc_start: 0.8871 (tt) cc_final: 0.8451 (tt) REVERT: A 303 LYS cc_start: 0.8658 (mttm) cc_final: 0.8411 (ptmm) REVERT: A 309 ASN cc_start: 0.9205 (m110) cc_final: 0.8741 (t0) REVERT: A 317 THR cc_start: 0.9788 (p) cc_final: 0.9447 (t) REVERT: A 320 MET cc_start: 0.8112 (ptt) cc_final: 0.7883 (ptt) REVERT: B 13 GLU cc_start: 0.8476 (pm20) cc_final: 0.8257 (pm20) REVERT: B 169 GLU cc_start: 0.7246 (tt0) cc_final: 0.6584 (tt0) REVERT: B 177 LYS cc_start: 0.8384 (pttt) cc_final: 0.8086 (ptmt) REVERT: B 227 GLU cc_start: 0.9094 (tp30) cc_final: 0.8804 (tt0) REVERT: B 251 GLU cc_start: 0.8563 (tt0) cc_final: 0.8083 (tm-30) REVERT: B 315 HIS cc_start: 0.8462 (m90) cc_final: 0.8174 (m90) REVERT: B 348 ILE cc_start: 0.9036 (pt) cc_final: 0.8638 (mp) REVERT: B 362 GLU cc_start: 0.7850 (tt0) cc_final: 0.7407 (tt0) REVERT: B 368 ASN cc_start: 0.9278 (t0) cc_final: 0.8062 (p0) REVERT: C 38 LYS cc_start: 0.8482 (mttt) cc_final: 0.8014 (ttmt) REVERT: C 60 CYS cc_start: 0.8070 (m) cc_final: 0.7378 (m) REVERT: C 84 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: C 90 ASN cc_start: 0.8473 (m-40) cc_final: 0.8107 (m-40) REVERT: C 116 CYS cc_start: 0.8183 (m) cc_final: 0.6496 (m) REVERT: C 121 CYS cc_start: 0.8273 (p) cc_final: 0.7975 (m) REVERT: C 175 TYR cc_start: 0.8372 (m-80) cc_final: 0.8075 (m-80) REVERT: C 205 VAL cc_start: 0.8648 (m) cc_final: 0.8413 (p) REVERT: C 228 MET cc_start: 0.8364 (ttm) cc_final: 0.7858 (tpp) REVERT: C 230 HIS cc_start: 0.7441 (m90) cc_final: 0.6857 (m170) REVERT: C 251 GLU cc_start: 0.8762 (tt0) cc_final: 0.8412 (tt0) REVERT: C 297 TYR cc_start: 0.7988 (m-10) cc_final: 0.7709 (m-80) REVERT: C 320 MET cc_start: 0.8237 (ptt) cc_final: 0.7704 (ptm) REVERT: C 346 LYS cc_start: 0.8817 (tptt) cc_final: 0.8487 (tppp) REVERT: C 375 TYR cc_start: 0.8713 (m-10) cc_final: 0.8490 (m-10) REVERT: D 30 THR cc_start: 0.9676 (p) cc_final: 0.9475 (t) REVERT: D 36 TRP cc_start: 0.8886 (m100) cc_final: 0.7941 (m100) REVERT: D 92 MET cc_start: 0.5358 (tpp) cc_final: 0.5088 (tpp) REVERT: E 35 TRP cc_start: 0.9154 (m100) cc_final: 0.8584 (m100) REVERT: E 69 GLN cc_start: 0.8448 (mt0) cc_final: 0.7923 (mt0) REVERT: E 90 GLN cc_start: 0.9192 (pp30) cc_final: 0.8950 (pp30) REVERT: E 92 ASP cc_start: 0.8622 (t70) cc_final: 0.8332 (t70) REVERT: F 36 TRP cc_start: 0.8658 (m100) cc_final: 0.8103 (m100) REVERT: F 44 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7265 (mmm160) REVERT: F 72 ASP cc_start: 0.7946 (t0) cc_final: 0.7453 (t0) REVERT: F 94 TYR cc_start: 0.8017 (m-80) cc_final: 0.7294 (m-80) REVERT: F 99 ASP cc_start: 0.8671 (p0) cc_final: 0.8279 (p0) REVERT: F 113 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8274 (tp40) REVERT: G 47 LEU cc_start: 0.8770 (mm) cc_final: 0.8428 (mt) REVERT: G 69 GLN cc_start: 0.8057 (pm20) cc_final: 0.7697 (pm20) REVERT: H 36 TRP cc_start: 0.8624 (m100) cc_final: 0.8085 (m100) REVERT: I 3 ARG cc_start: 0.9164 (tpt-90) cc_final: 0.8839 (tpp80) REVERT: I 4 MET cc_start: 0.8202 (mtm) cc_final: 0.7935 (ttm) REVERT: I 28 ASP cc_start: 0.7811 (m-30) cc_final: 0.7176 (t0) REVERT: I 31 SER cc_start: 0.9071 (m) cc_final: 0.8727 (p) REVERT: I 58 VAL cc_start: 0.8839 (t) cc_final: 0.8571 (p) REVERT: I 69 GLN cc_start: 0.8733 (pt0) cc_final: 0.8235 (pm20) REVERT: I 90 GLN cc_start: 0.9519 (pp30) cc_final: 0.9011 (pp30) REVERT: I 91 TYR cc_start: 0.9194 (p90) cc_final: 0.8460 (p90) REVERT: I 92 ASP cc_start: 0.8190 (t0) cc_final: 0.7988 (t0) REVERT: I 96 PHE cc_start: 0.9259 (m-80) cc_final: 0.8906 (m-80) outliers start: 57 outliers final: 31 residues processed: 600 average time/residue: 0.0960 time to fit residues: 85.7436 Evaluate side-chains 531 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 498 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 136 optimal weight: 8.9990 chunk 1 optimal weight: 0.0270 chunk 88 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN C 280 HIS I 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108885 restraints weight = 27968.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112834 restraints weight = 13752.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115478 restraints weight = 8570.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117223 restraints weight = 6118.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118456 restraints weight = 4822.252| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14694 Z= 0.121 Angle : 0.666 13.261 19911 Z= 0.347 Chirality : 0.046 0.220 2217 Planarity : 0.004 0.050 2544 Dihedral : 6.269 61.869 2064 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.21 % Allowed : 17.72 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 1836 helix: -1.55 (0.64), residues: 67 sheet: -0.12 (0.18), residues: 730 loop : -0.34 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 50 TYR 0.028 0.002 TYR B 194 PHE 0.032 0.002 PHE H 67 TRP 0.026 0.002 TRP G 35 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00273 (14691) covalent geometry : angle 0.66370 (19902) hydrogen bonds : bond 0.03881 ( 354) hydrogen bonds : angle 6.18492 ( 828) link_NAG-ASN : bond 0.00295 ( 3) link_NAG-ASN : angle 2.68833 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 528 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8091 (mmtp) REVERT: A 46 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8308 (tp30) REVERT: A 61 TYR cc_start: 0.7962 (p90) cc_final: 0.7477 (p90) REVERT: A 148 LYS cc_start: 0.8732 (ptpt) cc_final: 0.8505 (ptpp) REVERT: A 155 ASP cc_start: 0.8234 (t0) cc_final: 0.7761 (t0) REVERT: A 199 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 203 TRP cc_start: 0.8203 (m-90) cc_final: 0.7526 (m-90) REVERT: A 217 TRP cc_start: 0.8187 (p-90) cc_final: 0.7430 (p-90) REVERT: A 230 HIS cc_start: 0.7902 (t-90) cc_final: 0.7610 (t-90) REVERT: A 235 GLU cc_start: 0.8295 (pt0) cc_final: 0.8017 (pt0) REVERT: A 254 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 303 LYS cc_start: 0.8646 (mttm) cc_final: 0.8362 (ptmm) REVERT: A 309 ASN cc_start: 0.9253 (m110) cc_final: 0.8774 (t0) REVERT: A 317 THR cc_start: 0.9798 (p) cc_final: 0.9514 (t) REVERT: A 320 MET cc_start: 0.8140 (ptt) cc_final: 0.7931 (ptt) REVERT: B 60 CYS cc_start: 0.7872 (m) cc_final: 0.7545 (m) REVERT: B 70 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8579 (mm) REVERT: B 227 GLU cc_start: 0.9079 (tp30) cc_final: 0.8791 (mt-10) REVERT: B 228 MET cc_start: 0.8959 (tpp) cc_final: 0.8291 (tpp) REVERT: B 243 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7877 (ttp-110) REVERT: B 312 ASP cc_start: 0.8357 (t0) cc_final: 0.8150 (t0) REVERT: B 317 THR cc_start: 0.9381 (p) cc_final: 0.9067 (p) REVERT: B 321 GLN cc_start: 0.7727 (mt0) cc_final: 0.6960 (mt0) REVERT: B 348 ILE cc_start: 0.9056 (pt) cc_final: 0.8605 (mp) REVERT: B 368 ASN cc_start: 0.9301 (t0) cc_final: 0.8075 (p0) REVERT: C 37 ASP cc_start: 0.8243 (t0) cc_final: 0.8011 (t0) REVERT: C 38 LYS cc_start: 0.8425 (mttt) cc_final: 0.8032 (mtmt) REVERT: C 46 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: C 60 CYS cc_start: 0.8125 (m) cc_final: 0.7410 (m) REVERT: C 84 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: C 90 ASN cc_start: 0.8580 (m-40) cc_final: 0.8038 (m-40) REVERT: C 140 ARG cc_start: 0.8854 (mtp85) cc_final: 0.8591 (mtp180) REVERT: C 228 MET cc_start: 0.8311 (ttm) cc_final: 0.7932 (tpp) REVERT: C 251 GLU cc_start: 0.8750 (tt0) cc_final: 0.8368 (tt0) REVERT: C 297 TYR cc_start: 0.7999 (m-10) cc_final: 0.7675 (m-80) REVERT: C 320 MET cc_start: 0.8245 (ptt) cc_final: 0.7750 (ptm) REVERT: C 346 LYS cc_start: 0.8885 (tptt) cc_final: 0.8456 (tppp) REVERT: D 36 TRP cc_start: 0.8833 (m100) cc_final: 0.7940 (m100) REVERT: D 43 LYS cc_start: 0.8196 (mttt) cc_final: 0.7988 (tppt) REVERT: D 92 MET cc_start: 0.5271 (tpp) cc_final: 0.4954 (tpp) REVERT: E 35 TRP cc_start: 0.9163 (m100) cc_final: 0.8882 (m100) REVERT: E 50 ARG cc_start: 0.7560 (ttt-90) cc_final: 0.7331 (tpt-90) REVERT: E 69 GLN cc_start: 0.8474 (mt0) cc_final: 0.7877 (mt0) REVERT: E 85 ILE cc_start: 0.8991 (mm) cc_final: 0.8583 (pt) REVERT: F 36 TRP cc_start: 0.8520 (m100) cc_final: 0.8114 (m100) REVERT: F 59 TYR cc_start: 0.8249 (m-80) cc_final: 0.7683 (m-80) REVERT: F 68 THR cc_start: 0.8805 (t) cc_final: 0.8434 (p) REVERT: F 72 ASP cc_start: 0.7794 (t0) cc_final: 0.7253 (t0) REVERT: F 94 TYR cc_start: 0.8002 (m-80) cc_final: 0.7327 (m-80) REVERT: F 113 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8141 (tp40) REVERT: G 69 GLN cc_start: 0.7939 (pm20) cc_final: 0.7654 (pm20) REVERT: G 87 TYR cc_start: 0.8410 (m-80) cc_final: 0.8165 (m-80) REVERT: H 3 LYS cc_start: 0.8565 (mmtt) cc_final: 0.7998 (mmtt) REVERT: H 36 TRP cc_start: 0.8190 (m100) cc_final: 0.7773 (m100) REVERT: H 92 MET cc_start: 0.6664 (tpt) cc_final: 0.6395 (tpt) REVERT: I 3 ARG cc_start: 0.9198 (tpt-90) cc_final: 0.8894 (tpp80) REVERT: I 28 ASP cc_start: 0.7887 (m-30) cc_final: 0.7396 (t0) REVERT: I 31 SER cc_start: 0.9009 (m) cc_final: 0.8733 (p) REVERT: I 58 VAL cc_start: 0.8894 (t) cc_final: 0.8649 (p) REVERT: I 69 GLN cc_start: 0.8696 (pt0) cc_final: 0.7935 (mp10) REVERT: I 90 GLN cc_start: 0.9455 (pp30) cc_final: 0.8919 (pp30) REVERT: I 96 PHE cc_start: 0.9161 (m-80) cc_final: 0.8756 (m-80) outliers start: 66 outliers final: 45 residues processed: 556 average time/residue: 0.0954 time to fit residues: 78.6027 Evaluate side-chains 543 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 493 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 140 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107223 restraints weight = 28211.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111090 restraints weight = 14059.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113689 restraints weight = 8802.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115410 restraints weight = 6309.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116647 restraints weight = 4977.680| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14694 Z= 0.151 Angle : 0.667 13.935 19911 Z= 0.346 Chirality : 0.045 0.213 2217 Planarity : 0.004 0.055 2544 Dihedral : 6.075 59.438 2064 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.42 % Allowed : 20.08 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1836 helix: -1.62 (0.57), residues: 79 sheet: -0.16 (0.18), residues: 707 loop : -0.51 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 44 TYR 0.027 0.002 TYR B 194 PHE 0.029 0.002 PHE H 67 TRP 0.037 0.002 TRP G 35 HIS 0.016 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00345 (14691) covalent geometry : angle 0.66519 (19902) hydrogen bonds : bond 0.03797 ( 354) hydrogen bonds : angle 6.06730 ( 828) link_NAG-ASN : bond 0.00258 ( 3) link_NAG-ASN : angle 2.36613 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 515 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8487 (mmtp) cc_final: 0.7833 (mttt) REVERT: A 46 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: A 148 LYS cc_start: 0.8778 (ptpt) cc_final: 0.8544 (ptpp) REVERT: A 155 ASP cc_start: 0.8236 (t0) cc_final: 0.7746 (t0) REVERT: A 217 TRP cc_start: 0.8270 (p-90) cc_final: 0.7489 (p-90) REVERT: A 230 HIS cc_start: 0.8149 (t-90) cc_final: 0.7827 (t-90) REVERT: A 235 GLU cc_start: 0.8329 (pt0) cc_final: 0.8068 (pt0) REVERT: A 254 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8600 (mp) REVERT: A 303 LYS cc_start: 0.8650 (mttm) cc_final: 0.8328 (ptmm) REVERT: A 317 THR cc_start: 0.9809 (p) cc_final: 0.9532 (t) REVERT: A 320 MET cc_start: 0.8105 (ptt) cc_final: 0.7886 (ptt) REVERT: A 321 GLN cc_start: 0.8442 (tt0) cc_final: 0.8056 (tt0) REVERT: B 60 CYS cc_start: 0.7858 (m) cc_final: 0.7476 (m) REVERT: B 142 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: B 227 GLU cc_start: 0.9163 (tp30) cc_final: 0.8815 (mt-10) REVERT: B 228 MET cc_start: 0.9010 (tpp) cc_final: 0.8590 (tpp) REVERT: B 312 ASP cc_start: 0.8378 (t0) cc_final: 0.8117 (t0) REVERT: B 317 THR cc_start: 0.9449 (p) cc_final: 0.9161 (p) REVERT: B 321 GLN cc_start: 0.7696 (mt0) cc_final: 0.7030 (mt0) REVERT: B 348 ILE cc_start: 0.9126 (pt) cc_final: 0.8686 (mp) REVERT: B 362 GLU cc_start: 0.7409 (tt0) cc_final: 0.5872 (tt0) REVERT: B 368 ASN cc_start: 0.9362 (t0) cc_final: 0.8209 (p0) REVERT: C 37 ASP cc_start: 0.8230 (t0) cc_final: 0.8016 (t0) REVERT: C 38 LYS cc_start: 0.8382 (mttt) cc_final: 0.8001 (ttmt) REVERT: C 84 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7835 (tp30) REVERT: C 90 ASN cc_start: 0.8643 (m-40) cc_final: 0.8420 (m-40) REVERT: C 205 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8368 (p) REVERT: C 208 GLN cc_start: 0.8863 (mm-40) cc_final: 0.7985 (tm-30) REVERT: C 211 GLN cc_start: 0.8379 (pt0) cc_final: 0.8130 (pt0) REVERT: C 228 MET cc_start: 0.8368 (ttm) cc_final: 0.8066 (tpp) REVERT: C 251 GLU cc_start: 0.8818 (tt0) cc_final: 0.8408 (tt0) REVERT: C 320 MET cc_start: 0.8258 (ptt) cc_final: 0.7973 (ptm) REVERT: C 346 LYS cc_start: 0.8931 (tptt) cc_final: 0.8500 (tppp) REVERT: D 36 TRP cc_start: 0.8864 (m100) cc_final: 0.7926 (m100) REVERT: D 43 LYS cc_start: 0.8258 (mttt) cc_final: 0.8040 (tppt) REVERT: D 92 MET cc_start: 0.5486 (tpp) cc_final: 0.5108 (tpp) REVERT: E 35 TRP cc_start: 0.9190 (m100) cc_final: 0.8899 (m100) REVERT: E 50 ARG cc_start: 0.7750 (ttt-90) cc_final: 0.7521 (tpt-90) REVERT: E 69 GLN cc_start: 0.8474 (mt0) cc_final: 0.7822 (mt0) REVERT: E 85 ILE cc_start: 0.8757 (mm) cc_final: 0.8423 (tp) REVERT: E 102 THR cc_start: 0.7879 (t) cc_final: 0.7461 (m) REVERT: F 36 TRP cc_start: 0.8403 (m100) cc_final: 0.8033 (m100) REVERT: F 44 ARG cc_start: 0.7546 (mmm160) cc_final: 0.7301 (mmm160) REVERT: F 59 TYR cc_start: 0.8420 (m-80) cc_final: 0.7844 (m-80) REVERT: F 68 THR cc_start: 0.8786 (t) cc_final: 0.8444 (p) REVERT: F 72 ASP cc_start: 0.7944 (t0) cc_final: 0.7419 (t0) REVERT: F 94 TYR cc_start: 0.7999 (m-80) cc_final: 0.7400 (m-80) REVERT: F 111 TRP cc_start: 0.7635 (m100) cc_final: 0.7184 (m-10) REVERT: F 113 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8137 (tp40) REVERT: G 35 TRP cc_start: 0.7341 (m-10) cc_final: 0.6433 (m-10) REVERT: G 54 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8062 (mt) REVERT: G 69 GLN cc_start: 0.8125 (pm20) cc_final: 0.7710 (pm20) REVERT: H 36 TRP cc_start: 0.8201 (m100) cc_final: 0.7704 (m100) REVERT: H 92 MET cc_start: 0.6623 (tpt) cc_final: 0.6240 (tpt) REVERT: I 3 ARG cc_start: 0.9340 (tpt-90) cc_final: 0.9114 (tpp80) REVERT: I 28 ASP cc_start: 0.8076 (m-30) cc_final: 0.7571 (t0) REVERT: I 58 VAL cc_start: 0.8949 (t) cc_final: 0.8724 (p) REVERT: I 69 GLN cc_start: 0.8766 (pt0) cc_final: 0.7985 (mp10) REVERT: I 90 GLN cc_start: 0.9375 (pp30) cc_final: 0.8956 (pp30) REVERT: I 96 PHE cc_start: 0.9239 (m-80) cc_final: 0.8861 (m-80) outliers start: 85 outliers final: 66 residues processed: 550 average time/residue: 0.0983 time to fit residues: 80.4350 Evaluate side-chains 569 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 497 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 120 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS ** G 6 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 = 0.3666 r_free = 0.3666 target = 0.132189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106771 restraints weight = 28213.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.110584 restraints weight = 14163.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113120 restraints weight = 8933.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114854 restraints weight = 6433.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115987 restraints weight = 5076.168| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14694 Z= 0.155 Angle : 0.653 14.651 19911 Z= 0.339 Chirality : 0.045 0.207 2217 Planarity : 0.004 0.051 2544 Dihedral : 5.900 57.921 2064 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.99 % Allowed : 20.59 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 1836 helix: -1.46 (0.56), residues: 82 sheet: -0.17 (0.19), residues: 679 loop : -0.58 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 75 TYR 0.025 0.002 TYR B 194 PHE 0.028 0.002 PHE D 27 TRP 0.021 0.002 TRP G 35 HIS 0.016 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00356 (14691) covalent geometry : angle 0.65093 (19902) hydrogen bonds : bond 0.03692 ( 354) hydrogen bonds : angle 6.00623 ( 828) link_NAG-ASN : bond 0.00116 ( 3) link_NAG-ASN : angle 2.35006 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 499 time to evaluate : 0.481 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: A 38 LYS cc_start: 0.8546 (mmtp) cc_final: 0.7892 (mttt) REVERT: A 46 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8371 (tp30) REVERT: A 148 LYS cc_start: 0.8735 (ptpt) cc_final: 0.8533 (ptpp) REVERT: A 155 ASP cc_start: 0.8226 (t0) cc_final: 0.7747 (t0) REVERT: A 199 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 201 GLU cc_start: 0.8291 (mp0) cc_final: 0.8076 (mp0) REVERT: A 217 TRP cc_start: 0.8299 (p-90) cc_final: 0.7521 (p-90) REVERT: A 230 HIS cc_start: 0.8222 (t-90) cc_final: 0.7881 (t-90) REVERT: A 254 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 303 LYS cc_start: 0.8658 (mttm) cc_final: 0.8312 (ptmm) REVERT: A 317 THR cc_start: 0.9826 (p) cc_final: 0.9558 (t) REVERT: A 321 GLN cc_start: 0.8364 (tt0) cc_final: 0.7950 (tt0) REVERT: B 131 ASP cc_start: 0.7579 (m-30) cc_final: 0.7244 (p0) REVERT: B 142 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: B 227 GLU cc_start: 0.9179 (tp30) cc_final: 0.8835 (mt-10) REVERT: B 312 ASP cc_start: 0.8380 (t0) cc_final: 0.8170 (t0) REVERT: B 321 GLN cc_start: 0.7731 (mt0) cc_final: 0.7047 (mt0) REVERT: B 348 ILE cc_start: 0.9135 (pt) cc_final: 0.8652 (mp) REVERT: B 362 GLU cc_start: 0.7406 (tt0) cc_final: 0.5888 (tt0) REVERT: B 368 ASN cc_start: 0.9362 (t0) cc_final: 0.8242 (p0) REVERT: C 37 ASP cc_start: 0.8298 (t0) cc_final: 0.8067 (t0) REVERT: C 38 LYS cc_start: 0.8400 (mttt) cc_final: 0.8094 (mtmt) REVERT: C 84 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: C 90 ASN cc_start: 0.8651 (m-40) cc_final: 0.8376 (m-40) REVERT: C 125 MET cc_start: 0.8212 (ttt) cc_final: 0.7650 (ttm) REVERT: C 211 GLN cc_start: 0.8393 (pt0) cc_final: 0.8188 (pt0) REVERT: C 228 MET cc_start: 0.8568 (ttm) cc_final: 0.8336 (tpp) REVERT: C 251 GLU cc_start: 0.8817 (tt0) cc_final: 0.8424 (tt0) REVERT: C 320 MET cc_start: 0.8297 (ptt) cc_final: 0.7887 (ptm) REVERT: C 346 LYS cc_start: 0.8987 (tptt) cc_final: 0.8245 (tppp) REVERT: C 366 GLU cc_start: 0.9084 (mp0) cc_final: 0.8635 (mp0) REVERT: D 36 TRP cc_start: 0.8756 (m100) cc_final: 0.7966 (m100) REVERT: D 92 MET cc_start: 0.5550 (tpp) cc_final: 0.4973 (tpp) REVERT: E 35 TRP cc_start: 0.9225 (m100) cc_final: 0.8948 (m100) REVERT: E 50 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7504 (tpt-90) REVERT: E 72 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8164 (m) REVERT: E 85 ILE cc_start: 0.8711 (mm) cc_final: 0.8376 (tp) REVERT: E 102 THR cc_start: 0.8022 (t) cc_final: 0.7676 (m) REVERT: F 36 TRP cc_start: 0.8347 (m100) cc_final: 0.7939 (m100) REVERT: F 44 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7299 (mmm160) REVERT: F 46 GLU cc_start: 0.8012 (tp30) cc_final: 0.7652 (tp30) REVERT: F 59 TYR cc_start: 0.8503 (m-80) cc_final: 0.7941 (m-80) REVERT: F 72 ASP cc_start: 0.7931 (t0) cc_final: 0.7424 (t0) REVERT: F 94 TYR cc_start: 0.7938 (m-80) cc_final: 0.7390 (m-80) REVERT: F 111 TRP cc_start: 0.7767 (m100) cc_final: 0.7413 (m-10) REVERT: F 113 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8103 (tp40) REVERT: G 69 GLN cc_start: 0.8187 (pm20) cc_final: 0.7692 (pm20) REVERT: H 36 TRP cc_start: 0.8191 (m100) cc_final: 0.7676 (m100) REVERT: I 3 ARG cc_start: 0.9354 (tpt-90) cc_final: 0.9113 (tpp80) REVERT: I 28 ASP cc_start: 0.8128 (m-30) cc_final: 0.7570 (t0) REVERT: I 69 GLN cc_start: 0.8806 (pt0) cc_final: 0.8066 (mp10) REVERT: I 90 GLN cc_start: 0.9249 (pp30) cc_final: 0.8849 (pp30) REVERT: I 96 PHE cc_start: 0.9242 (m-80) cc_final: 0.8886 (m-80) outliers start: 94 outliers final: 73 residues processed: 540 average time/residue: 0.0974 time to fit residues: 78.3329 Evaluate side-chains 566 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 488 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 55 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 123 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 113 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN C 211 GLN C 280 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109173 restraints weight = 27952.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113058 restraints weight = 13996.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115667 restraints weight = 8807.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117428 restraints weight = 6310.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118613 restraints weight = 4964.710| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14694 Z= 0.109 Angle : 0.630 15.166 19911 Z= 0.322 Chirality : 0.044 0.206 2217 Planarity : 0.004 0.048 2544 Dihedral : 5.511 58.295 2064 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.27 % Allowed : 23.01 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1836 helix: -1.15 (0.56), residues: 81 sheet: -0.12 (0.19), residues: 678 loop : -0.52 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 18 TYR 0.022 0.001 TYR B 194 PHE 0.027 0.002 PHE D 27 TRP 0.013 0.001 TRP G 35 HIS 0.008 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00247 (14691) covalent geometry : angle 0.62880 (19902) hydrogen bonds : bond 0.03236 ( 354) hydrogen bonds : angle 5.76125 ( 828) link_NAG-ASN : bond 0.00306 ( 3) link_NAG-ASN : angle 2.21761 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 505 time to evaluate : 0.521 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: A 38 LYS cc_start: 0.8593 (mmtp) cc_final: 0.7954 (mttt) REVERT: A 46 GLU cc_start: 0.8678 (tt0) cc_final: 0.8374 (tp30) REVERT: A 155 ASP cc_start: 0.8197 (t0) cc_final: 0.7703 (t0) REVERT: A 199 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 217 TRP cc_start: 0.8290 (p-90) cc_final: 0.7956 (p90) REVERT: A 228 MET cc_start: 0.8860 (mtm) cc_final: 0.8381 (mpp) REVERT: A 230 HIS cc_start: 0.8297 (t-90) cc_final: 0.7921 (t-90) REVERT: A 254 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 303 LYS cc_start: 0.8606 (mttm) cc_final: 0.8250 (ptmm) REVERT: A 317 THR cc_start: 0.9823 (p) cc_final: 0.9560 (t) REVERT: A 320 MET cc_start: 0.7906 (ptt) cc_final: 0.7651 (ptp) REVERT: A 321 GLN cc_start: 0.8302 (tt0) cc_final: 0.7883 (tt0) REVERT: B 142 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: B 227 GLU cc_start: 0.9166 (tp30) cc_final: 0.8823 (mt-10) REVERT: B 228 MET cc_start: 0.9026 (tpp) cc_final: 0.8660 (tpp) REVERT: B 312 ASP cc_start: 0.8295 (t0) cc_final: 0.8071 (t0) REVERT: B 317 THR cc_start: 0.9445 (p) cc_final: 0.9156 (p) REVERT: B 321 GLN cc_start: 0.7701 (mt0) cc_final: 0.7002 (mt0) REVERT: B 348 ILE cc_start: 0.9062 (pt) cc_final: 0.8546 (mp) REVERT: B 362 GLU cc_start: 0.7348 (tt0) cc_final: 0.5920 (tt0) REVERT: B 368 ASN cc_start: 0.9321 (t0) cc_final: 0.8123 (p0) REVERT: C 37 ASP cc_start: 0.8178 (t0) cc_final: 0.7935 (t0) REVERT: C 38 LYS cc_start: 0.8270 (mttt) cc_final: 0.7573 (mttt) REVERT: C 90 ASN cc_start: 0.8638 (m-40) cc_final: 0.8087 (t0) REVERT: C 125 MET cc_start: 0.8231 (ttt) cc_final: 0.7637 (ttm) REVERT: C 169 GLU cc_start: 0.8659 (mp0) cc_final: 0.8133 (pt0) REVERT: C 251 GLU cc_start: 0.8765 (tt0) cc_final: 0.8343 (tt0) REVERT: C 288 SER cc_start: 0.9081 (t) cc_final: 0.8542 (t) REVERT: C 320 MET cc_start: 0.8302 (ptt) cc_final: 0.7962 (ptm) REVERT: C 346 LYS cc_start: 0.8876 (tptt) cc_final: 0.8175 (tppp) REVERT: D 29 PHE cc_start: 0.8688 (t80) cc_final: 0.8290 (t80) REVERT: D 36 TRP cc_start: 0.8625 (m100) cc_final: 0.7979 (m100) REVERT: D 44 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6733 (ptt-90) REVERT: E 35 TRP cc_start: 0.9248 (m100) cc_final: 0.9020 (m100) REVERT: E 37 GLN cc_start: 0.6894 (tp-100) cc_final: 0.6682 (tp-100) REVERT: E 85 ILE cc_start: 0.8506 (mm) cc_final: 0.8042 (tp) REVERT: E 102 THR cc_start: 0.8023 (t) cc_final: 0.7669 (m) REVERT: F 36 TRP cc_start: 0.8043 (m100) cc_final: 0.7554 (m100) REVERT: F 44 ARG cc_start: 0.7497 (mmm160) cc_final: 0.7218 (mmm160) REVERT: F 46 GLU cc_start: 0.7971 (tp30) cc_final: 0.7602 (tp30) REVERT: F 59 TYR cc_start: 0.8382 (m-80) cc_final: 0.7839 (m-80) REVERT: F 72 ASP cc_start: 0.7972 (t0) cc_final: 0.7484 (t0) REVERT: F 94 TYR cc_start: 0.7699 (m-80) cc_final: 0.7268 (m-80) REVERT: F 111 TRP cc_start: 0.7639 (m100) cc_final: 0.7273 (m-10) REVERT: G 2 ILE cc_start: 0.8903 (tp) cc_final: 0.8498 (pt) REVERT: G 35 TRP cc_start: 0.7503 (m100) cc_final: 0.6411 (m-10) REVERT: G 55 PHE cc_start: 0.6688 (m-10) cc_final: 0.6043 (m-10) REVERT: G 69 GLN cc_start: 0.8154 (pm20) cc_final: 0.7694 (pm20) REVERT: G 90 GLN cc_start: 0.9418 (pp30) cc_final: 0.8988 (pp30) REVERT: H 21 SER cc_start: 0.7612 (p) cc_final: 0.7146 (t) REVERT: H 36 TRP cc_start: 0.8154 (m100) cc_final: 0.7643 (m100) REVERT: I 3 ARG cc_start: 0.9323 (tpt-90) cc_final: 0.9099 (tpp80) REVERT: I 28 ASP cc_start: 0.7994 (m-30) cc_final: 0.7454 (t0) REVERT: I 31 SER cc_start: 0.8955 (m) cc_final: 0.8657 (p) REVERT: I 69 GLN cc_start: 0.8769 (pt0) cc_final: 0.8020 (mp10) REVERT: I 90 GLN cc_start: 0.9136 (pp30) cc_final: 0.8874 (pp30) REVERT: I 91 TYR cc_start: 0.9023 (p90) cc_final: 0.8328 (p90) REVERT: I 96 PHE cc_start: 0.9184 (m-80) cc_final: 0.8803 (m-80) outliers start: 67 outliers final: 50 residues processed: 534 average time/residue: 0.1020 time to fit residues: 80.2309 Evaluate side-chains 535 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 482 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 118 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 57 optimal weight: 0.0010 chunk 88 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN B 81 HIS C 211 GLN C 280 HIS C 390 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107050 restraints weight = 28027.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110909 restraints weight = 14004.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113470 restraints weight = 8777.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115154 restraints weight = 6283.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116436 restraints weight = 4960.187| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14694 Z= 0.145 Angle : 0.645 16.275 19911 Z= 0.332 Chirality : 0.044 0.201 2217 Planarity : 0.004 0.049 2544 Dihedral : 5.530 56.020 2064 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.61 % Allowed : 21.92 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.19), residues: 1836 helix: -0.86 (0.60), residues: 81 sheet: -0.17 (0.19), residues: 674 loop : -0.58 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 50 TYR 0.039 0.002 TYR H 110 PHE 0.027 0.002 PHE D 27 TRP 0.035 0.002 TRP B 152 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00331 (14691) covalent geometry : angle 0.64376 (19902) hydrogen bonds : bond 0.03460 ( 354) hydrogen bonds : angle 5.74775 ( 828) link_NAG-ASN : bond 0.00208 ( 3) link_NAG-ASN : angle 2.09519 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 491 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8667 (mmtp) cc_final: 0.8057 (mttt) REVERT: A 46 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8246 (tp30) REVERT: A 155 ASP cc_start: 0.8202 (t0) cc_final: 0.7818 (t0) REVERT: A 193 SER cc_start: 0.9529 (m) cc_final: 0.9329 (p) REVERT: A 199 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 201 GLU cc_start: 0.8287 (mp0) cc_final: 0.8085 (mp0) REVERT: A 217 TRP cc_start: 0.8258 (p-90) cc_final: 0.7970 (p90) REVERT: A 230 HIS cc_start: 0.8293 (t-90) cc_final: 0.7913 (t-90) REVERT: A 235 GLU cc_start: 0.8390 (pm20) cc_final: 0.7849 (pm20) REVERT: A 254 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8606 (mp) REVERT: A 303 LYS cc_start: 0.8645 (mttm) cc_final: 0.8285 (ptmm) REVERT: A 317 THR cc_start: 0.9835 (p) cc_final: 0.9575 (t) REVERT: A 320 MET cc_start: 0.7964 (ptt) cc_final: 0.7729 (ptt) REVERT: B 142 GLN cc_start: 0.8432 (pt0) cc_final: 0.7897 (pt0) REVERT: B 227 GLU cc_start: 0.9180 (tp30) cc_final: 0.8818 (mt-10) REVERT: B 228 MET cc_start: 0.9124 (tpp) cc_final: 0.8723 (tpp) REVERT: B 317 THR cc_start: 0.9480 (p) cc_final: 0.9193 (p) REVERT: B 321 GLN cc_start: 0.7694 (mt0) cc_final: 0.7029 (mt0) REVERT: B 348 ILE cc_start: 0.9142 (pt) cc_final: 0.8619 (mp) REVERT: B 362 GLU cc_start: 0.7338 (tt0) cc_final: 0.5912 (tt0) REVERT: B 368 ASN cc_start: 0.9345 (t0) cc_final: 0.8157 (p0) REVERT: C 37 ASP cc_start: 0.8240 (t0) cc_final: 0.8019 (t0) REVERT: C 38 LYS cc_start: 0.8322 (mttt) cc_final: 0.7557 (mttt) REVERT: C 125 MET cc_start: 0.8247 (ttt) cc_final: 0.7732 (ttm) REVERT: C 226 ARG cc_start: 0.8607 (mpt-90) cc_final: 0.8349 (mmt90) REVERT: C 251 GLU cc_start: 0.8806 (tt0) cc_final: 0.8579 (tt0) REVERT: C 320 MET cc_start: 0.8301 (ptt) cc_final: 0.7916 (ptm) REVERT: C 346 LYS cc_start: 0.8904 (tptt) cc_final: 0.8208 (tppp) REVERT: C 366 GLU cc_start: 0.9009 (mp0) cc_final: 0.8742 (mp0) REVERT: D 36 TRP cc_start: 0.8720 (m100) cc_final: 0.8164 (m100) REVERT: D 44 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6873 (ptt-90) REVERT: D 51 ILE cc_start: 0.9345 (tt) cc_final: 0.9068 (mp) REVERT: D 113 GLN cc_start: 0.7515 (tm-30) cc_final: 0.6998 (tm-30) REVERT: E 72 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8163 (m) REVERT: E 85 ILE cc_start: 0.8423 (mm) cc_final: 0.8060 (tp) REVERT: E 102 THR cc_start: 0.8057 (t) cc_final: 0.7783 (m) REVERT: F 36 TRP cc_start: 0.8105 (m100) cc_final: 0.7579 (m100) REVERT: F 44 ARG cc_start: 0.7552 (mmm160) cc_final: 0.7252 (mmm160) REVERT: F 46 GLU cc_start: 0.8109 (tp30) cc_final: 0.7738 (tp30) REVERT: F 59 TYR cc_start: 0.8480 (m-80) cc_final: 0.7940 (m-80) REVERT: F 67 PHE cc_start: 0.8217 (m-10) cc_final: 0.7624 (m-80) REVERT: F 72 ASP cc_start: 0.7998 (t0) cc_final: 0.7509 (t0) REVERT: F 94 TYR cc_start: 0.7695 (m-80) cc_final: 0.7212 (m-80) REVERT: G 2 ILE cc_start: 0.8920 (tp) cc_final: 0.8514 (pt) REVERT: G 69 GLN cc_start: 0.8288 (pm20) cc_final: 0.7863 (pm20) REVERT: H 36 TRP cc_start: 0.8250 (m100) cc_final: 0.7631 (m100) REVERT: I 4 MET cc_start: 0.7933 (ttp) cc_final: 0.7532 (tmm) REVERT: I 28 ASP cc_start: 0.8083 (m-30) cc_final: 0.7539 (t0) REVERT: I 61 ARG cc_start: 0.9104 (ptp-110) cc_final: 0.8802 (ptp-110) REVERT: I 69 GLN cc_start: 0.8812 (pt0) cc_final: 0.8084 (mp10) REVERT: I 90 GLN cc_start: 0.9182 (pp30) cc_final: 0.8814 (pp30) REVERT: I 96 PHE cc_start: 0.9217 (m-80) cc_final: 0.8819 (m-80) outliers start: 88 outliers final: 72 residues processed: 531 average time/residue: 0.1013 time to fit residues: 80.0825 Evaluate side-chains 558 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 482 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS C 211 GLN C 280 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107545 restraints weight = 28130.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111307 restraints weight = 14278.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113833 restraints weight = 9052.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115541 restraints weight = 6530.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116752 restraints weight = 5161.956| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14694 Z= 0.133 Angle : 0.648 15.499 19911 Z= 0.331 Chirality : 0.044 0.204 2217 Planarity : 0.004 0.049 2544 Dihedral : 5.462 56.294 2064 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.97 % Allowed : 23.33 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1836 helix: -0.82 (0.60), residues: 81 sheet: -0.17 (0.19), residues: 674 loop : -0.59 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 18 TYR 0.025 0.002 TYR H 110 PHE 0.029 0.002 PHE D 27 TRP 0.037 0.002 TRP E 35 HIS 0.004 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00308 (14691) covalent geometry : angle 0.64700 (19902) hydrogen bonds : bond 0.03342 ( 354) hydrogen bonds : angle 5.66987 ( 828) link_NAG-ASN : bond 0.00222 ( 3) link_NAG-ASN : angle 2.02701 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 498 time to evaluate : 0.439 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: A 38 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8065 (mttt) REVERT: A 46 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: A 155 ASP cc_start: 0.8166 (t0) cc_final: 0.7785 (t0) REVERT: A 199 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7822 (tm-30) REVERT: A 201 GLU cc_start: 0.8245 (mp0) cc_final: 0.8036 (mp0) REVERT: A 217 TRP cc_start: 0.8236 (p-90) cc_final: 0.7954 (p90) REVERT: A 230 HIS cc_start: 0.8364 (t-90) cc_final: 0.7943 (t-90) REVERT: A 235 GLU cc_start: 0.8491 (pm20) cc_final: 0.7846 (pm20) REVERT: A 254 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8586 (mp) REVERT: A 303 LYS cc_start: 0.8614 (mttm) cc_final: 0.8196 (ptmm) REVERT: A 317 THR cc_start: 0.9844 (p) cc_final: 0.9588 (t) REVERT: A 320 MET cc_start: 0.7950 (ptt) cc_final: 0.7704 (ptt) REVERT: B 142 GLN cc_start: 0.8491 (pt0) cc_final: 0.8047 (pt0) REVERT: B 227 GLU cc_start: 0.9178 (tp30) cc_final: 0.8825 (mt-10) REVERT: B 228 MET cc_start: 0.9156 (tpp) cc_final: 0.8731 (tpp) REVERT: B 317 THR cc_start: 0.9458 (p) cc_final: 0.9175 (p) REVERT: B 321 GLN cc_start: 0.7702 (mt0) cc_final: 0.7043 (mt0) REVERT: B 348 ILE cc_start: 0.9115 (pt) cc_final: 0.8592 (mp) REVERT: B 362 GLU cc_start: 0.7348 (tt0) cc_final: 0.5943 (tt0) REVERT: B 368 ASN cc_start: 0.9335 (t0) cc_final: 0.8150 (p0) REVERT: C 37 ASP cc_start: 0.8235 (t0) cc_final: 0.8009 (t0) REVERT: C 38 LYS cc_start: 0.8317 (mttt) cc_final: 0.7505 (mttt) REVERT: C 125 MET cc_start: 0.8364 (ttt) cc_final: 0.7851 (ttm) REVERT: C 169 GLU cc_start: 0.8655 (mp0) cc_final: 0.8141 (pt0) REVERT: C 226 ARG cc_start: 0.8599 (mpt-90) cc_final: 0.8332 (mmt90) REVERT: C 251 GLU cc_start: 0.8798 (tt0) cc_final: 0.8568 (tt0) REVERT: C 288 SER cc_start: 0.9170 (t) cc_final: 0.8511 (t) REVERT: C 320 MET cc_start: 0.8337 (ptt) cc_final: 0.7987 (ptm) REVERT: C 346 LYS cc_start: 0.8905 (tptt) cc_final: 0.8420 (mmmm) REVERT: D 36 TRP cc_start: 0.8711 (m100) cc_final: 0.8162 (m100) REVERT: D 44 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6968 (ptt-90) REVERT: D 51 ILE cc_start: 0.9269 (tt) cc_final: 0.9024 (mp) REVERT: D 92 MET cc_start: 0.4913 (tpp) cc_final: 0.4651 (tpp) REVERT: D 108 MET cc_start: 0.7607 (mpp) cc_final: 0.7376 (mpp) REVERT: E 85 ILE cc_start: 0.8555 (mm) cc_final: 0.8179 (tp) REVERT: E 102 THR cc_start: 0.8080 (t) cc_final: 0.7782 (m) REVERT: F 21 SER cc_start: 0.9163 (m) cc_final: 0.8903 (p) REVERT: F 36 TRP cc_start: 0.8057 (m100) cc_final: 0.7559 (m100) REVERT: F 44 ARG cc_start: 0.7519 (mmm160) cc_final: 0.7213 (mmm160) REVERT: F 46 GLU cc_start: 0.8083 (tp30) cc_final: 0.7742 (tp30) REVERT: F 59 TYR cc_start: 0.8466 (m-80) cc_final: 0.7926 (m-80) REVERT: F 67 PHE cc_start: 0.8248 (m-10) cc_final: 0.7628 (m-80) REVERT: F 72 ASP cc_start: 0.8030 (t0) cc_final: 0.7562 (t0) REVERT: F 94 TYR cc_start: 0.7690 (m-80) cc_final: 0.7143 (m-80) REVERT: G 2 ILE cc_start: 0.8913 (tp) cc_final: 0.8493 (pt) REVERT: G 69 GLN cc_start: 0.8267 (pm20) cc_final: 0.7854 (pm20) REVERT: H 36 TRP cc_start: 0.8269 (m100) cc_final: 0.7603 (m100) REVERT: I 4 MET cc_start: 0.8020 (ttp) cc_final: 0.7489 (tmm) REVERT: I 28 ASP cc_start: 0.8058 (m-30) cc_final: 0.7505 (t0) REVERT: I 55 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7576 (t80) REVERT: I 61 ARG cc_start: 0.9066 (ptp-110) cc_final: 0.8738 (ptp-110) REVERT: I 69 GLN cc_start: 0.8786 (pt0) cc_final: 0.8068 (mp10) REVERT: I 90 GLN cc_start: 0.9171 (pp30) cc_final: 0.8809 (pp30) REVERT: I 96 PHE cc_start: 0.9203 (m-80) cc_final: 0.8771 (m-80) outliers start: 78 outliers final: 66 residues processed: 533 average time/residue: 0.0978 time to fit residues: 76.9567 Evaluate side-chains 555 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 485 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 55 PHE Chi-restraints excluded: chain I residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 160 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 60 optimal weight: 0.0170 chunk 149 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS C 211 GLN C 280 HIS C 390 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112885 restraints weight = 27543.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116836 restraints weight = 13567.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119427 restraints weight = 8438.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121268 restraints weight = 6001.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122464 restraints weight = 4678.379| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14694 Z= 0.113 Angle : 0.663 15.806 19911 Z= 0.331 Chirality : 0.044 0.204 2217 Planarity : 0.004 0.048 2544 Dihedral : 5.228 56.625 2064 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.63 % Allowed : 25.94 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1836 helix: -0.80 (0.65), residues: 69 sheet: -0.16 (0.19), residues: 678 loop : -0.47 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 18 TYR 0.021 0.001 TYR I 87 PHE 0.029 0.002 PHE D 27 TRP 0.056 0.002 TRP E 35 HIS 0.006 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00263 (14691) covalent geometry : angle 0.66136 (19902) hydrogen bonds : bond 0.03114 ( 354) hydrogen bonds : angle 5.59730 ( 828) link_NAG-ASN : bond 0.00394 ( 3) link_NAG-ASN : angle 1.96093 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 503 time to evaluate : 0.476 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: A 46 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: A 142 GLN cc_start: 0.8345 (tp40) cc_final: 0.7694 (tp-100) REVERT: A 148 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8207 (mtmm) REVERT: A 155 ASP cc_start: 0.8117 (t0) cc_final: 0.7636 (t0) REVERT: A 199 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 217 TRP cc_start: 0.8307 (p-90) cc_final: 0.8049 (p90) REVERT: A 230 HIS cc_start: 0.8285 (t-90) cc_final: 0.7904 (t-90) REVERT: A 235 GLU cc_start: 0.8487 (pm20) cc_final: 0.7833 (pm20) REVERT: A 254 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8562 (mp) REVERT: A 308 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8608 (pttt) REVERT: A 317 THR cc_start: 0.9810 (p) cc_final: 0.9570 (t) REVERT: A 320 MET cc_start: 0.7905 (ptt) cc_final: 0.7623 (ptp) REVERT: B 60 CYS cc_start: 0.7557 (m) cc_final: 0.6729 (m) REVERT: B 142 GLN cc_start: 0.8406 (pt0) cc_final: 0.7869 (pt0) REVERT: B 227 GLU cc_start: 0.9116 (tp30) cc_final: 0.8797 (mt-10) REVERT: B 228 MET cc_start: 0.9196 (tpp) cc_final: 0.8995 (tpp) REVERT: B 317 THR cc_start: 0.9398 (p) cc_final: 0.9112 (p) REVERT: B 321 GLN cc_start: 0.7633 (mt0) cc_final: 0.6967 (mt0) REVERT: B 340 LEU cc_start: 0.8864 (mt) cc_final: 0.8622 (mm) REVERT: B 348 ILE cc_start: 0.9085 (pt) cc_final: 0.8501 (mp) REVERT: B 362 GLU cc_start: 0.7249 (tt0) cc_final: 0.5846 (tt0) REVERT: B 368 ASN cc_start: 0.9329 (t0) cc_final: 0.8114 (p0) REVERT: C 37 ASP cc_start: 0.8029 (t0) cc_final: 0.7768 (t0) REVERT: C 125 MET cc_start: 0.8374 (ttt) cc_final: 0.7859 (ttm) REVERT: C 169 GLU cc_start: 0.8616 (mp0) cc_final: 0.8183 (pt0) REVERT: C 208 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8762 (mm-40) REVERT: C 251 GLU cc_start: 0.8758 (tt0) cc_final: 0.8361 (tt0) REVERT: C 320 MET cc_start: 0.8405 (ptt) cc_final: 0.8070 (ptm) REVERT: C 346 LYS cc_start: 0.8896 (tptt) cc_final: 0.8319 (mmmm) REVERT: D 36 TRP cc_start: 0.8612 (m100) cc_final: 0.8068 (m100) REVERT: D 51 ILE cc_start: 0.9221 (tt) cc_final: 0.9016 (mp) REVERT: D 66 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.7297 (ptm160) REVERT: D 108 MET cc_start: 0.7624 (mpp) cc_final: 0.7389 (mpp) REVERT: E 85 ILE cc_start: 0.8585 (mm) cc_final: 0.8201 (tp) REVERT: F 21 SER cc_start: 0.9084 (m) cc_final: 0.8852 (p) REVERT: F 36 TRP cc_start: 0.7940 (m100) cc_final: 0.7591 (m100) REVERT: F 44 ARG cc_start: 0.7528 (mmm160) cc_final: 0.7219 (mmm160) REVERT: F 46 GLU cc_start: 0.8101 (tp30) cc_final: 0.7801 (tp30) REVERT: F 59 TYR cc_start: 0.8410 (m-80) cc_final: 0.7885 (m-80) REVERT: F 67 PHE cc_start: 0.8228 (m-10) cc_final: 0.7573 (m-80) REVERT: F 72 ASP cc_start: 0.8126 (t0) cc_final: 0.7676 (t0) REVERT: F 94 TYR cc_start: 0.7645 (m-80) cc_final: 0.7278 (m-80) REVERT: G 2 ILE cc_start: 0.8903 (tp) cc_final: 0.8514 (pt) REVERT: G 69 GLN cc_start: 0.8243 (pm20) cc_final: 0.8004 (pm20) REVERT: G 90 GLN cc_start: 0.9460 (pp30) cc_final: 0.9026 (pp30) REVERT: H 36 TRP cc_start: 0.8173 (m100) cc_final: 0.7647 (m100) REVERT: H 72 ASP cc_start: 0.8274 (m-30) cc_final: 0.8033 (m-30) REVERT: I 4 MET cc_start: 0.8166 (ttp) cc_final: 0.7320 (tmm) REVERT: I 28 ASP cc_start: 0.7928 (m-30) cc_final: 0.7430 (t0) REVERT: I 31 SER cc_start: 0.8894 (m) cc_final: 0.8582 (p) REVERT: I 55 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7676 (t80) REVERT: I 61 ARG cc_start: 0.9082 (ptp-110) cc_final: 0.8780 (ptp-110) REVERT: I 69 GLN cc_start: 0.8814 (pt0) cc_final: 0.8075 (mp10) REVERT: I 90 GLN cc_start: 0.9202 (pp30) cc_final: 0.8840 (pp30) REVERT: I 96 PHE cc_start: 0.9205 (m-80) cc_final: 0.8851 (m-80) REVERT: I 102 THR cc_start: 0.8753 (m) cc_final: 0.8206 (p) outliers start: 57 outliers final: 49 residues processed: 526 average time/residue: 0.0989 time to fit residues: 77.0631 Evaluate side-chains 537 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 485 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 55 PHE Chi-restraints excluded: chain I residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 57 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 142 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 162 optimal weight: 0.0570 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 211 GLN C 390 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114751 restraints weight = 27482.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118545 restraints weight = 13937.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121095 restraints weight = 8777.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122744 restraints weight = 6275.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123959 restraints weight = 4948.774| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14694 Z= 0.114 Angle : 0.668 16.261 19911 Z= 0.332 Chirality : 0.044 0.206 2217 Planarity : 0.004 0.048 2544 Dihedral : 5.135 56.177 2064 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.82 % Allowed : 26.45 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 1836 helix: -0.75 (0.66), residues: 70 sheet: -0.17 (0.19), residues: 706 loop : -0.52 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 18 TYR 0.019 0.001 TYR B 194 PHE 0.029 0.002 PHE D 27 TRP 0.049 0.002 TRP E 35 HIS 0.003 0.001 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00267 (14691) covalent geometry : angle 0.66663 (19902) hydrogen bonds : bond 0.03095 ( 354) hydrogen bonds : angle 5.54799 ( 828) link_NAG-ASN : bond 0.00349 ( 3) link_NAG-ASN : angle 1.92938 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 487 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8255 (tp30) REVERT: A 142 GLN cc_start: 0.8307 (tp40) cc_final: 0.7588 (tp-100) REVERT: A 148 LYS cc_start: 0.8774 (mtmm) cc_final: 0.8519 (mtmm) REVERT: A 155 ASP cc_start: 0.8136 (t0) cc_final: 0.7597 (t0) REVERT: A 199 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 201 GLU cc_start: 0.8171 (mp0) cc_final: 0.7800 (mp0) REVERT: A 217 TRP cc_start: 0.8297 (p-90) cc_final: 0.8067 (p90) REVERT: A 230 HIS cc_start: 0.8340 (t-90) cc_final: 0.7937 (t-90) REVERT: A 235 GLU cc_start: 0.8478 (pm20) cc_final: 0.7851 (pm20) REVERT: A 254 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 308 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8622 (pttt) REVERT: A 317 THR cc_start: 0.9820 (p) cc_final: 0.9562 (t) REVERT: A 320 MET cc_start: 0.7950 (ptt) cc_final: 0.7667 (ptp) REVERT: B 60 CYS cc_start: 0.7549 (m) cc_final: 0.6730 (m) REVERT: B 142 GLN cc_start: 0.8394 (pt0) cc_final: 0.7887 (pt0) REVERT: B 227 GLU cc_start: 0.9088 (tp30) cc_final: 0.8773 (mt-10) REVERT: B 228 MET cc_start: 0.9175 (tpp) cc_final: 0.8961 (tpp) REVERT: B 317 THR cc_start: 0.9389 (p) cc_final: 0.9102 (p) REVERT: B 321 GLN cc_start: 0.7616 (mt0) cc_final: 0.7016 (mt0) REVERT: B 340 LEU cc_start: 0.8853 (mt) cc_final: 0.8622 (mm) REVERT: B 348 ILE cc_start: 0.9040 (pt) cc_final: 0.8520 (mp) REVERT: B 362 GLU cc_start: 0.7259 (tt0) cc_final: 0.5898 (tt0) REVERT: B 368 ASN cc_start: 0.9324 (t0) cc_final: 0.8130 (p0) REVERT: B 369 PRO cc_start: 0.9229 (Cg_endo) cc_final: 0.8954 (Cg_exo) REVERT: C 37 ASP cc_start: 0.8041 (t0) cc_final: 0.7818 (t0) REVERT: C 38 LYS cc_start: 0.8026 (mttt) cc_final: 0.7180 (mttt) REVERT: C 125 MET cc_start: 0.8462 (ttt) cc_final: 0.7964 (ttm) REVERT: C 169 GLU cc_start: 0.8615 (mp0) cc_final: 0.8205 (pt0) REVERT: C 251 GLU cc_start: 0.8759 (tt0) cc_final: 0.8362 (tt0) REVERT: C 284 ARG cc_start: 0.8668 (mtt90) cc_final: 0.8465 (ttp-170) REVERT: C 320 MET cc_start: 0.8416 (ptt) cc_final: 0.8179 (ptm) REVERT: C 346 LYS cc_start: 0.8806 (tptt) cc_final: 0.8453 (mmmm) REVERT: D 36 TRP cc_start: 0.8551 (m100) cc_final: 0.8050 (m100) REVERT: D 44 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7143 (ptt-90) REVERT: D 51 ILE cc_start: 0.9211 (tt) cc_final: 0.9009 (mp) REVERT: D 66 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7284 (ptm160) REVERT: D 108 MET cc_start: 0.7582 (mpp) cc_final: 0.7366 (mpp) REVERT: E 85 ILE cc_start: 0.8733 (mm) cc_final: 0.8104 (pt) REVERT: E 87 TYR cc_start: 0.7833 (m-80) cc_final: 0.7568 (m-80) REVERT: E 90 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: F 21 SER cc_start: 0.9040 (m) cc_final: 0.8832 (p) REVERT: F 36 TRP cc_start: 0.7964 (m100) cc_final: 0.7626 (m100) REVERT: F 46 GLU cc_start: 0.8110 (tp30) cc_final: 0.7800 (tp30) REVERT: F 59 TYR cc_start: 0.8396 (m-80) cc_final: 0.7855 (m-80) REVERT: F 67 PHE cc_start: 0.8234 (m-10) cc_final: 0.7555 (m-80) REVERT: F 72 ASP cc_start: 0.8155 (t0) cc_final: 0.7697 (t0) REVERT: F 94 TYR cc_start: 0.7643 (m-80) cc_final: 0.7351 (m-80) REVERT: G 2 ILE cc_start: 0.8878 (tp) cc_final: 0.8483 (pt) REVERT: H 36 TRP cc_start: 0.8198 (m100) cc_final: 0.7663 (m100) REVERT: H 38 ARG cc_start: 0.8255 (ptm-80) cc_final: 0.7478 (ttp-170) REVERT: H 82 MET cc_start: 0.7322 (mtt) cc_final: 0.6831 (mmt) REVERT: I 4 MET cc_start: 0.8302 (ttp) cc_final: 0.7427 (tmm) REVERT: I 28 ASP cc_start: 0.7965 (m-30) cc_final: 0.7452 (t0) REVERT: I 31 SER cc_start: 0.8884 (m) cc_final: 0.8592 (p) REVERT: I 37 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6712 (tp-100) REVERT: I 55 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7709 (t80) REVERT: I 61 ARG cc_start: 0.9087 (ptp-110) cc_final: 0.8779 (ptp-110) REVERT: I 69 GLN cc_start: 0.8824 (pt0) cc_final: 0.8076 (mp10) REVERT: I 86 PHE cc_start: 0.7896 (m-10) cc_final: 0.7631 (m-10) REVERT: I 90 GLN cc_start: 0.9222 (pp30) cc_final: 0.8836 (pp30) REVERT: I 96 PHE cc_start: 0.9168 (m-80) cc_final: 0.8822 (m-80) REVERT: I 102 THR cc_start: 0.8690 (m) cc_final: 0.8160 (p) outliers start: 60 outliers final: 49 residues processed: 516 average time/residue: 0.0957 time to fit residues: 73.4277 Evaluate side-chains 534 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 479 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 55 PHE Chi-restraints excluded: chain I residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 55 optimal weight: 0.0570 chunk 15 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 161 optimal weight: 0.0470 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 173 optimal weight: 0.0270 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN C 390 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112816 restraints weight = 27599.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116775 restraints weight = 13585.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119427 restraints weight = 8427.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121226 restraints weight = 5979.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122477 restraints weight = 4647.977| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.335 14694 Z= 0.291 Angle : 0.961 59.199 19911 Z= 0.552 Chirality : 0.047 0.684 2217 Planarity : 0.006 0.201 2544 Dihedral : 5.147 56.172 2064 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.95 % Allowed : 26.70 % Favored : 69.34 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1836 helix: -0.72 (0.66), residues: 70 sheet: -0.19 (0.19), residues: 706 loop : -0.52 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.019 0.001 TYR B 194 PHE 0.028 0.001 PHE D 27 TRP 0.042 0.002 TRP E 35 HIS 0.003 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00604 (14691) covalent geometry : angle 0.96046 (19902) hydrogen bonds : bond 0.03149 ( 354) hydrogen bonds : angle 5.55593 ( 828) link_NAG-ASN : bond 0.00366 ( 3) link_NAG-ASN : angle 1.92898 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.45 seconds wall clock time: 44 minutes 23.27 seconds (2663.27 seconds total)