Starting phenix.real_space_refine on Fri Mar 6 02:13:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vbt_64933/03_2026/9vbt_64933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vbt_64933/03_2026/9vbt_64933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vbt_64933/03_2026/9vbt_64933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vbt_64933/03_2026/9vbt_64933.map" model { file = "/net/cci-nas-00/data/ceres_data/9vbt_64933/03_2026/9vbt_64933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vbt_64933/03_2026/9vbt_64933.cif" } resolution = 2.32 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= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 126 5.16 5 C 17138 2.51 5 N 4493 2.21 5 O 5184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 313 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26945 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2774 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2771 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 8, 'TRANS': 345} Chain: "C" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2771 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 8, 'TRANS': 345} Chain: "D" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2780 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 346} Chain: "H" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 140} Chain: "I" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2843 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SCY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2752 Classifications: {'peptide': 366} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 354} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SCY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1127 Classifications: {'peptide': 140} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 134} Chain breaks: 1 Chain: "L" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1098 Classifications: {'peptide': 137} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "E" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2915 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SCY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2809 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 360} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SCY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1128 Classifications: {'peptide': 141} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 135} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11356 SG CYS H 33 120.753 70.538 30.687 1.00 63.63 S ATOM 11379 SG CYS H 36 124.304 69.483 31.423 1.00 68.07 S ATOM 11480 SG CYS H 47 121.822 70.452 34.293 1.00 59.36 S ATOM 11505 SG CYS H 50 123.283 73.018 31.810 1.00 62.63 S ATOM 18116 SG CYS K 33 33.198 55.346 30.754 1.00 63.54 S ATOM 18139 SG CYS K 36 29.594 56.441 31.387 1.00 67.32 S ATOM 18240 SG CYS K 47 31.986 55.575 34.299 1.00 58.83 S ATOM 18265 SG CYS K 50 30.599 52.895 31.819 1.00 61.70 S ATOM 19232 SG CYS L 33 40.069 38.149 92.329 1.00 73.87 S ATOM 19255 SG CYS L 36 38.008 35.016 91.798 1.00 77.37 S ATOM 19356 SG CYS L 47 38.934 37.551 88.891 1.00 69.56 S ATOM 19381 SG CYS L 50 36.351 38.379 91.565 1.00 71.46 S ATOM 26054 SG CYS G 33 113.816 87.787 92.285 1.00 73.24 S ATOM 26077 SG CYS G 36 115.823 90.929 91.915 1.00 76.33 S ATOM 26178 SG CYS G 47 114.948 88.515 88.887 1.00 69.33 S ATOM 26203 SG CYS G 50 117.562 87.635 91.569 1.00 71.56 S Time building chain proxies: 6.24, per 1000 atoms: 0.23 Number of scatterers: 26945 At special positions: 0 Unit cell: (155.736, 126.999, 124.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 126 16.00 O 5184 8.00 N 4493 7.00 C 17138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 47 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 50 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 36 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 33 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 50 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 36 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 47 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 33 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 50 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 47 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 47 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 36 " Number of angles added : 24 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6332 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 25 sheets defined 40.9% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.697A pdb=" N VAL A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.773A pdb=" N GLN A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.504A pdb=" N ILE A 151 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.993A pdb=" N ILE A 161 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 216 through 233 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 278 through 290 removed outlier: 4.623A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.634A pdb=" N LYS A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'B' and resid 22 through 30 removed outlier: 3.848A pdb=" N VAL B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.794A pdb=" N GLN B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 133 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.519A pdb=" N ILE B 151 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.995A pdb=" N ILE B 161 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 216 through 233 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 278 through 290 removed outlier: 4.631A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.501A pdb=" N ASP B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.663A pdb=" N VAL C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.727A pdb=" N GLN C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 118 through 133 Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.531A pdb=" N ILE C 151 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 216 through 232 Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 279 through 292 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'D' and resid 22 through 30 removed outlier: 3.663A pdb=" N VAL D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP D 29 " --> pdb=" O THR D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.732A pdb=" N GLN D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 118 through 133 Processing helix chain 'D' and resid 146 through 151 removed outlier: 3.524A pdb=" N ILE D 151 " --> pdb=" O SER D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 216 through 232 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 279 through 292 Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 337 through 345 Processing helix chain 'H' and resid 15 through 21 removed outlier: 3.634A pdb=" N GLU H 21 " --> pdb=" O LYS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 27 Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'I' and resid 24 through 41 Processing helix chain 'I' and resid 43 through 47 Processing helix chain 'I' and resid 56 through 61 removed outlier: 4.161A pdb=" N ILE I 60 " --> pdb=" O GLY I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 73 removed outlier: 4.519A pdb=" N THR I 68 " --> pdb=" O GLY I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 87 No H-bonds generated for 'chain 'I' and resid 85 through 87' Processing helix chain 'I' and resid 88 through 103 Processing helix chain 'I' and resid 116 through 120 removed outlier: 3.503A pdb=" N ASP I 119 " --> pdb=" O LYS I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 136 through 140 Processing helix chain 'I' and resid 142 through 150 removed outlier: 3.885A pdb=" N ALA I 146 " --> pdb=" O SER I 142 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE I 147 " --> pdb=" O HIS I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 157 removed outlier: 3.926A pdb=" N SER I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 181 removed outlier: 3.883A pdb=" N VAL I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 200 Processing helix chain 'I' and resid 201 through 206 Processing helix chain 'I' and resid 248 through 253 Processing helix chain 'I' and resid 273 through 288 Processing helix chain 'I' and resid 290 through 294 Processing helix chain 'I' and resid 304 through 313 Processing helix chain 'I' and resid 320 through 327 Processing helix chain 'I' and resid 342 through 347 Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 353 through 367 removed outlier: 4.214A pdb=" N TYR I 357 " --> pdb=" O GLY I 353 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN I 358 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 359 " --> pdb=" O SER I 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 41 Processing helix chain 'J' and resid 43 through 47 Processing helix chain 'J' and resid 56 through 61 removed outlier: 4.039A pdb=" N ILE J 60 " --> pdb=" O GLY J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 74 Processing helix chain 'J' and resid 85 through 87 No H-bonds generated for 'chain 'J' and resid 85 through 87' Processing helix chain 'J' and resid 88 through 104 Processing helix chain 'J' and resid 116 through 120 removed outlier: 3.504A pdb=" N ILE J 120 " --> pdb=" O MET J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 127 Processing helix chain 'J' and resid 128 through 130 No H-bonds generated for 'chain 'J' and resid 128 through 130' Processing helix chain 'J' and resid 143 through 150 removed outlier: 3.755A pdb=" N PHE J 147 " --> pdb=" O HIS J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 157 removed outlier: 3.857A pdb=" N SER J 155 " --> pdb=" O GLN J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 182 removed outlier: 3.860A pdb=" N VAL J 181 " --> pdb=" O LYS J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 206 Processing helix chain 'J' and resid 247 through 253 Processing helix chain 'J' and resid 273 through 288 Processing helix chain 'J' and resid 304 through 314 Processing helix chain 'J' and resid 320 through 327 Processing helix chain 'J' and resid 342 through 347 Processing helix chain 'J' and resid 350 through 353 Processing helix chain 'J' and resid 354 through 368 removed outlier: 4.160A pdb=" N GLN J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE J 359 " --> pdb=" O SER J 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 21 Processing helix chain 'K' and resid 21 through 27 Processing helix chain 'K' and resid 74 through 78 Processing helix chain 'L' and resid 15 through 21 removed outlier: 3.579A pdb=" N GLU L 21 " --> pdb=" O LYS L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 28 Processing helix chain 'L' and resid 74 through 78 removed outlier: 3.558A pdb=" N VAL L 77 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 41 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 56 through 61 removed outlier: 4.169A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 73 Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.766A pdb=" N LEU E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 142 through 150 removed outlier: 3.907A pdb=" N ALA E 146 " --> pdb=" O SER E 142 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE E 147 " --> pdb=" O HIS E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 157 removed outlier: 3.959A pdb=" N SER E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 181 removed outlier: 3.882A pdb=" N VAL E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.525A pdb=" N GLU E 199 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 Processing helix chain 'E' and resid 248 through 257 removed outlier: 5.713A pdb=" N GLU E 254 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS E 255 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 256 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 304 through 313 Processing helix chain 'E' and resid 320 through 327 Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 353 through 367 removed outlier: 4.185A pdb=" N TYR E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 40 Processing helix chain 'F' and resid 43 through 47 Processing helix chain 'F' and resid 56 through 61 removed outlier: 4.011A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 88 through 103 Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.722A pdb=" N ILE F 120 " --> pdb=" O MET F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 143 through 150 removed outlier: 4.042A pdb=" N PHE F 147 " --> pdb=" O HIS F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 157 removed outlier: 3.866A pdb=" N SER F 155 " --> pdb=" O GLN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 182 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 247 through 257 removed outlier: 5.716A pdb=" N GLU F 254 " --> pdb=" O ARG F 251 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS F 255 " --> pdb=" O TYR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 304 through 314 Processing helix chain 'F' and resid 320 through 327 Processing helix chain 'F' and resid 342 through 347 Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.629A pdb=" N ALA F 354 " --> pdb=" O GLY F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 368 removed outlier: 3.904A pdb=" N ILE F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 21 removed outlier: 3.554A pdb=" N GLU G 21 " --> pdb=" O LYS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 28 Processing helix chain 'G' and resid 74 through 78 removed outlier: 3.617A pdb=" N VAL G 77 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 244 removed outlier: 6.287A pdb=" N TYR A 241 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N CYS A 301 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 243 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 309 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN A 185 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A 311 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 183 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE A 313 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 178 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE A 6 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 169 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR A 11 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER A 167 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE A 13 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A 165 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 138 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 79 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP A 78 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N CYS A 111 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 80 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 113 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 82 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP B 78 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N CYS B 111 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 80 " --> pdb=" O CYS B 111 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE B 113 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 82 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR B 138 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 79 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 165 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE B 13 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER B 167 " --> pdb=" O TYR B 11 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR B 11 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 169 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE B 6 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B 178 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 313 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 183 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR B 311 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN B 185 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER B 309 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR B 241 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N CYS B 301 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 243 " --> pdb=" O CYS B 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 4.249A pdb=" N PHE A 18 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 48 removed outlier: 4.254A pdb=" N PHE B 18 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 Processing sheet with id=AA6, first strand: chain 'C' and resid 241 through 244 removed outlier: 6.444A pdb=" N TYR C 241 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N CYS C 301 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 243 " --> pdb=" O CYS C 301 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR C 303 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER C 309 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN C 185 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR C 311 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE C 183 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 313 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 178 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C 169 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR C 11 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER C 167 " --> pdb=" O TYR C 11 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE C 13 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA C 165 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR C 138 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 79 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP C 78 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N CYS C 111 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 80 " --> pdb=" O CYS C 111 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE C 113 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU C 82 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP D 78 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N CYS D 111 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE D 80 " --> pdb=" O CYS D 111 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE D 113 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU D 82 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR D 138 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER D 79 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA D 165 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE D 13 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER D 167 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR D 11 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE D 169 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE D 6 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 178 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE D 313 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE D 183 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR D 311 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN D 185 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER D 309 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR D 241 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS D 301 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL D 243 " --> pdb=" O CYS D 301 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N TYR D 303 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 48 removed outlier: 4.235A pdb=" N PHE C 18 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 193 through 194 Processing sheet with id=AA9, first strand: chain 'D' and resid 45 through 48 removed outlier: 4.216A pdb=" N PHE D 18 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 193 through 194 Processing sheet with id=AB2, first strand: chain 'H' and resid 38 through 40 Processing sheet with id=AB3, first strand: chain 'H' and resid 63 through 72 removed outlier: 5.691A pdb=" N ILE H 66 " --> pdb=" O GLU H 94 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU H 94 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR H 89 " --> pdb=" O ILE H 105 " (cutoff:3.500A) removed outlier: 18.606A pdb=" N ASP H 100 " --> pdb=" O TYR H 139 " (cutoff:3.500A) removed outlier: 13.262A pdb=" N TYR H 141 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU H 102 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE H 143 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU H 104 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU H 145 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER H 130 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY H 140 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS H 128 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS H 142 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL H 126 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS H 144 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER H 124 " --> pdb=" O LYS H 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.484A pdb=" N ILE I 218 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL I 10 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA I 216 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N CYS I 12 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA I 214 " --> pdb=" O CYS I 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 234 through 243 removed outlier: 5.541A pdb=" N ILE I 236 " --> pdb=" O LYS I 399 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS I 399 " --> pdb=" O ILE I 236 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE I 296 " --> pdb=" O LEU I 382 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR I 384 " --> pdb=" O ILE I 296 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU I 298 " --> pdb=" O THR I 384 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ILE I 386 " --> pdb=" O GLU I 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 6 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 6 through 12 current: chain 'J' and resid 79 through 81 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 79 through 81 current: chain 'J' and resid 213 through 221 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 213 through 221 current: chain 'J' and resid 337 through 338 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 337 through 338 current: chain 'J' and resid 392 through 399 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'K' and resid 38 through 40 removed outlier: 3.680A pdb=" N GLU K 38 " --> pdb=" O CYS K 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 63 through 72 removed outlier: 5.593A pdb=" N ILE K 66 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU K 94 " --> pdb=" O ILE K 66 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR K 89 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 18.641A pdb=" N ASP K 100 " --> pdb=" O TYR K 139 " (cutoff:3.500A) removed outlier: 13.310A pdb=" N TYR K 141 " --> pdb=" O ASP K 100 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU K 102 " --> pdb=" O TYR K 141 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE K 143 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU K 104 " --> pdb=" O PHE K 143 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU K 145 " --> pdb=" O GLU K 104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER K 130 " --> pdb=" O LYS K 138 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY K 140 " --> pdb=" O LYS K 128 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS K 128 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS K 142 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL K 126 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS K 144 " --> pdb=" O SER K 124 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER K 124 " --> pdb=" O LYS K 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 38 through 40 Processing sheet with id=AC1, first strand: chain 'L' and resid 63 through 72 removed outlier: 5.553A pdb=" N ILE L 66 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU L 94 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR L 89 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 18.726A pdb=" N ASP L 100 " --> pdb=" O TYR L 139 " (cutoff:3.500A) removed outlier: 13.233A pdb=" N TYR L 141 " --> pdb=" O ASP L 100 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LEU L 102 " --> pdb=" O TYR L 141 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE L 143 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU L 104 " --> pdb=" O PHE L 143 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU L 145 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE L 106 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS L 138 " --> pdb=" O GLN L 129 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 12 removed outlier: 6.509A pdb=" N ILE E 218 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL E 10 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA E 216 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS E 12 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA E 214 " --> pdb=" O CYS E 12 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY E 49 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALA E 112 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER E 51 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N PHE E 114 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER E 53 " --> pdb=" O PHE E 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 234 through 243 removed outlier: 5.526A pdb=" N ILE E 236 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS E 399 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE E 296 " --> pdb=" O LEU E 382 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR E 384 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU E 298 " --> pdb=" O THR E 384 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE E 386 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 6 through 12 removed outlier: 5.754A pdb=" N VAL F 7 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER F 220 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY F 9 " --> pdb=" O ILE F 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 234 through 243 removed outlier: 6.364A pdb=" N VAL F 397 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG F 239 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA F 395 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR F 241 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA F 393 " --> pdb=" O TYR F 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 38 through 40 Processing sheet with id=AC7, first strand: chain 'G' and resid 63 through 72 removed outlier: 5.498A pdb=" N ILE G 66 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU G 94 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR G 89 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 18.764A pdb=" N ASP G 100 " --> pdb=" O TYR G 139 " (cutoff:3.500A) removed outlier: 13.270A pdb=" N TYR G 141 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU G 102 " --> pdb=" O TYR G 141 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE G 143 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU G 104 " --> pdb=" O PHE G 143 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU G 145 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ILE G 106 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS G 138 " --> pdb=" O GLN G 129 " (cutoff:3.500A) 1108 hydrogen bonds defined for protein. 3006 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: 5.55 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5083 1.32 - 1.45: 6685 1.45 - 1.57: 15455 1.57 - 1.69: 0 1.69 - 1.82: 200 Bond restraints: 27423 Sorted by residual: bond pdb=" N GLY J 63 " pdb=" CA GLY J 63 " ideal model delta sigma weight residual 1.443 1.475 -0.032 8.60e-03 1.35e+04 1.38e+01 bond pdb=" N SER A 280 " pdb=" CA SER A 280 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.33e+01 bond pdb=" N SER B 280 " pdb=" CA SER B 280 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.32e+01 bond pdb=" N GLY I 63 " pdb=" CA GLY I 63 " ideal model delta sigma weight residual 1.444 1.478 -0.034 9.60e-03 1.09e+04 1.25e+01 bond pdb=" N ILE J 60 " pdb=" CA ILE J 60 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.07e-02 8.73e+03 1.17e+01 ... (remaining 27418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 35435 1.76 - 3.51: 1336 3.51 - 5.27: 150 5.27 - 7.03: 23 7.03 - 8.78: 7 Bond angle restraints: 36951 Sorted by residual: angle pdb=" N ASN B 118 " pdb=" CA ASN B 118 " pdb=" C ASN B 118 " ideal model delta sigma weight residual 113.17 106.07 7.10 1.26e+00 6.30e-01 3.17e+01 angle pdb=" N ASN A 118 " pdb=" CA ASN A 118 " pdb=" C ASN A 118 " ideal model delta sigma weight residual 113.17 106.23 6.94 1.26e+00 6.30e-01 3.03e+01 angle pdb=" N ASN C 118 " pdb=" CA ASN C 118 " pdb=" C ASN C 118 " ideal model delta sigma weight residual 113.17 107.03 6.14 1.26e+00 6.30e-01 2.38e+01 angle pdb=" N ASN D 118 " pdb=" CA ASN D 118 " pdb=" C ASN D 118 " ideal model delta sigma weight residual 113.17 107.18 5.99 1.26e+00 6.30e-01 2.26e+01 angle pdb=" N TYR J 252 " pdb=" CA TYR J 252 " pdb=" C TYR J 252 " ideal model delta sigma weight residual 113.61 106.67 6.94 1.50e+00 4.44e-01 2.14e+01 ... (remaining 36946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 14376 17.66 - 35.32: 1526 35.32 - 52.98: 374 52.98 - 70.64: 123 70.64 - 88.30: 30 Dihedral angle restraints: 16429 sinusoidal: 6474 harmonic: 9955 Sorted by residual: dihedral pdb=" CA ASP I 132 " pdb=" C ASP I 132 " pdb=" N SER I 133 " pdb=" CA SER I 133 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLY F 64 " pdb=" C GLY F 64 " pdb=" N ILE F 65 " pdb=" CA ILE F 65 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ASP E 132 " pdb=" C ASP E 132 " pdb=" N SER E 133 " pdb=" CA SER E 133 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 16426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3132 0.059 - 0.118: 834 0.118 - 0.177: 115 0.177 - 0.236: 15 0.236 - 0.295: 6 Chirality restraints: 4102 Sorted by residual: chirality pdb=" CA ARG C 200 " pdb=" N ARG C 200 " pdb=" C ARG C 200 " pdb=" CB ARG C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ARG D 200 " pdb=" N ARG D 200 " pdb=" C ARG D 200 " pdb=" CB ARG D 200 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ILE D 113 " pdb=" N ILE D 113 " pdb=" C ILE D 113 " pdb=" CB ILE D 113 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4099 not shown) Planarity restraints: 4754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SCY F 87 " 0.022 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C SCY F 87 " -0.080 2.00e-02 2.50e+03 pdb=" O SCY F 87 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA F 88 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SCY J 87 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C SCY J 87 " 0.079 2.00e-02 2.50e+03 pdb=" O SCY J 87 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA J 88 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 27 " -0.362 9.50e-02 1.11e+02 1.62e-01 1.63e+01 pdb=" NE ARG L 27 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG L 27 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG L 27 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 27 " -0.011 2.00e-02 2.50e+03 ... (remaining 4751 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3575 2.75 - 3.29: 26169 3.29 - 3.83: 49139 3.83 - 4.36: 64298 4.36 - 4.90: 103186 Nonbonded interactions: 246367 Sorted by model distance: nonbonded pdb=" OD1 ASN G 134 " pdb=" OG SER G 136 " model vdw 2.214 3.040 nonbonded pdb=" O ASN J 138 " pdb=" OH TYR K 82 " model vdw 2.221 3.040 nonbonded pdb=" O ASN E 86 " pdb=" OG SER E 89 " model vdw 2.246 3.040 nonbonded pdb=" O THR J 331 " pdb=" OG SER J 334 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLU A 352 " pdb=" N MET H 1 " model vdw 2.253 3.120 ... (remaining 246362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 358) selection = (chain 'B' and (resid 5 through 261 or (resid 262 and (name N or name CA or name \ C or name O or name CB )) or resid 263 through 358)) selection = (chain 'C' and (resid 5 through 261 or (resid 262 and (name N or name CA or name \ C or name O or name CB )) or resid 263 through 358)) selection = (chain 'D' and (resid 5 through 261 or (resid 262 and (name N or name CA or name \ C or name O or name CB )) or resid 263 through 358)) } ncs_group { reference = (chain 'E' and (resid 4 through 189 or resid 202 through 221 or resid 234 throug \ h 256 or resid 269 through 401)) selection = (chain 'F' and (resid 4 through 221 or resid 234 through 256 or resid 269 throug \ h 401)) selection = (chain 'I' and (resid 4 through 189 or resid 202 through 221 or resid 234 throug \ h 401)) selection = (chain 'J' and (resid 4 through 256 or resid 269 through 401)) } ncs_group { reference = (chain 'G' and (resid 3 through 108 or resid 117 through 201)) selection = (chain 'H' and (resid 3 through 108 or resid 117 through 201)) selection = (chain 'K' and (resid 3 through 108 or resid 117 through 201)) selection = (chain 'L' and (resid 3 through 108 or resid 117 through 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.970 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 27439 Z= 0.363 Angle : 0.755 8.783 36975 Z= 0.483 Chirality : 0.054 0.295 4102 Planarity : 0.006 0.162 4754 Dihedral : 16.361 88.300 10097 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.86 % Allowed : 16.15 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.40 (0.14), residues: 3420 helix: -0.06 (0.15), residues: 1167 sheet: -0.11 (0.19), residues: 701 loop : -0.33 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 20 TYR 0.018 0.002 TYR I 153 PHE 0.035 0.002 PHE H 2 TRP 0.009 0.002 TRP K 19 HIS 0.006 0.001 HIS J 62 Details of bonding type rmsd covalent geometry : bond 0.00655 (27423) covalent geometry : angle 0.74941 (36951) hydrogen bonds : bond 0.14658 ( 1108) hydrogen bonds : angle 7.15560 ( 3006) metal coordination : bond 0.00689 ( 16) metal coordination : angle 3.55417 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 319 time to evaluate : 1.115 Fit side-chains REVERT: H 65 LYS cc_start: 0.7987 (pttm) cc_final: 0.7572 (ptpp) REVERT: J 106 TYR cc_start: 0.8083 (m-80) cc_final: 0.7875 (m-80) REVERT: K 29 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8494 (mt-10) REVERT: L 59 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6860 (tttm) outliers start: 25 outliers final: 18 residues processed: 340 average time/residue: 0.7968 time to fit residues: 309.1986 Evaluate side-chains 306 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 215 SER Chi-restraints excluded: chain I residue 254 GLU Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 335 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN B 5 GLN B 104 ASN C 97 GLN H 35 HIS H 129 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN J 125 ASN K 35 HIS K 72 ASN K 129 GLN L 35 HIS E 45 HIS E 302 GLN E 305 ASN G 35 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105426 restraints weight = 26104.384| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.39 r_work: 0.3120 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27439 Z= 0.196 Angle : 0.566 7.360 36975 Z= 0.308 Chirality : 0.046 0.166 4102 Planarity : 0.004 0.038 4754 Dihedral : 5.503 59.348 3771 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.92 % Allowed : 15.74 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.07 (0.14), residues: 3420 helix: 0.55 (0.15), residues: 1187 sheet: -0.09 (0.19), residues: 723 loop : -0.13 (0.17), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 220 TYR 0.023 0.002 TYR I 153 PHE 0.031 0.002 PHE H 2 TRP 0.010 0.002 TRP G 137 HIS 0.004 0.001 HIS J 45 Details of bonding type rmsd covalent geometry : bond 0.00450 (27423) covalent geometry : angle 0.55929 (36951) hydrogen bonds : bond 0.04683 ( 1108) hydrogen bonds : angle 5.51570 ( 3006) metal coordination : bond 0.00514 ( 16) metal coordination : angle 3.49970 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 1.038 Fit side-chains REVERT: A 72 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: B 72 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: B 265 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7091 (pt) REVERT: D 73 ASP cc_start: 0.8288 (t0) cc_final: 0.8055 (t70) REVERT: H 65 LYS cc_start: 0.8222 (pttm) cc_final: 0.7766 (ptpp) REVERT: I 90 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.8011 (t) REVERT: I 99 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6968 (mt-10) REVERT: I 288 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7164 (mtmm) REVERT: J 4 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6659 (tttp) REVERT: J 106 TYR cc_start: 0.8201 (m-80) cc_final: 0.7815 (m-80) REVERT: K 29 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8664 (mt-10) REVERT: E 288 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7001 (mtmm) REVERT: F 311 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7501 (mt-10) outliers start: 56 outliers final: 17 residues processed: 344 average time/residue: 0.7783 time to fit residues: 306.3298 Evaluate side-chains 310 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 288 LYS Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN B 5 GLN B 104 ASN C 64 GLN H 35 HIS I 125 ASN I 305 ASN K 35 HIS L 35 HIS G 35 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102801 restraints weight = 26231.064| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.40 r_work: 0.3096 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 27439 Z= 0.287 Angle : 0.630 8.527 36975 Z= 0.341 Chirality : 0.050 0.175 4102 Planarity : 0.004 0.043 4754 Dihedral : 5.438 58.911 3746 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.50 % Allowed : 15.26 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.02 (0.14), residues: 3420 helix: 0.48 (0.15), residues: 1185 sheet: -0.07 (0.19), residues: 736 loop : -0.22 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 127 TYR 0.023 0.002 TYR E 153 PHE 0.031 0.002 PHE H 2 TRP 0.010 0.002 TRP K 19 HIS 0.006 0.001 HIS J 45 Details of bonding type rmsd covalent geometry : bond 0.00674 (27423) covalent geometry : angle 0.62345 (36951) hydrogen bonds : bond 0.05052 ( 1108) hydrogen bonds : angle 5.54639 ( 3006) metal coordination : bond 0.00636 ( 16) metal coordination : angle 3.63467 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 1.087 Fit side-chains REVERT: B 72 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: B 155 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: B 217 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8047 (ttm110) REVERT: B 265 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7078 (pt) REVERT: C 155 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: C 235 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7962 (mmtp) REVERT: D 155 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: D 172 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8328 (mtmm) REVERT: H 65 LYS cc_start: 0.8265 (pttm) cc_final: 0.7734 (ptpp) REVERT: I 90 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.8052 (t) REVERT: J 106 TYR cc_start: 0.8154 (m-80) cc_final: 0.7779 (m-80) REVERT: J 292 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6411 (ptmm) REVERT: E 402 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.5456 (mp0) REVERT: F 233 LYS cc_start: 0.5541 (mtpp) cc_final: 0.5323 (tttt) REVERT: F 311 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7540 (mt-10) REVERT: G 121 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6962 (mm-30) outliers start: 73 outliers final: 27 residues processed: 346 average time/residue: 0.7701 time to fit residues: 304.2570 Evaluate side-chains 321 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 254 GLU Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain I residue 301 ASP Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 136 ASP Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 292 LYS Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 208 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 106 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN B 5 GLN B 104 ASN H 35 HIS I 125 ASN I 305 ASN K 35 HIS L 35 HIS G 35 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106870 restraints weight = 26208.531| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.41 r_work: 0.3154 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27439 Z= 0.115 Angle : 0.487 7.704 36975 Z= 0.266 Chirality : 0.043 0.160 4102 Planarity : 0.003 0.035 4754 Dihedral : 4.915 59.070 3746 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.89 % Allowed : 16.60 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.23 (0.14), residues: 3420 helix: 0.67 (0.15), residues: 1210 sheet: 0.05 (0.20), residues: 674 loop : -0.06 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 107 TYR 0.016 0.001 TYR I 153 PHE 0.026 0.001 PHE H 2 TRP 0.006 0.001 TRP K 19 HIS 0.004 0.001 HIS J 246 Details of bonding type rmsd covalent geometry : bond 0.00249 (27423) covalent geometry : angle 0.47973 (36951) hydrogen bonds : bond 0.03722 ( 1108) hydrogen bonds : angle 5.14826 ( 3006) metal coordination : bond 0.00383 ( 16) metal coordination : angle 3.29163 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 309 time to evaluate : 0.984 Fit side-chains REVERT: A 72 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: B 72 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: C 155 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: C 235 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7902 (mmtp) REVERT: D 73 ASP cc_start: 0.8269 (t0) cc_final: 0.8025 (t70) REVERT: D 172 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8251 (mtmm) REVERT: H 65 LYS cc_start: 0.8165 (pttm) cc_final: 0.7691 (ptpp) REVERT: I 90 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7940 (t) REVERT: I 288 LYS cc_start: 0.7264 (mtmm) cc_final: 0.6912 (mptm) REVERT: J 23 LYS cc_start: 0.8133 (mttt) cc_final: 0.7644 (mttm) REVERT: J 106 TYR cc_start: 0.8153 (m-80) cc_final: 0.7886 (m-80) REVERT: K 138 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8744 (mmmm) REVERT: E 90 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7942 (t) REVERT: E 288 LYS cc_start: 0.7108 (mttm) cc_final: 0.6808 (mptm) REVERT: F 253 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6748 (tmtm) REVERT: F 311 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7333 (mt-10) REVERT: G 121 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6866 (mm-30) outliers start: 55 outliers final: 19 residues processed: 351 average time/residue: 0.6947 time to fit residues: 280.0381 Evaluate side-chains 322 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 294 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 253 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 100 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 303 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 330 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN B 5 GLN B 104 ASN B 267 GLN H 35 HIS I 125 ASN I 305 ASN J 379 GLN K 35 HIS L 35 HIS E 282 GLN G 35 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105164 restraints weight = 25994.280| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.38 r_work: 0.3115 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27439 Z= 0.207 Angle : 0.557 7.031 36975 Z= 0.302 Chirality : 0.047 0.161 4102 Planarity : 0.004 0.035 4754 Dihedral : 5.133 58.712 3746 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.06 % Allowed : 16.50 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.19 (0.14), residues: 3420 helix: 0.67 (0.15), residues: 1201 sheet: 0.01 (0.19), residues: 711 loop : -0.11 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 107 TYR 0.018 0.002 TYR E 153 PHE 0.031 0.002 PHE H 2 TRP 0.008 0.002 TRP H 19 HIS 0.004 0.001 HIS J 45 Details of bonding type rmsd covalent geometry : bond 0.00482 (27423) covalent geometry : angle 0.55094 (36951) hydrogen bonds : bond 0.04373 ( 1108) hydrogen bonds : angle 5.26645 ( 3006) metal coordination : bond 0.00485 ( 16) metal coordination : angle 3.38973 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 0.988 Fit side-chains REVERT: A 264 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7479 (p) REVERT: B 72 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: C 155 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: C 235 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7959 (mmtp) REVERT: D 172 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8311 (mtmm) REVERT: H 65 LYS cc_start: 0.8236 (pttm) cc_final: 0.7742 (ptpp) REVERT: I 90 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.8003 (t) REVERT: I 288 LYS cc_start: 0.7266 (mtmm) cc_final: 0.6910 (mptm) REVERT: I 310 MET cc_start: 0.7979 (mtp) cc_final: 0.7773 (mtm) REVERT: J 4 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6662 (tttp) REVERT: J 23 LYS cc_start: 0.8046 (mttt) cc_final: 0.7546 (mttm) REVERT: J 106 TYR cc_start: 0.8173 (m-80) cc_final: 0.7914 (m-80) REVERT: E 90 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.8023 (t) REVERT: F 233 LYS cc_start: 0.5494 (mtpt) cc_final: 0.5277 (mtpp) REVERT: F 253 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6473 (tmtm) REVERT: F 292 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6467 (ptmm) REVERT: F 311 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7495 (mt-10) REVERT: G 121 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6858 (mm-30) outliers start: 60 outliers final: 33 residues processed: 340 average time/residue: 0.7182 time to fit residues: 279.9710 Evaluate side-chains 330 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 254 GLU Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 292 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 229 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 151 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN B 5 GLN B 104 ASN B 267 GLN H 35 HIS I 125 ASN I 305 ASN J 379 GLN K 35 HIS L 35 HIS G 35 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104045 restraints weight = 26226.801| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.43 r_work: 0.3115 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27439 Z= 0.220 Angle : 0.569 7.135 36975 Z= 0.308 Chirality : 0.047 0.164 4102 Planarity : 0.004 0.035 4754 Dihedral : 5.205 57.814 3746 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.16 % Allowed : 16.63 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.12 (0.14), residues: 3420 helix: 0.60 (0.15), residues: 1199 sheet: -0.02 (0.19), residues: 705 loop : -0.15 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 107 TYR 0.020 0.002 TYR E 153 PHE 0.031 0.002 PHE H 2 TRP 0.008 0.002 TRP K 19 HIS 0.004 0.001 HIS J 45 Details of bonding type rmsd covalent geometry : bond 0.00512 (27423) covalent geometry : angle 0.56223 (36951) hydrogen bonds : bond 0.04442 ( 1108) hydrogen bonds : angle 5.31020 ( 3006) metal coordination : bond 0.00525 ( 16) metal coordination : angle 3.52886 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 1.093 Fit side-chains REVERT: A 264 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7465 (p) REVERT: B 72 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: C 155 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: C 235 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7936 (mmtp) REVERT: D 172 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8268 (mtmm) REVERT: H 65 LYS cc_start: 0.8200 (pttm) cc_final: 0.7688 (ptpp) REVERT: I 90 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7932 (t) REVERT: I 288 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6838 (mptm) REVERT: J 4 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6715 (tttp) REVERT: J 23 LYS cc_start: 0.8055 (mttt) cc_final: 0.7561 (mttm) REVERT: J 106 TYR cc_start: 0.8145 (m-80) cc_final: 0.7868 (m-80) REVERT: E 90 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7949 (t) REVERT: F 233 LYS cc_start: 0.5436 (mtpt) cc_final: 0.5195 (mtpp) REVERT: F 253 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6421 (tmtm) REVERT: F 292 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.6310 (ptmm) REVERT: F 311 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7363 (mt-10) REVERT: G 121 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7008 (mm-30) outliers start: 63 outliers final: 30 residues processed: 340 average time/residue: 0.7535 time to fit residues: 292.7410 Evaluate side-chains 324 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 254 GLU Chi-restraints excluded: chain I residue 288 LYS Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 292 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 27 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN B 5 GLN B 104 ASN B 199 ASN H 35 HIS I 305 ASN J 379 GLN K 35 HIS L 35 HIS F 349 HIS G 35 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107042 restraints weight = 25987.401| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.41 r_work: 0.3153 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27439 Z= 0.120 Angle : 0.484 7.393 36975 Z= 0.263 Chirality : 0.044 0.156 4102 Planarity : 0.003 0.034 4754 Dihedral : 4.846 57.776 3746 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.82 % Allowed : 17.04 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.35 (0.15), residues: 3420 helix: 0.77 (0.15), residues: 1212 sheet: 0.08 (0.20), residues: 684 loop : 0.02 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 107 TYR 0.015 0.001 TYR I 153 PHE 0.027 0.001 PHE H 2 TRP 0.006 0.001 TRP K 19 HIS 0.003 0.001 HIS J 246 Details of bonding type rmsd covalent geometry : bond 0.00268 (27423) covalent geometry : angle 0.47715 (36951) hydrogen bonds : bond 0.03642 ( 1108) hydrogen bonds : angle 5.06432 ( 3006) metal coordination : bond 0.00399 ( 16) metal coordination : angle 3.23497 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 1.130 Fit side-chains REVERT: A 264 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7387 (p) REVERT: B 72 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: C 235 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7901 (mmtp) REVERT: D 172 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8274 (mtmm) REVERT: H 65 LYS cc_start: 0.8146 (pttm) cc_final: 0.7690 (ptpp) REVERT: I 90 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7941 (t) REVERT: I 288 LYS cc_start: 0.7216 (mtmm) cc_final: 0.6835 (mptm) REVERT: J 23 LYS cc_start: 0.8046 (mttt) cc_final: 0.7538 (mttm) REVERT: E 90 SER cc_start: 0.8175 (OUTLIER) cc_final: 0.7948 (t) REVERT: E 91 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.7968 (m170) REVERT: E 402 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.5383 (mp0) REVERT: F 253 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6469 (tmtm) REVERT: F 292 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.6234 (ptmm) REVERT: F 311 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7345 (mt-10) REVERT: G 121 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6817 (mm-30) outliers start: 53 outliers final: 24 residues processed: 338 average time/residue: 0.7437 time to fit residues: 287.7746 Evaluate side-chains 322 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 91 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 292 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN B 5 GLN B 104 ASN B 199 ASN I 151 GLN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 GLN K 35 HIS L 35 HIS E 282 GLN F 379 GLN G 35 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107009 restraints weight = 26190.066| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.41 r_work: 0.3155 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27439 Z= 0.124 Angle : 0.485 6.673 36975 Z= 0.263 Chirality : 0.044 0.153 4102 Planarity : 0.003 0.034 4754 Dihedral : 4.771 57.995 3746 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.58 % Allowed : 17.46 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.44 (0.15), residues: 3420 helix: 0.89 (0.15), residues: 1212 sheet: 0.08 (0.20), residues: 693 loop : 0.06 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 107 TYR 0.015 0.001 TYR I 153 PHE 0.025 0.001 PHE H 2 TRP 0.006 0.001 TRP K 19 HIS 0.003 0.001 HIS J 246 Details of bonding type rmsd covalent geometry : bond 0.00279 (27423) covalent geometry : angle 0.47843 (36951) hydrogen bonds : bond 0.03637 ( 1108) hydrogen bonds : angle 5.00625 ( 3006) metal coordination : bond 0.00393 ( 16) metal coordination : angle 3.06437 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 1.088 Fit side-chains REVERT: A 264 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7386 (p) REVERT: B 72 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: C 235 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7900 (mmtp) REVERT: D 172 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8245 (mtmm) REVERT: H 65 LYS cc_start: 0.8143 (pttm) cc_final: 0.7716 (ptpp) REVERT: I 90 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7894 (t) REVERT: I 91 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7952 (m170) REVERT: I 288 LYS cc_start: 0.7238 (mtmm) cc_final: 0.6859 (mptm) REVERT: J 23 LYS cc_start: 0.8094 (mttt) cc_final: 0.7552 (mttp) REVERT: E 90 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7940 (t) REVERT: E 91 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.7928 (m170) REVERT: F 253 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6408 (tmtm) REVERT: F 292 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6230 (ptmm) REVERT: F 311 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7331 (mt-10) REVERT: G 121 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6734 (mm-30) outliers start: 46 outliers final: 25 residues processed: 332 average time/residue: 0.7387 time to fit residues: 281.1518 Evaluate side-chains 324 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 91 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 292 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 334 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN B 5 GLN B 104 ASN B 199 ASN H 35 HIS I 125 ASN J 379 GLN K 35 HIS L 35 HIS E 282 GLN F 187 ASN F 379 GLN G 35 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105134 restraints weight = 25906.308| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.38 r_work: 0.3115 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27439 Z= 0.231 Angle : 0.574 7.406 36975 Z= 0.310 Chirality : 0.048 0.165 4102 Planarity : 0.004 0.035 4754 Dihedral : 5.125 57.376 3746 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.54 % Allowed : 17.56 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.23 (0.14), residues: 3420 helix: 0.72 (0.15), residues: 1202 sheet: 0.05 (0.19), residues: 711 loop : -0.10 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 107 TYR 0.021 0.002 TYR I 153 PHE 0.029 0.002 PHE H 2 TRP 0.008 0.002 TRP K 19 HIS 0.005 0.001 HIS J 45 Details of bonding type rmsd covalent geometry : bond 0.00540 (27423) covalent geometry : angle 0.56713 (36951) hydrogen bonds : bond 0.04448 ( 1108) hydrogen bonds : angle 5.25751 ( 3006) metal coordination : bond 0.00504 ( 16) metal coordination : angle 3.40290 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 1.186 Fit side-chains REVERT: A 264 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7520 (p) REVERT: B 72 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: C 235 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7967 (mmtp) REVERT: D 172 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8299 (mtmm) REVERT: H 65 LYS cc_start: 0.8238 (pttm) cc_final: 0.7747 (ptpp) REVERT: I 90 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7994 (t) REVERT: I 99 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6995 (mt-10) REVERT: I 288 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6856 (mptm) REVERT: J 23 LYS cc_start: 0.8024 (mttt) cc_final: 0.7530 (mttm) REVERT: J 106 TYR cc_start: 0.8050 (m-80) cc_final: 0.7817 (m-80) REVERT: E 90 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.8028 (t) REVERT: E 91 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8047 (m170) REVERT: F 253 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6499 (tmtm) REVERT: F 292 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6319 (ptmm) REVERT: F 311 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7406 (mt-10) REVERT: G 121 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6935 (mm-30) outliers start: 45 outliers final: 25 residues processed: 331 average time/residue: 0.7760 time to fit residues: 293.9825 Evaluate side-chains 323 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 288 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 288 LYS Chi-restraints excluded: chain I residue 292 LYS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 91 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 292 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 160 optimal weight: 0.7980 chunk 304 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 320 optimal weight: 0.0170 chunk 104 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 94 ASN A 104 ASN A 199 ASN B 5 GLN B 104 ASN B 199 ASN B 266 ASN D 5 GLN H 35 HIS J 246 HIS J 379 GLN K 35 HIS L 35 HIS E 282 GLN G 35 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.145389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108792 restraints weight = 26008.321| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.41 r_work: 0.3179 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27439 Z= 0.098 Angle : 0.466 7.199 36975 Z= 0.254 Chirality : 0.043 0.158 4102 Planarity : 0.003 0.035 4754 Dihedral : 4.662 57.038 3746 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.99 % Allowed : 18.11 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.48 (0.15), residues: 3420 helix: 0.92 (0.15), residues: 1212 sheet: 0.11 (0.20), residues: 675 loop : 0.09 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 107 TYR 0.014 0.001 TYR J 153 PHE 0.025 0.001 PHE H 2 TRP 0.007 0.001 TRP D 29 HIS 0.004 0.000 HIS J 246 Details of bonding type rmsd covalent geometry : bond 0.00211 (27423) covalent geometry : angle 0.45999 (36951) hydrogen bonds : bond 0.03325 ( 1108) hydrogen bonds : angle 4.95324 ( 3006) metal coordination : bond 0.00418 ( 16) metal coordination : angle 3.06907 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 306 time to evaluate : 1.053 Fit side-chains REVERT: A 264 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7320 (p) REVERT: B 72 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: C 235 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7895 (mmtp) REVERT: H 65 LYS cc_start: 0.8116 (pttm) cc_final: 0.7689 (ptpp) REVERT: I 90 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7831 (t) REVERT: I 288 LYS cc_start: 0.7246 (mtmm) cc_final: 0.6832 (mptm) REVERT: J 23 LYS cc_start: 0.8103 (mttt) cc_final: 0.7547 (mttp) REVERT: E 90 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7926 (t) REVERT: E 91 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7926 (m170) REVERT: F 253 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6464 (tmtm) REVERT: F 292 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6208 (ptmm) REVERT: F 311 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7329 (mt-10) REVERT: G 121 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6711 (mm-30) outliers start: 29 outliers final: 16 residues processed: 328 average time/residue: 0.7430 time to fit residues: 279.4254 Evaluate side-chains 321 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 297 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 91 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 292 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 1 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 304 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 104 ASN A 199 ASN A 266 ASN B 5 GLN B 104 ASN B 332 ASN J 160 GLN J 379 GLN L 35 HIS E 282 GLN E 305 ASN F 379 GLN G 35 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.106819 restraints weight = 25900.828| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.41 r_work: 0.3152 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27439 Z= 0.138 Angle : 0.497 6.247 36975 Z= 0.269 Chirality : 0.044 0.153 4102 Planarity : 0.003 0.035 4754 Dihedral : 4.762 56.881 3746 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.99 % Allowed : 18.24 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.49 (0.15), residues: 3420 helix: 0.92 (0.15), residues: 1212 sheet: 0.10 (0.20), residues: 693 loop : 0.11 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 107 TYR 0.015 0.001 TYR I 153 PHE 0.028 0.001 PHE H 2 TRP 0.006 0.001 TRP K 19 HIS 0.003 0.001 HIS J 246 Details of bonding type rmsd covalent geometry : bond 0.00313 (27423) covalent geometry : angle 0.49086 (36951) hydrogen bonds : bond 0.03729 ( 1108) hydrogen bonds : angle 5.00330 ( 3006) metal coordination : bond 0.00399 ( 16) metal coordination : angle 3.04127 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10318.08 seconds wall clock time: 176 minutes 27.79 seconds (10587.79 seconds total)