Starting phenix.real_space_refine on Sat Mar 7 02:24:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i3m_4404/03_2026/6i3m_4404.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i3m_4404/03_2026/6i3m_4404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i3m_4404/03_2026/6i3m_4404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i3m_4404/03_2026/6i3m_4404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i3m_4404/03_2026/6i3m_4404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i3m_4404/03_2026/6i3m_4404.map" } resolution = 3.93 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 168 5.16 5 C 23570 2.51 5 N 6300 2.21 5 O 6972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s 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: 37012 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2393 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "C" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "D" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "E" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 395} Chain: "I" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2187 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Chain: "J" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2187 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2393 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 395} Chain: "F" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "K" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2010 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "M" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "O" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2010 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "P" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 8.35, per 1000 atoms: 0.23 Number of scatterers: 37012 At special positions: 0 Unit cell: (296.14, 143.38, 121.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 2 15.00 O 6972 8.00 N 6300 7.00 C 23570 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8904 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 48 sheets defined 33.9% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 4.155A pdb=" N PHE A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 14 " --> pdb=" O TYR A 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 9 through 14' Processing helix chain 'A' and resid 21 through 37 removed outlier: 3.755A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.796A pdb=" N MET A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 removed outlier: 3.991A pdb=" N MET A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 removed outlier: 4.425A pdb=" N ILE A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 117 removed outlier: 4.077A pdb=" N LYS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 145 removed outlier: 3.507A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 removed outlier: 4.033A pdb=" N LEU A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 167' Processing helix chain 'A' and resid 180 through 184 removed outlier: 4.107A pdb=" N VAL A 184 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.903A pdb=" N MET A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 283 removed outlier: 3.697A pdb=" N HIS C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 removed outlier: 4.147A pdb=" N ILE C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.931A pdb=" N LEU C 329 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 353 removed outlier: 3.729A pdb=" N ALA C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 378 removed outlier: 4.187A pdb=" N LYS C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 391 Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.707A pdb=" N LEU C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 448 removed outlier: 3.735A pdb=" N MET C 440 " --> pdb=" O GLU C 436 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 443 " --> pdb=" O LYS C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.947A pdb=" N ILE C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 removed outlier: 4.036A pdb=" N LEU C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 639 through 647 removed outlier: 4.211A pdb=" N ILE C 643 " --> pdb=" O SER C 639 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 647 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 283 removed outlier: 3.697A pdb=" N HIS D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 306 removed outlier: 4.147A pdb=" N ILE D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.931A pdb=" N LEU D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU D 330 " --> pdb=" O GLN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 353 removed outlier: 3.729A pdb=" N ALA D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 378 removed outlier: 4.187A pdb=" N LYS D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 391 Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.706A pdb=" N LEU D 412 " --> pdb=" O VAL D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 448 removed outlier: 3.736A pdb=" N MET D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 443 " --> pdb=" O LYS D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 464 removed outlier: 3.947A pdb=" N ILE D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE D 463 " --> pdb=" O LEU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 499 removed outlier: 4.036A pdb=" N LEU D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 639 through 647 removed outlier: 4.212A pdb=" N ILE D 643 " --> pdb=" O SER D 639 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 647 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 31 removed outlier: 3.682A pdb=" N ASP E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 53 removed outlier: 3.649A pdb=" N ALA E 41 " --> pdb=" O SER E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 78 removed outlier: 3.812A pdb=" N GLU E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 71 " --> pdb=" O ILE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 107 removed outlier: 3.938A pdb=" N VAL E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE E 88 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU E 98 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR E 107 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.888A pdb=" N LEU E 124 " --> pdb=" O MET E 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN E 126 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 166 removed outlier: 3.689A pdb=" N GLN E 152 " --> pdb=" O THR E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 removed outlier: 4.006A pdb=" N ILE E 172 " --> pdb=" O ILE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 206 removed outlier: 4.304A pdb=" N ARG E 204 " --> pdb=" O LEU E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 224 removed outlier: 3.812A pdb=" N LYS E 224 " --> pdb=" O ASN E 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 221 through 224' Processing helix chain 'E' and resid 225 through 236 removed outlier: 3.744A pdb=" N HIS E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 288 removed outlier: 3.602A pdb=" N CYS E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 308 through 313 Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 361 through 369 Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 59 through 70 removed outlier: 3.761A pdb=" N THR G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE G 66 " --> pdb=" O TYR G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 92 removed outlier: 4.885A pdb=" N TYR G 89 " --> pdb=" O GLN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 126 Processing helix chain 'G' and resid 145 through 159 removed outlier: 3.939A pdb=" N GLU G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 249 removed outlier: 4.139A pdb=" N LEU G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU G 248 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN G 249 " --> pdb=" O ILE G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 300 removed outlier: 4.847A pdb=" N THR G 293 " --> pdb=" O GLN G 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 84 removed outlier: 3.639A pdb=" N VAL I 80 " --> pdb=" O MET I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 128 removed outlier: 3.743A pdb=" N TYR I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU I 126 " --> pdb=" O ILE I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 157 removed outlier: 4.102A pdb=" N LYS I 157 " --> pdb=" O GLU I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 189 Processing helix chain 'I' and resid 257 through 262 removed outlier: 3.525A pdb=" N ASN I 262 " --> pdb=" O HIS I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 287 Processing helix chain 'I' and resid 403 through 411 Processing helix chain 'J' and resid 75 through 84 removed outlier: 3.641A pdb=" N VAL J 80 " --> pdb=" O MET J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 128 removed outlier: 3.743A pdb=" N TYR J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 157 removed outlier: 4.102A pdb=" N LYS J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 257 through 262 removed outlier: 3.525A pdb=" N ASN J 262 " --> pdb=" O HIS J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 287 Processing helix chain 'J' and resid 403 through 411 Processing helix chain 'B' and resid 9 through 14 removed outlier: 4.154A pdb=" N PHE B 13 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 14 " --> pdb=" O TYR B 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 9 through 14' Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.754A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 60 removed outlier: 3.797A pdb=" N MET B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 82 removed outlier: 3.991A pdb=" N MET B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 99 removed outlier: 4.424A pdb=" N ILE B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 removed outlier: 4.078A pdb=" N LYS B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 removed outlier: 3.508A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 4.033A pdb=" N LEU B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 167' Processing helix chain 'B' and resid 180 through 184 removed outlier: 4.107A pdb=" N VAL B 184 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 291 through 302 removed outlier: 3.902A pdb=" N MET B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 Processing helix chain 'H' and resid 59 through 70 removed outlier: 3.761A pdb=" N THR H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE H 66 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 removed outlier: 4.886A pdb=" N TYR H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 126 Processing helix chain 'H' and resid 145 through 159 removed outlier: 3.939A pdb=" N GLU H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 249 removed outlier: 4.139A pdb=" N LEU H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU H 248 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN H 249 " --> pdb=" O ILE H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 300 removed outlier: 4.847A pdb=" N THR H 293 " --> pdb=" O GLN H 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 31 removed outlier: 3.682A pdb=" N ASP F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 53 removed outlier: 3.649A pdb=" N ALA F 41 " --> pdb=" O SER F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 78 removed outlier: 3.812A pdb=" N GLU F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU F 70 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY F 71 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 107 removed outlier: 3.938A pdb=" N VAL F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE F 88 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER F 105 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.888A pdb=" N LEU F 124 " --> pdb=" O MET F 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN F 126 " --> pdb=" O ASN F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 166 removed outlier: 3.688A pdb=" N GLN F 152 " --> pdb=" O THR F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 4.006A pdb=" N ILE F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 removed outlier: 4.304A pdb=" N ARG F 204 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 224 removed outlier: 3.812A pdb=" N LYS F 224 " --> pdb=" O ASN F 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 221 through 224' Processing helix chain 'F' and resid 225 through 236 removed outlier: 3.744A pdb=" N HIS F 236 " --> pdb=" O LYS F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 288 removed outlier: 3.602A pdb=" N CYS F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 308 through 313 Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 361 through 369 Processing helix chain 'K' and resid 57 through 65 removed outlier: 4.144A pdb=" N ILE K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG K 64 " --> pdb=" O GLN K 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL K 65 " --> pdb=" O LYS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 120 removed outlier: 3.770A pdb=" N ILE K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYS K 115 " --> pdb=" O ILE K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 138 removed outlier: 4.424A pdb=" N LEU K 126 " --> pdb=" O PRO K 122 " (cutoff:3.500A) Proline residue: K 133 - end of helix removed outlier: 3.622A pdb=" N PHE K 138 " --> pdb=" O LEU K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 149 removed outlier: 3.788A pdb=" N ALA K 144 " --> pdb=" O HIS K 140 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU K 147 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE K 149 " --> pdb=" O PHE K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 158 removed outlier: 3.836A pdb=" N GLU K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE K 158 " --> pdb=" O VAL K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.088A pdb=" N ILE K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 209 removed outlier: 3.604A pdb=" N SER K 207 " --> pdb=" O ASP K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 257 removed outlier: 3.560A pdb=" N GLU K 245 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER K 246 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR K 256 " --> pdb=" O THR K 252 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 130 through 135 removed outlier: 4.011A pdb=" N ARG O 134 " --> pdb=" O ASP O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 209 Processing helix chain 'O' and resid 226 through 239 Processing helix chain 'O' and resid 257 through 270 Processing helix chain 'O' and resid 290 through 301 removed outlier: 4.242A pdb=" N VAL O 294 " --> pdb=" O ASN O 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 65 removed outlier: 4.144A pdb=" N ILE L 63 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG L 64 " --> pdb=" O GLN L 60 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 65 " --> pdb=" O LYS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 120 removed outlier: 3.770A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE L 111 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU L 112 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 138 removed outlier: 4.423A pdb=" N LEU L 126 " --> pdb=" O PRO L 122 " (cutoff:3.500A) Proline residue: L 133 - end of helix removed outlier: 3.621A pdb=" N PHE L 138 " --> pdb=" O LEU L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 149 removed outlier: 3.789A pdb=" N ALA L 144 " --> pdb=" O HIS L 140 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 147 " --> pdb=" O GLU L 143 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE L 149 " --> pdb=" O PHE L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 158 removed outlier: 3.837A pdb=" N GLU L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE L 158 " --> pdb=" O VAL L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.088A pdb=" N ILE L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER L 174 " --> pdb=" O LYS L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 209 removed outlier: 3.602A pdb=" N SER L 207 " --> pdb=" O ASP L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 257 removed outlier: 3.560A pdb=" N GLU L 245 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER L 246 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 141 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'P' and resid 130 through 135 removed outlier: 4.011A pdb=" N ARG P 134 " --> pdb=" O ASP P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 209 Processing helix chain 'P' and resid 226 through 239 Processing helix chain 'P' and resid 257 through 270 Processing helix chain 'P' and resid 290 through 301 removed outlier: 4.242A pdb=" N VAL P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.029A pdb=" N ILE A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 125 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE A 195 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 127 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE A 227 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE A 284 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 229 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 288 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 398 through 401 removed outlier: 6.959A pdb=" N THR C 398 " --> pdb=" O LYS C 425 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE C 427 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE C 400 " --> pdb=" O ILE C 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 429 through 430 removed outlier: 4.152A pdb=" N ASP C 430 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 470 through 473 removed outlier: 6.439A pdb=" N VAL C 470 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS C 506 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 472 " --> pdb=" O CYS C 506 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 503 " --> pdb=" O LYS C 627 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 629 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 505 " --> pdb=" O ILE C 629 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 476 through 477 removed outlier: 3.798A pdb=" N SER C 485 " --> pdb=" O ASP C 618 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 618 " --> pdb=" O SER C 485 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 398 through 401 removed outlier: 6.960A pdb=" N THR D 398 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE D 427 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE D 400 " --> pdb=" O ILE D 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 429 through 430 removed outlier: 4.150A pdb=" N ASP D 430 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 470 through 473 removed outlier: 6.439A pdb=" N VAL D 470 " --> pdb=" O LEU D 504 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS D 506 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU D 472 " --> pdb=" O CYS D 506 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 503 " --> pdb=" O LYS D 627 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE D 629 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL D 505 " --> pdb=" O ILE D 629 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 476 through 477 removed outlier: 3.799A pdb=" N SER D 485 " --> pdb=" O ASP D 618 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP D 618 " --> pdb=" O SER D 485 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 241 through 242 removed outlier: 5.933A pdb=" N VAL E 213 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU E 186 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS E 257 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL E 258 " --> pdb=" O PHE E 293 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL E 295 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE E 260 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 264 through 265 Processing sheet with id=AB3, first strand: chain 'E' and resid 349 through 351 Processing sheet with id=AB4, first strand: chain 'G' and resid 103 through 108 removed outlier: 6.343A pdb=" N HIS G 73 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR G 105 " --> pdb=" O HIS G 73 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL G 75 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE G 107 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU G 77 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU G 27 " --> pdb=" O HIS G 73 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL G 75 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA G 29 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU G 77 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL G 31 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS G 79 " --> pdb=" O VAL G 31 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE G 133 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 139 through 141 Processing sheet with id=AB6, first strand: chain 'G' and resid 236 through 238 removed outlier: 6.898A pdb=" N TYR G 276 " --> pdb=" O SER G 164 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N MET G 166 " --> pdb=" O TYR G 276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 194 through 196 removed outlier: 7.013A pdb=" N CYS G 194 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP G 188 " --> pdb=" O CYS G 194 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 186 " --> pdb=" O TYR G 196 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG G 227 " --> pdb=" O PHE G 185 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE G 224 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL J 268 " --> pdb=" O PHE G 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 211 through 212 Processing sheet with id=AB9, first strand: chain 'G' and resid 319 through 320 removed outlier: 3.514A pdb=" N LYS G 327 " --> pdb=" O SER G 319 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR G 326 " --> pdb=" O ILE G 345 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA G 344 " --> pdb=" O ILE G 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 338 through 339 removed outlier: 6.614A pdb=" N LYS G 338 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS G 356 " --> pdb=" O ILE G 374 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 367 through 368 removed outlier: 6.404A pdb=" N GLN G 367 " --> pdb=" O ILE G 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'I' and resid 201 through 202 removed outlier: 3.920A pdb=" N TYR I 201 " --> pdb=" O LEU I 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 254 through 255 Processing sheet with id=AC6, first strand: chain 'I' and resid 265 through 269 removed outlier: 3.589A pdb=" N VAL I 268 " --> pdb=" O PHE H 224 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE H 224 " --> pdb=" O VAL I 268 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG H 227 " --> pdb=" O PHE H 185 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 186 " --> pdb=" O TYR H 196 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP H 188 " --> pdb=" O CYS H 194 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS H 194 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AC8, first strand: chain 'J' and resid 201 through 202 removed outlier: 3.920A pdb=" N TYR J 201 " --> pdb=" O LEU J 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.029A pdb=" N ILE B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE B 125 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE B 195 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU B 127 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 194 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 230 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 196 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE B 227 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE B 284 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL B 229 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 288 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 103 through 108 removed outlier: 6.342A pdb=" N HIS H 73 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR H 105 " --> pdb=" O HIS H 73 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL H 75 " --> pdb=" O THR H 105 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE H 107 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU H 77 " --> pdb=" O ILE H 107 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU H 27 " --> pdb=" O HIS H 73 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL H 75 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA H 29 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU H 77 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL H 31 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS H 79 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE H 133 " --> pdb=" O GLN H 28 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 139 through 141 Processing sheet with id=AD3, first strand: chain 'H' and resid 236 through 238 removed outlier: 6.898A pdb=" N TYR H 276 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N MET H 166 " --> pdb=" O TYR H 276 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 319 through 320 removed outlier: 3.514A pdb=" N LYS H 327 " --> pdb=" O SER H 319 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR H 326 " --> pdb=" O ILE H 345 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA H 344 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 338 through 339 removed outlier: 6.614A pdb=" N LYS H 338 " --> pdb=" O ILE H 357 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS H 356 " --> pdb=" O ILE H 374 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 367 through 368 removed outlier: 6.404A pdb=" N GLN H 367 " --> pdb=" O ILE H 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 241 through 242 removed outlier: 5.933A pdb=" N VAL F 213 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU F 186 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS F 257 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL F 258 " --> pdb=" O PHE F 293 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL F 295 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE F 260 " --> pdb=" O VAL F 295 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 264 through 265 Processing sheet with id=AD9, first strand: chain 'F' and resid 349 through 351 Processing sheet with id=AE1, first strand: chain 'K' and resid 35 through 36 removed outlier: 3.643A pdb=" N LYS K 35 " --> pdb=" O ASN K 23 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN K 23 " --> pdb=" O LYS K 35 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 219 through 222 Processing sheet with id=AE3, first strand: chain 'O' and resid 144 through 149 removed outlier: 5.732A pdb=" N LYS O 149 " --> pdb=" O LEU O 185 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU O 185 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 385 through 387 removed outlier: 4.247A pdb=" N ALA O 382 " --> pdb=" O ASN O 385 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU O 387 " --> pdb=" O LEU O 380 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU O 380 " --> pdb=" O LEU O 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY O 394 " --> pdb=" O ILE O 342 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL O 337 " --> pdb=" O SER O 320 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER O 320 " --> pdb=" O VAL O 337 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY O 339 " --> pdb=" O ILE O 318 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU O 343 " --> pdb=" O ARG O 314 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG O 314 " --> pdb=" O LEU O 343 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL O 416 " --> pdb=" O ARG O 356 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS O 371 " --> pdb=" O PRO O 357 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 347 through 348 Processing sheet with id=AE6, first strand: chain 'O' and resid 425 through 441 removed outlier: 9.812A pdb=" N ILE O 426 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N SER O 489 " --> pdb=" O ILE O 426 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR O 428 " --> pdb=" O LEU O 487 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET O 482 " --> pdb=" O VAL O 478 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL O 478 " --> pdb=" O MET O 482 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG O 484 " --> pdb=" O VAL O 476 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY O 472 " --> pdb=" O THR O 488 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ALA O 470 " --> pdb=" O PRO O 490 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL O 461 " --> pdb=" O ARG O 504 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG O 504 " --> pdb=" O VAL O 461 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE O 499 " --> pdb=" O TRP O 514 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP O 514 " --> pdb=" O ILE O 499 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU O 501 " --> pdb=" O ILE O 512 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE O 512 " --> pdb=" O LEU O 501 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ARG O 510 " --> pdb=" O ARG O 439 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ARG O 439 " --> pdb=" O ARG O 510 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE O 512 " --> pdb=" O LEU O 437 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.643A pdb=" N LYS L 35 " --> pdb=" O ASN L 23 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN L 23 " --> pdb=" O LYS L 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 183 through 189 Processing sheet with id=AE9, first strand: chain 'P' and resid 144 through 149 removed outlier: 5.733A pdb=" N LYS P 149 " --> pdb=" O LEU P 185 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU P 185 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 385 through 387 removed outlier: 4.247A pdb=" N ALA P 382 " --> pdb=" O ASN P 385 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU P 387 " --> pdb=" O LEU P 380 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU P 380 " --> pdb=" O LEU P 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY P 394 " --> pdb=" O ILE P 342 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL P 337 " --> pdb=" O SER P 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER P 320 " --> pdb=" O VAL P 337 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY P 339 " --> pdb=" O ILE P 318 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU P 343 " --> pdb=" O ARG P 314 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG P 314 " --> pdb=" O LEU P 343 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL P 416 " --> pdb=" O ARG P 356 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS P 371 " --> pdb=" O PRO P 357 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 347 through 348 Processing sheet with id=AF3, first strand: chain 'P' and resid 425 through 441 removed outlier: 9.812A pdb=" N ILE P 426 " --> pdb=" O SER P 489 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N SER P 489 " --> pdb=" O ILE P 426 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N THR P 428 " --> pdb=" O LEU P 487 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET P 482 " --> pdb=" O VAL P 478 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL P 478 " --> pdb=" O MET P 482 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG P 484 " --> pdb=" O VAL P 476 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLY P 472 " --> pdb=" O THR P 488 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA P 470 " --> pdb=" O PRO P 490 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL P 461 " --> pdb=" O ARG P 504 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG P 504 " --> pdb=" O VAL P 461 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE P 499 " --> pdb=" O TRP P 514 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP P 514 " --> pdb=" O ILE P 499 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU P 501 " --> pdb=" O ILE P 512 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE P 512 " --> pdb=" O LEU P 501 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ARG P 510 " --> pdb=" O ARG P 439 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ARG P 439 " --> pdb=" O ARG P 510 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE P 512 " --> pdb=" O LEU P 437 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3162 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: 7.20 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11354 1.34 - 1.46: 6037 1.46 - 1.58: 19997 1.58 - 1.70: 8 1.70 - 1.82: 254 Bond restraints: 37650 Sorted by residual: bond pdb=" CA VAL O 453 " pdb=" CB VAL O 453 " ideal model delta sigma weight residual 1.530 1.562 -0.032 1.05e-02 9.07e+03 9.23e+00 bond pdb=" CZ ARG P 503 " pdb=" NH1 ARG P 503 " ideal model delta sigma weight residual 1.323 1.365 -0.042 1.40e-02 5.10e+03 8.95e+00 bond pdb=" CZ ARG O 503 " pdb=" NH1 ARG O 503 " ideal model delta sigma weight residual 1.323 1.364 -0.041 1.40e-02 5.10e+03 8.75e+00 bond pdb=" CA VAL P 453 " pdb=" CB VAL P 453 " ideal model delta sigma weight residual 1.530 1.561 -0.031 1.05e-02 9.07e+03 8.57e+00 bond pdb=" C CYS O 194 " pdb=" N PRO O 195 " ideal model delta sigma weight residual 1.333 1.366 -0.033 1.17e-02 7.31e+03 8.20e+00 ... (remaining 37645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 48726 2.68 - 5.35: 1837 5.35 - 8.03: 309 8.03 - 10.70: 68 10.70 - 13.38: 12 Bond angle restraints: 50952 Sorted by residual: angle pdb=" N THR E 109 " pdb=" CA THR E 109 " pdb=" C THR E 109 " ideal model delta sigma weight residual 111.07 120.32 -9.25 1.07e+00 8.73e-01 7.47e+01 angle pdb=" N THR F 109 " pdb=" CA THR F 109 " pdb=" C THR F 109 " ideal model delta sigma weight residual 111.07 120.29 -9.22 1.07e+00 8.73e-01 7.42e+01 angle pdb=" N ILE E 238 " pdb=" CA ILE E 238 " pdb=" C ILE E 238 " ideal model delta sigma weight residual 106.21 113.48 -7.27 1.07e+00 8.73e-01 4.61e+01 angle pdb=" N ILE F 238 " pdb=" CA ILE F 238 " pdb=" C ILE F 238 " ideal model delta sigma weight residual 106.21 113.47 -7.26 1.07e+00 8.73e-01 4.60e+01 angle pdb=" C GLU F 115 " pdb=" N PRO F 116 " pdb=" CA PRO F 116 " ideal model delta sigma weight residual 119.05 126.40 -7.35 1.11e+00 8.12e-01 4.38e+01 ... (remaining 50947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 20763 16.20 - 32.39: 1685 32.39 - 48.59: 478 48.59 - 64.79: 80 64.79 - 80.99: 54 Dihedral angle restraints: 23060 sinusoidal: 9368 harmonic: 13692 Sorted by residual: dihedral pdb=" CA ARG H 178 " pdb=" C ARG H 178 " pdb=" N THR H 179 " pdb=" CA THR H 179 " ideal model delta harmonic sigma weight residual -180.00 -134.64 -45.36 0 5.00e+00 4.00e-02 8.23e+01 dihedral pdb=" CA ARG G 178 " pdb=" C ARG G 178 " pdb=" N THR G 179 " pdb=" CA THR G 179 " ideal model delta harmonic sigma weight residual -180.00 -134.65 -45.35 0 5.00e+00 4.00e-02 8.22e+01 dihedral pdb=" CA HIS K 140 " pdb=" C HIS K 140 " pdb=" N ALA K 141 " pdb=" CA ALA K 141 " ideal model delta harmonic sigma weight residual -180.00 -144.25 -35.75 0 5.00e+00 4.00e-02 5.11e+01 ... (remaining 23057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 5446 0.122 - 0.243: 472 0.243 - 0.365: 38 0.365 - 0.487: 0 0.487 - 0.608: 2 Chirality restraints: 5958 Sorted by residual: chirality pdb=" CA ARG P 356 " pdb=" N ARG P 356 " pdb=" C ARG P 356 " pdb=" CB ARG P 356 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" CA ARG O 356 " pdb=" N ARG O 356 " pdb=" C ARG O 356 " pdb=" CB ARG O 356 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" CA ASP P 130 " pdb=" N ASP P 130 " pdb=" C ASP P 130 " pdb=" CB ASP P 130 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 5955 not shown) Planarity restraints: 6490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 181 " -0.051 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO H 182 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO H 182 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 182 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 181 " 0.051 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO G 182 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO G 182 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 182 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 341 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO E 342 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 342 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 342 " 0.038 5.00e-02 4.00e+02 ... (remaining 6487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3099 2.74 - 3.28: 36021 3.28 - 3.82: 60463 3.82 - 4.36: 71205 4.36 - 4.90: 117816 Nonbonded interactions: 288604 Sorted by model distance: nonbonded pdb=" O GLY E 269 " pdb=" OH TYR E 349 " model vdw 2.201 3.040 nonbonded pdb=" O GLY F 269 " pdb=" OH TYR F 349 " model vdw 2.202 3.040 nonbonded pdb=" OG SER E 37 " pdb=" OG SER E 83 " model vdw 2.302 3.040 nonbonded pdb=" OG SER F 37 " pdb=" OG SER F 83 " model vdw 2.302 3.040 nonbonded pdb=" OG SER H 169 " pdb=" O ALA H 282 " model vdw 2.304 3.040 ... (remaining 288599 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.910 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 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 0.071 37650 Z= 0.402 Angle : 1.240 13.376 50952 Z= 0.712 Chirality : 0.073 0.608 5958 Planarity : 0.007 0.078 6490 Dihedral : 13.811 80.985 14156 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.25 % Favored : 88.40 % Rotamer: Outliers : 2.83 % Allowed : 8.25 % Favored : 88.92 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.16 (0.10), residues: 4604 helix: -2.65 (0.11), residues: 1376 sheet: -2.53 (0.19), residues: 592 loop : -2.98 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 324 TYR 0.038 0.003 TYR K 9 PHE 0.038 0.003 PHE J 119 TRP 0.042 0.004 TRP K 132 HIS 0.010 0.002 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00711 (37650) covalent geometry : angle 1.23958 (50952) hydrogen bonds : bond 0.17327 ( 1104) hydrogen bonds : angle 8.06662 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 669 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7820 (tpt) cc_final: 0.7499 (tpt) REVERT: A 78 LEU cc_start: 0.8431 (tt) cc_final: 0.7901 (mm) REVERT: A 214 TYR cc_start: 0.9240 (t80) cc_final: 0.8744 (t80) REVERT: A 264 GLU cc_start: 0.8128 (tp30) cc_final: 0.7627 (mm-30) REVERT: A 277 GLN cc_start: 0.8443 (pp30) cc_final: 0.8197 (pt0) REVERT: C 274 ILE cc_start: 0.9057 (tt) cc_final: 0.8828 (tt) REVERT: C 296 MET cc_start: 0.8361 (tmm) cc_final: 0.7959 (tmm) REVERT: C 317 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.8057 (ttm110) REVERT: C 319 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8696 (tt) REVERT: C 326 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8054 (mm-40) REVERT: C 364 LYS cc_start: 0.8334 (mttt) cc_final: 0.8133 (mtpt) REVERT: C 383 ASP cc_start: 0.8045 (m-30) cc_final: 0.7675 (m-30) REVERT: C 384 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8030 (tp-100) REVERT: D 296 MET cc_start: 0.8332 (tmm) cc_final: 0.8116 (tmm) REVERT: D 317 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8096 (ttm110) REVERT: D 326 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8002 (mm-40) REVERT: D 383 ASP cc_start: 0.8057 (m-30) cc_final: 0.7659 (m-30) REVERT: D 384 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8047 (tp-100) REVERT: D 402 THR cc_start: 0.9267 (p) cc_final: 0.9044 (m) REVERT: E 97 ASP cc_start: 0.8307 (t0) cc_final: 0.7728 (t0) REVERT: E 127 LYS cc_start: 0.5971 (mmpt) cc_final: 0.5649 (tptp) REVERT: E 144 MET cc_start: 0.3755 (ttm) cc_final: 0.3292 (tpp) REVERT: E 289 ARG cc_start: 0.8612 (mmt-90) cc_final: 0.8307 (mpt180) REVERT: G 26 ARG cc_start: 0.8055 (mpt180) cc_final: 0.7762 (mmt180) REVERT: G 294 ILE cc_start: 0.9108 (pt) cc_final: 0.8716 (mt) REVERT: I 80 VAL cc_start: 0.5961 (m) cc_final: 0.5672 (m) REVERT: I 174 PHE cc_start: 0.6807 (t80) cc_final: 0.6441 (t80) REVERT: I 200 TYR cc_start: 0.5710 (m-10) cc_final: 0.5465 (m-10) REVERT: I 399 ASN cc_start: 0.2247 (p0) cc_final: 0.1924 (p0) REVERT: J 197 MET cc_start: 0.6575 (ptm) cc_final: 0.6276 (ppp) REVERT: J 199 ILE cc_start: 0.6747 (tp) cc_final: 0.6372 (tp) REVERT: J 200 TYR cc_start: 0.5640 (m-10) cc_final: 0.5416 (m-10) REVERT: J 393 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6899 (pp) REVERT: J 394 ARG cc_start: 0.4454 (mtm180) cc_final: 0.4183 (mmp80) REVERT: J 399 ASN cc_start: 0.2711 (p0) cc_final: 0.2410 (p0) REVERT: B 74 MET cc_start: 0.7806 (tpt) cc_final: 0.7058 (tpt) REVERT: B 78 LEU cc_start: 0.8350 (tt) cc_final: 0.7742 (mm) REVERT: B 264 GLU cc_start: 0.8015 (tp30) cc_final: 0.7546 (mm-30) REVERT: B 277 GLN cc_start: 0.8417 (pp30) cc_final: 0.8095 (pt0) REVERT: H 26 ARG cc_start: 0.7852 (mpt180) cc_final: 0.7596 (mmt180) REVERT: H 294 ILE cc_start: 0.9168 (pt) cc_final: 0.8733 (mt) REVERT: H 413 ILE cc_start: 0.8667 (mt) cc_final: 0.8425 (mm) REVERT: F 97 ASP cc_start: 0.8351 (t0) cc_final: 0.7772 (t0) REVERT: F 127 LYS cc_start: 0.6131 (mmpt) cc_final: 0.5817 (tptp) REVERT: F 144 MET cc_start: 0.3696 (ttm) cc_final: 0.3233 (tpp) REVERT: F 289 ARG cc_start: 0.8606 (mmt-90) cc_final: 0.8297 (mpt180) REVERT: K 23 ASN cc_start: 0.7700 (p0) cc_final: 0.7276 (p0) REVERT: K 171 ASN cc_start: 0.8166 (t0) cc_final: 0.7901 (m-40) REVERT: O 192 VAL cc_start: 0.2765 (OUTLIER) cc_final: 0.2226 (t) REVERT: O 201 MET cc_start: 0.1527 (mmm) cc_final: -0.1342 (ppp) REVERT: O 257 GLU cc_start: 0.2332 (OUTLIER) cc_final: 0.1236 (pt0) REVERT: O 354 GLU cc_start: 0.0932 (OUTLIER) cc_final: 0.0187 (tt0) REVERT: O 476 VAL cc_start: 0.0629 (t) cc_final: 0.0126 (t) REVERT: L 119 PHE cc_start: 0.6509 (t80) cc_final: 0.6048 (t80) REVERT: P 192 VAL cc_start: 0.2238 (OUTLIER) cc_final: 0.1611 (t) REVERT: P 201 MET cc_start: 0.0791 (mmm) cc_final: -0.1972 (ttp) REVERT: P 354 GLU cc_start: 0.0948 (OUTLIER) cc_final: -0.0088 (tt0) REVERT: P 463 MET cc_start: 0.3110 (ttp) cc_final: 0.2793 (ttm) outliers start: 118 outliers final: 10 residues processed: 768 average time/residue: 0.2298 time to fit residues: 279.0625 Evaluate side-chains 384 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 367 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain J residue 393 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 192 VAL Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 354 GLU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 236 ILE Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 432 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS C 373 GLN C 389 ASN C 416 ASN C 446 ASN C 517 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN D 389 ASN D 416 ASN D 517 GLN E 78 HIS E 227 HIS G 85 GLN G 87 ASN G 96 ASN ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 ASN I 118 GLN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 GLN ** I 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 GLN ** J 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 GLN ** J 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN H 87 ASN H 96 ASN H 212 GLN H 371 ASN F 78 HIS F 227 HIS K 103 GLN O 433 ASN L 103 GLN ** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.175034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130848 restraints weight = 73989.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123416 restraints weight = 58341.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125526 restraints weight = 48896.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125472 restraints weight = 35935.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125412 restraints weight = 32934.272| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37650 Z= 0.151 Angle : 0.742 14.060 50952 Z= 0.384 Chirality : 0.049 0.334 5958 Planarity : 0.005 0.059 6490 Dihedral : 7.548 78.744 5062 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.64 % Favored : 91.27 % Rotamer: Outliers : 3.41 % Allowed : 13.08 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.12 (0.12), residues: 4604 helix: -1.37 (0.13), residues: 1434 sheet: -2.27 (0.20), residues: 604 loop : -2.50 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 234 TYR 0.017 0.002 TYR C 624 PHE 0.026 0.002 PHE A 149 TRP 0.027 0.001 TRP L 132 HIS 0.007 0.001 HIS O 232 Details of bonding type rmsd covalent geometry : bond 0.00333 (37650) covalent geometry : angle 0.74212 (50952) hydrogen bonds : bond 0.04187 ( 1104) hydrogen bonds : angle 5.65893 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 473 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7768 (tpt) cc_final: 0.7524 (tpt) REVERT: A 78 LEU cc_start: 0.8469 (tt) cc_final: 0.7864 (mm) REVERT: A 99 GLN cc_start: 0.8542 (pm20) cc_final: 0.8215 (pm20) REVERT: C 319 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8573 (tt) REVERT: C 339 THR cc_start: 0.8963 (p) cc_final: 0.8662 (t) REVERT: C 349 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 383 ASP cc_start: 0.7904 (m-30) cc_final: 0.7592 (m-30) REVERT: C 384 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7786 (tp-100) REVERT: C 465 MET cc_start: 0.8134 (mtp) cc_final: 0.7481 (mtp) REVERT: D 326 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8027 (mm-40) REVERT: D 339 THR cc_start: 0.8934 (p) cc_final: 0.8615 (t) REVERT: D 349 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7901 (tm-30) REVERT: D 353 LEU cc_start: 0.8644 (pp) cc_final: 0.8432 (mp) REVERT: D 383 ASP cc_start: 0.7922 (m-30) cc_final: 0.7533 (m-30) REVERT: D 384 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7803 (tp-100) REVERT: E 144 MET cc_start: 0.3852 (ttm) cc_final: 0.3316 (tpp) REVERT: E 150 TYR cc_start: 0.8548 (m-80) cc_final: 0.8348 (m-10) REVERT: G 47 LYS cc_start: 0.8663 (ptpp) cc_final: 0.8348 (ptmt) REVERT: G 119 MET cc_start: 0.8202 (mpp) cc_final: 0.7150 (ttp) REVERT: G 162 HIS cc_start: 0.6854 (p90) cc_final: 0.6415 (p90) REVERT: G 288 TRP cc_start: 0.8570 (m100) cc_final: 0.8289 (m100) REVERT: I 80 VAL cc_start: 0.5601 (m) cc_final: 0.5312 (m) REVERT: I 174 PHE cc_start: 0.6943 (t80) cc_final: 0.6419 (t80) REVERT: J 115 ARG cc_start: 0.3116 (tpp-160) cc_final: 0.1114 (tmm160) REVERT: J 174 PHE cc_start: 0.7104 (t80) cc_final: 0.6758 (t80) REVERT: J 197 MET cc_start: 0.6688 (ptm) cc_final: 0.6238 (ppp) REVERT: J 252 TYR cc_start: 0.6453 (m-80) cc_final: 0.6085 (m-80) REVERT: B 74 MET cc_start: 0.7579 (tpt) cc_final: 0.7306 (tpt) REVERT: B 78 LEU cc_start: 0.8429 (tt) cc_final: 0.7800 (mm) REVERT: H 47 LYS cc_start: 0.8751 (ptpp) cc_final: 0.8429 (ptmt) REVERT: H 288 TRP cc_start: 0.8645 (m100) cc_final: 0.8254 (m100) REVERT: F 144 MET cc_start: 0.3892 (ttm) cc_final: 0.3263 (tpp) REVERT: F 289 ARG cc_start: 0.8512 (mmt-90) cc_final: 0.8300 (mpt180) REVERT: O 201 MET cc_start: 0.2553 (mmm) cc_final: -0.0619 (ppp) REVERT: O 211 MET cc_start: -0.1284 (mtt) cc_final: -0.1515 (mtt) REVERT: O 257 GLU cc_start: -0.0731 (OUTLIER) cc_final: -0.1110 (pt0) REVERT: O 354 GLU cc_start: 0.1339 (OUTLIER) cc_final: 0.0711 (tt0) REVERT: O 373 ILE cc_start: -0.1396 (OUTLIER) cc_final: -0.1945 (mm) REVERT: O 502 SER cc_start: 0.0963 (OUTLIER) cc_final: 0.0191 (p) REVERT: P 201 MET cc_start: 0.2861 (mmm) cc_final: -0.0954 (ttp) REVERT: P 284 SER cc_start: -0.0187 (p) cc_final: -0.0597 (t) REVERT: P 354 GLU cc_start: 0.1700 (OUTLIER) cc_final: 0.0694 (tt0) REVERT: P 455 LYS cc_start: 0.5646 (mttm) cc_final: 0.4914 (mptt) outliers start: 142 outliers final: 48 residues processed: 597 average time/residue: 0.2049 time to fit residues: 201.9454 Evaluate side-chains 409 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 355 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain K residue 195 TYR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain O residue 354 GLU Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 426 ILE Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 502 SER Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain P residue 496 ASN Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 357 optimal weight: 30.0000 chunk 107 optimal weight: 0.0870 chunk 402 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 359 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 chunk 396 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 ASN G 212 GLN G 393 HIS ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 393 HIS ** H 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 508 HIS ** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 262 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.169486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127278 restraints weight = 74232.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122295 restraints weight = 54436.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122989 restraints weight = 51676.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.122895 restraints weight = 37820.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.123410 restraints weight = 30508.570| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37650 Z= 0.223 Angle : 0.766 12.214 50952 Z= 0.395 Chirality : 0.050 0.309 5958 Planarity : 0.005 0.055 6490 Dihedral : 7.142 75.121 5047 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.93 % Favored : 89.99 % Rotamer: Outliers : 4.13 % Allowed : 15.38 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.86 (0.12), residues: 4604 helix: -1.02 (0.13), residues: 1452 sheet: -2.32 (0.18), residues: 672 loop : -2.34 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 234 TYR 0.024 0.002 TYR D 624 PHE 0.023 0.002 PHE I 223 TRP 0.044 0.002 TRP K 132 HIS 0.012 0.002 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00512 (37650) covalent geometry : angle 0.76584 (50952) hydrogen bonds : bond 0.04022 ( 1104) hydrogen bonds : angle 5.30533 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 380 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8185 (pt) REVERT: A 74 MET cc_start: 0.7888 (tpt) cc_final: 0.7110 (tpt) REVERT: A 78 LEU cc_start: 0.8553 (tt) cc_final: 0.7889 (mm) REVERT: A 100 LEU cc_start: 0.7938 (mt) cc_final: 0.7466 (tt) REVERT: C 269 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7209 (tt) REVERT: C 319 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8453 (tt) REVERT: C 326 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7709 (mm-40) REVERT: C 349 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 383 ASP cc_start: 0.8184 (m-30) cc_final: 0.7898 (m-30) REVERT: C 384 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7519 (tp-100) REVERT: C 465 MET cc_start: 0.8481 (mtp) cc_final: 0.8147 (mtm) REVERT: C 491 MET cc_start: 0.8048 (mmm) cc_final: 0.7762 (mmm) REVERT: D 269 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7325 (tt) REVERT: D 326 GLN cc_start: 0.8484 (mm-40) cc_final: 0.7920 (mm-40) REVERT: D 339 THR cc_start: 0.8901 (p) cc_final: 0.8669 (t) REVERT: D 349 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7908 (tm-30) REVERT: D 384 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7581 (tp-100) REVERT: D 440 MET cc_start: 0.8152 (ttp) cc_final: 0.7900 (ttp) REVERT: D 465 MET cc_start: 0.8263 (mtp) cc_final: 0.7990 (mtm) REVERT: D 491 MET cc_start: 0.8077 (mmm) cc_final: 0.7794 (mmm) REVERT: E 121 MET cc_start: 0.7849 (tmm) cc_final: 0.7610 (tmm) REVERT: E 144 MET cc_start: 0.3427 (ttm) cc_final: 0.3058 (tpp) REVERT: E 239 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: E 362 TYR cc_start: 0.8218 (p90) cc_final: 0.8006 (p90) REVERT: G 47 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8583 (ptmt) REVERT: G 119 MET cc_start: 0.8165 (mpp) cc_final: 0.7857 (ttp) REVERT: G 288 TRP cc_start: 0.8779 (m100) cc_final: 0.8070 (m100) REVERT: G 294 ILE cc_start: 0.9155 (pt) cc_final: 0.8659 (mt) REVERT: I 80 VAL cc_start: 0.5722 (m) cc_final: 0.5455 (m) REVERT: I 174 PHE cc_start: 0.6497 (t80) cc_final: 0.6276 (t80) REVERT: I 197 MET cc_start: 0.7286 (ttt) cc_final: 0.6410 (ttp) REVERT: I 389 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7518 (tm-30) REVERT: J 6 PHE cc_start: 0.5715 (t80) cc_final: 0.5381 (t80) REVERT: J 197 MET cc_start: 0.7134 (ptm) cc_final: 0.6600 (ppp) REVERT: J 234 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7009 (mmm160) REVERT: J 389 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 71 ASP cc_start: 0.7574 (t0) cc_final: 0.7234 (t0) REVERT: B 74 MET cc_start: 0.7824 (tpt) cc_final: 0.7083 (tpt) REVERT: B 78 LEU cc_start: 0.8676 (tt) cc_final: 0.7961 (mm) REVERT: B 300 ILE cc_start: 0.9066 (tt) cc_final: 0.6569 (tt) REVERT: B 304 TYR cc_start: 0.7738 (m-10) cc_final: 0.6719 (m-10) REVERT: H 47 LYS cc_start: 0.8848 (ptpp) cc_final: 0.8563 (ptmt) REVERT: H 288 TRP cc_start: 0.8806 (m100) cc_final: 0.8090 (m100) REVERT: H 294 ILE cc_start: 0.9160 (pt) cc_final: 0.8641 (mt) REVERT: F 144 MET cc_start: 0.3590 (ttm) cc_final: 0.3307 (tpp) REVERT: K 119 PHE cc_start: 0.6717 (t80) cc_final: 0.6395 (t80) REVERT: O 186 VAL cc_start: -0.0752 (t) cc_final: -0.1024 (t) REVERT: O 201 MET cc_start: 0.3323 (mmm) cc_final: -0.0755 (ppp) REVERT: O 239 MET cc_start: -0.0157 (tpp) cc_final: -0.1467 (mtm) REVERT: O 257 GLU cc_start: -0.0322 (OUTLIER) cc_final: -0.0882 (pt0) REVERT: O 354 GLU cc_start: 0.1768 (OUTLIER) cc_final: 0.0288 (tt0) REVERT: O 373 ILE cc_start: -0.0218 (OUTLIER) cc_final: -0.0570 (mm) REVERT: O 502 SER cc_start: 0.1209 (OUTLIER) cc_final: 0.0716 (p) REVERT: P 201 MET cc_start: 0.3120 (mmm) cc_final: -0.0770 (tmm) REVERT: P 354 GLU cc_start: 0.1746 (OUTLIER) cc_final: 0.0387 (tt0) REVERT: P 455 LYS cc_start: 0.5836 (mttm) cc_final: 0.4938 (mptt) outliers start: 172 outliers final: 80 residues processed: 521 average time/residue: 0.1880 time to fit residues: 166.6985 Evaluate side-chains 418 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 328 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 517 GLN Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 195 TYR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 111 HIS Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 354 GLU Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 403 ASP Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 476 VAL Chi-restraints excluded: chain O residue 502 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 257 GLU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 97 optimal weight: 0.9980 chunk 337 optimal weight: 8.9990 chunk 384 optimal weight: 0.0570 chunk 417 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 375 optimal weight: 4.9990 chunk 395 optimal weight: 0.4980 chunk 243 optimal weight: 3.9990 chunk 274 optimal weight: 0.0970 chunk 100 optimal weight: 0.4980 chunk 127 optimal weight: 0.5980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN D 393 GLN E 368 ASN G 82 HIS I 156 GLN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS F 368 ASN K 103 GLN ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.174362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.133828 restraints weight = 73242.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129874 restraints weight = 62572.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130307 restraints weight = 56441.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130530 restraints weight = 45522.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130771 restraints weight = 35156.016| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37650 Z= 0.120 Angle : 0.670 13.626 50952 Z= 0.339 Chirality : 0.047 0.227 5958 Planarity : 0.004 0.054 6490 Dihedral : 6.527 71.971 5047 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.84 % Favored : 92.07 % Rotamer: Outliers : 2.33 % Allowed : 18.69 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.53 (0.12), residues: 4604 helix: -0.71 (0.13), residues: 1456 sheet: -2.24 (0.18), residues: 664 loop : -2.14 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 234 TYR 0.018 0.001 TYR D 624 PHE 0.024 0.001 PHE J 223 TRP 0.030 0.001 TRP K 132 HIS 0.010 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00259 (37650) covalent geometry : angle 0.67043 (50952) hydrogen bonds : bond 0.03247 ( 1104) hydrogen bonds : angle 4.91564 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 429 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7732 (tpt) cc_final: 0.7410 (tpt) REVERT: A 78 LEU cc_start: 0.8570 (tt) cc_final: 0.7952 (mm) REVERT: A 99 GLN cc_start: 0.8504 (pm20) cc_final: 0.8296 (pm20) REVERT: A 100 LEU cc_start: 0.7932 (mt) cc_final: 0.7573 (tt) REVERT: A 249 MET cc_start: 0.7098 (pmm) cc_final: 0.6808 (ppp) REVERT: A 297 GLU cc_start: 0.8576 (tt0) cc_final: 0.8227 (tt0) REVERT: C 269 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7333 (tp) REVERT: C 319 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8504 (tt) REVERT: C 325 HIS cc_start: 0.6667 (t-90) cc_final: 0.6301 (t-170) REVERT: C 326 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7704 (mm-40) REVERT: C 349 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 383 ASP cc_start: 0.7866 (m-30) cc_final: 0.7543 (m-30) REVERT: C 384 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7460 (tp-100) REVERT: C 465 MET cc_start: 0.8072 (mtp) cc_final: 0.7569 (mtp) REVERT: C 491 MET cc_start: 0.7914 (mmm) cc_final: 0.7673 (mmm) REVERT: D 326 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7816 (mm-40) REVERT: D 339 THR cc_start: 0.8880 (p) cc_final: 0.8570 (t) REVERT: D 349 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7983 (tm-30) REVERT: D 383 ASP cc_start: 0.8159 (m-30) cc_final: 0.7917 (m-30) REVERT: D 384 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7496 (tp-100) REVERT: D 465 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7480 (mtp) REVERT: D 491 MET cc_start: 0.7956 (mmm) cc_final: 0.7702 (mmm) REVERT: G 47 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8402 (ptmt) REVERT: G 288 TRP cc_start: 0.8689 (m100) cc_final: 0.7871 (m100) REVERT: G 294 ILE cc_start: 0.9065 (pt) cc_final: 0.8508 (mt) REVERT: I 6 PHE cc_start: 0.6610 (t80) cc_final: 0.4840 (t80) REVERT: I 80 VAL cc_start: 0.5540 (m) cc_final: 0.5226 (m) REVERT: I 174 PHE cc_start: 0.6510 (t80) cc_final: 0.6199 (t80) REVERT: I 197 MET cc_start: 0.7508 (ttt) cc_final: 0.7282 (ttt) REVERT: I 389 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7463 (tm-30) REVERT: J 6 PHE cc_start: 0.5668 (t80) cc_final: 0.5306 (t80) REVERT: J 197 MET cc_start: 0.7008 (ptm) cc_final: 0.5886 (ptm) REVERT: J 389 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7525 (tm-30) REVERT: J 397 ASN cc_start: 0.4367 (OUTLIER) cc_final: 0.4013 (t0) REVERT: B 71 ASP cc_start: 0.7463 (t0) cc_final: 0.7177 (t0) REVERT: B 78 LEU cc_start: 0.8611 (tt) cc_final: 0.7924 (mm) REVERT: B 100 LEU cc_start: 0.7858 (mt) cc_final: 0.7495 (tt) REVERT: B 300 ILE cc_start: 0.9006 (tt) cc_final: 0.6658 (tt) REVERT: B 304 TYR cc_start: 0.7724 (m-10) cc_final: 0.6967 (m-10) REVERT: H 47 LYS cc_start: 0.8745 (ptpp) cc_final: 0.8511 (ptmt) REVERT: H 200 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8761 (tp) REVERT: H 288 TRP cc_start: 0.8722 (m100) cc_final: 0.7899 (m100) REVERT: H 294 ILE cc_start: 0.9088 (pt) cc_final: 0.8528 (mt) REVERT: F 144 MET cc_start: 0.3641 (ttm) cc_final: 0.3366 (tpp) REVERT: K 120 GLN cc_start: 0.6520 (mp10) cc_final: 0.6033 (pp30) REVERT: O 192 VAL cc_start: 0.0992 (OUTLIER) cc_final: 0.0655 (t) REVERT: O 201 MET cc_start: 0.3331 (mmm) cc_final: -0.0442 (ppp) REVERT: O 239 MET cc_start: -0.0750 (tpp) cc_final: -0.1856 (mpt) REVERT: O 257 GLU cc_start: 0.0340 (OUTLIER) cc_final: -0.0357 (pt0) REVERT: O 379 SER cc_start: 0.3728 (p) cc_final: 0.3445 (p) REVERT: P 149 LYS cc_start: 0.0808 (mttt) cc_final: 0.0296 (tptp) REVERT: P 201 MET cc_start: 0.3081 (mmm) cc_final: -0.1087 (ttp) REVERT: P 312 SER cc_start: 0.2042 (p) cc_final: 0.1820 (m) REVERT: P 354 GLU cc_start: 0.2178 (OUTLIER) cc_final: 0.0498 (tt0) REVERT: P 455 LYS cc_start: 0.5780 (mttm) cc_final: 0.4894 (mptt) outliers start: 97 outliers final: 44 residues processed: 505 average time/residue: 0.1905 time to fit residues: 163.4026 Evaluate side-chains 414 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 362 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 195 TYR Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 192 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 403 ASP Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 397 optimal weight: 0.8980 chunk 347 optimal weight: 8.9990 chunk 337 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 206 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 209 optimal weight: 0.0040 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** G 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 ASN ** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 221 ASN ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 450 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.167684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.125863 restraints weight = 73451.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.120750 restraints weight = 52808.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.121461 restraints weight = 45739.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122211 restraints weight = 32567.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122181 restraints weight = 28074.841| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 37650 Z= 0.241 Angle : 0.751 11.447 50952 Z= 0.385 Chirality : 0.050 0.200 5958 Planarity : 0.005 0.063 6490 Dihedral : 6.558 72.389 5041 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.27 % Favored : 89.64 % Rotamer: Outliers : 4.37 % Allowed : 17.78 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.52 (0.12), residues: 4604 helix: -0.62 (0.13), residues: 1460 sheet: -2.14 (0.18), residues: 712 loop : -2.21 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 120 TYR 0.022 0.002 TYR A 304 PHE 0.036 0.002 PHE G 246 TRP 0.014 0.002 TRP J 261 HIS 0.013 0.002 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00560 (37650) covalent geometry : angle 0.75092 (50952) hydrogen bonds : bond 0.03591 ( 1104) hydrogen bonds : angle 5.01440 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 375 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7747 (t0) cc_final: 0.7457 (t0) REVERT: A 101 PHE cc_start: 0.7879 (m-10) cc_final: 0.7444 (m-10) REVERT: C 269 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7491 (tp) REVERT: C 319 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8480 (tm) REVERT: C 326 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7809 (mm-40) REVERT: C 349 GLN cc_start: 0.8348 (tm-30) cc_final: 0.8013 (tm-30) REVERT: C 384 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7132 (tp-100) REVERT: C 388 ASP cc_start: 0.8054 (m-30) cc_final: 0.7676 (m-30) REVERT: C 491 MET cc_start: 0.8026 (mmm) cc_final: 0.7713 (mmm) REVERT: D 326 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7835 (mm-40) REVERT: D 349 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 384 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7257 (tp-100) REVERT: D 388 ASP cc_start: 0.8066 (m-30) cc_final: 0.7769 (m-30) REVERT: D 465 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8236 (mtm) REVERT: D 626 LYS cc_start: 0.8531 (tppp) cc_final: 0.8078 (tptt) REVERT: E 23 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: E 362 TYR cc_start: 0.8375 (p90) cc_final: 0.8159 (p90) REVERT: G 212 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: G 294 ILE cc_start: 0.9142 (pt) cc_final: 0.8707 (mt) REVERT: I 80 VAL cc_start: 0.5796 (m) cc_final: 0.5594 (m) REVERT: I 174 PHE cc_start: 0.6594 (t80) cc_final: 0.6304 (t80) REVERT: I 389 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7496 (tm-30) REVERT: J 184 VAL cc_start: 0.7835 (t) cc_final: 0.7478 (p) REVERT: J 188 ARG cc_start: 0.8176 (mmp-170) cc_final: 0.7946 (mmm160) REVERT: J 197 MET cc_start: 0.7315 (ptm) cc_final: 0.6062 (ptm) REVERT: J 201 TYR cc_start: 0.7315 (t80) cc_final: 0.7070 (t80) REVERT: B 71 ASP cc_start: 0.7697 (t0) cc_final: 0.7410 (t0) REVERT: B 101 PHE cc_start: 0.7934 (m-10) cc_final: 0.7445 (m-10) REVERT: B 249 MET cc_start: 0.6989 (pmm) cc_final: 0.6619 (ppp) REVERT: B 300 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.7196 (tt) REVERT: B 304 TYR cc_start: 0.7979 (m-10) cc_final: 0.7008 (m-10) REVERT: H 47 LYS cc_start: 0.8899 (ptpp) cc_final: 0.8615 (ptmt) REVERT: H 294 ILE cc_start: 0.9138 (pt) cc_final: 0.8705 (mt) REVERT: F 127 LYS cc_start: 0.5101 (tptp) cc_final: 0.4835 (tptp) REVERT: F 144 MET cc_start: 0.3607 (ttm) cc_final: 0.3327 (tpp) REVERT: F 362 TYR cc_start: 0.8376 (p90) cc_final: 0.8175 (p90) REVERT: K 120 GLN cc_start: 0.7070 (mp-120) cc_final: 0.6123 (pp30) REVERT: O 106 ILE cc_start: 0.2173 (OUTLIER) cc_final: 0.1791 (mm) REVERT: O 201 MET cc_start: 0.3132 (mmm) cc_final: -0.0602 (ppp) REVERT: O 239 MET cc_start: -0.0792 (tpp) cc_final: -0.1743 (mpp) REVERT: O 257 GLU cc_start: 0.0415 (mp0) cc_final: -0.0373 (pt0) REVERT: O 379 SER cc_start: 0.3609 (p) cc_final: 0.3344 (p) REVERT: P 201 MET cc_start: 0.3290 (mmm) cc_final: -0.0527 (tmm) REVERT: P 354 GLU cc_start: 0.2067 (OUTLIER) cc_final: 0.0276 (tt0) REVERT: P 455 LYS cc_start: 0.5805 (mttm) cc_final: 0.4911 (mptt) outliers start: 182 outliers final: 116 residues processed: 518 average time/residue: 0.1861 time to fit residues: 165.3641 Evaluate side-chains 471 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 347 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 517 GLN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 6 CYS Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain K residue 195 TYR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 290 ASN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain P residue 111 HIS Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 257 GLU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 403 ASP Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 405 optimal weight: 0.5980 chunk 213 optimal weight: 0.0060 chunk 185 optimal weight: 7.9990 chunk 200 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 338 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 322 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN I 258 HIS ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 221 ASN ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 GLN ** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 422 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.173172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132320 restraints weight = 73033.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128429 restraints weight = 59138.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128719 restraints weight = 50962.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.129227 restraints weight = 35182.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.129551 restraints weight = 29629.511| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37650 Z= 0.118 Angle : 0.667 10.647 50952 Z= 0.335 Chirality : 0.046 0.227 5958 Planarity : 0.004 0.056 6490 Dihedral : 6.000 68.877 5038 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.84 % Favored : 92.07 % Rotamer: Outliers : 2.83 % Allowed : 19.96 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.30 (0.12), residues: 4604 helix: -0.44 (0.14), residues: 1460 sheet: -1.97 (0.19), residues: 704 loop : -2.10 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 234 TYR 0.017 0.001 TYR I 201 PHE 0.030 0.001 PHE G 246 TRP 0.040 0.002 TRP A 87 HIS 0.006 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00267 (37650) covalent geometry : angle 0.66748 (50952) hydrogen bonds : bond 0.02994 ( 1104) hydrogen bonds : angle 4.70540 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 407 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7600 (t0) cc_final: 0.7282 (t0) REVERT: A 99 GLN cc_start: 0.8530 (pm20) cc_final: 0.8130 (pm20) REVERT: A 101 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: A 235 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8369 (mttt) REVERT: C 269 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7383 (tp) REVERT: C 319 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8252 (tp) REVERT: C 326 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7776 (mm-40) REVERT: C 349 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8069 (tm-30) REVERT: C 383 ASP cc_start: 0.8377 (m-30) cc_final: 0.8139 (m-30) REVERT: C 384 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7142 (tp-100) REVERT: C 388 ASP cc_start: 0.8015 (m-30) cc_final: 0.7614 (m-30) REVERT: C 491 MET cc_start: 0.7940 (mmm) cc_final: 0.7672 (mmm) REVERT: D 326 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7793 (mm-40) REVERT: D 349 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 384 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7190 (tp-100) REVERT: D 388 ASP cc_start: 0.7991 (m-30) cc_final: 0.7708 (m-30) REVERT: D 491 MET cc_start: 0.7987 (mmm) cc_final: 0.7752 (mmm) REVERT: G 294 ILE cc_start: 0.9051 (pt) cc_final: 0.8603 (mt) REVERT: I 174 PHE cc_start: 0.6504 (t80) cc_final: 0.6230 (t80) REVERT: I 389 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7561 (tm-30) REVERT: I 397 ASN cc_start: 0.4861 (OUTLIER) cc_final: 0.4280 (t0) REVERT: J 76 MET cc_start: 0.5457 (pmm) cc_final: 0.4040 (mtm) REVERT: J 184 VAL cc_start: 0.7644 (t) cc_final: 0.7375 (p) REVERT: J 197 MET cc_start: 0.6999 (ptm) cc_final: 0.5762 (ptm) REVERT: J 201 TYR cc_start: 0.6796 (t80) cc_final: 0.6443 (t80) REVERT: J 389 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7615 (tm-30) REVERT: J 397 ASN cc_start: 0.4642 (OUTLIER) cc_final: 0.4165 (t0) REVERT: B 71 ASP cc_start: 0.7533 (t0) cc_final: 0.7203 (t0) REVERT: B 101 PHE cc_start: 0.7871 (m-10) cc_final: 0.7486 (m-10) REVERT: B 235 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8387 (mttt) REVERT: B 300 ILE cc_start: 0.9063 (tt) cc_final: 0.6975 (tt) REVERT: B 304 TYR cc_start: 0.7793 (m-10) cc_final: 0.7116 (m-10) REVERT: H 47 LYS cc_start: 0.8775 (ptpp) cc_final: 0.8523 (ptmt) REVERT: H 294 ILE cc_start: 0.9099 (pt) cc_final: 0.8609 (mt) REVERT: F 127 LYS cc_start: 0.5117 (tptp) cc_final: 0.4867 (tptp) REVERT: F 144 MET cc_start: 0.3636 (ttm) cc_final: 0.3383 (tpp) REVERT: K 120 GLN cc_start: 0.7061 (mp-120) cc_final: 0.6089 (pp30) REVERT: O 106 ILE cc_start: 0.1973 (OUTLIER) cc_final: 0.1588 (mm) REVERT: O 201 MET cc_start: 0.3176 (mmm) cc_final: -0.0686 (ppp) REVERT: O 239 MET cc_start: -0.0545 (tpp) cc_final: -0.1422 (mpp) REVERT: O 257 GLU cc_start: 0.0963 (mp0) cc_final: 0.0271 (pt0) REVERT: O 412 LEU cc_start: 0.3548 (tp) cc_final: 0.3115 (pp) REVERT: P 201 MET cc_start: 0.2880 (mmm) cc_final: -0.1710 (tmm) REVERT: P 354 GLU cc_start: 0.2169 (OUTLIER) cc_final: 0.0260 (tt0) REVERT: P 455 LYS cc_start: 0.5740 (mttm) cc_final: 0.4859 (mptt) outliers start: 118 outliers final: 68 residues processed: 499 average time/residue: 0.1862 time to fit residues: 158.7561 Evaluate side-chains 448 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 373 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 173 GLN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 351 ILE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain P residue 111 HIS Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 215 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 335 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 330 optimal weight: 0.9990 chunk 416 optimal weight: 20.0000 chunk 247 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 232 HIS P 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.171363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131092 restraints weight = 73164.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127418 restraints weight = 61339.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.128288 restraints weight = 52628.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127911 restraints weight = 41928.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.128199 restraints weight = 34949.553| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37650 Z= 0.141 Angle : 0.670 12.807 50952 Z= 0.336 Chirality : 0.047 0.205 5958 Planarity : 0.004 0.054 6490 Dihedral : 5.865 68.992 5036 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.77 % Favored : 91.18 % Rotamer: Outliers : 3.38 % Allowed : 19.70 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.19 (0.12), residues: 4604 helix: -0.38 (0.14), residues: 1454 sheet: -1.89 (0.19), residues: 710 loop : -2.01 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 234 TYR 0.033 0.002 TYR K 195 PHE 0.047 0.002 PHE B 73 TRP 0.027 0.002 TRP A 87 HIS 0.006 0.001 HIS G 162 Details of bonding type rmsd covalent geometry : bond 0.00330 (37650) covalent geometry : angle 0.66956 (50952) hydrogen bonds : bond 0.03037 ( 1104) hydrogen bonds : angle 4.68299 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 385 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7612 (t0) cc_final: 0.7337 (t0) REVERT: A 99 GLN cc_start: 0.8554 (pm20) cc_final: 0.8243 (pm20) REVERT: A 101 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: A 235 LYS cc_start: 0.8923 (mmmt) cc_final: 0.8425 (mttt) REVERT: C 326 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7799 (mm-40) REVERT: C 340 MET cc_start: 0.7226 (mmm) cc_final: 0.6841 (mmm) REVERT: C 349 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 384 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7195 (tp-100) REVERT: C 388 ASP cc_start: 0.8043 (m-30) cc_final: 0.7671 (m-30) REVERT: D 326 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7857 (mm-40) REVERT: D 384 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7306 (tp-100) REVERT: D 491 MET cc_start: 0.8001 (mmm) cc_final: 0.7719 (mmm) REVERT: G 294 ILE cc_start: 0.9076 (pt) cc_final: 0.8620 (mt) REVERT: I 174 PHE cc_start: 0.6451 (t80) cc_final: 0.6225 (t80) REVERT: I 201 TYR cc_start: 0.6925 (t80) cc_final: 0.6613 (t80) REVERT: I 389 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7585 (tm-30) REVERT: I 397 ASN cc_start: 0.4650 (OUTLIER) cc_final: 0.4162 (t0) REVERT: J 76 MET cc_start: 0.5492 (pmm) cc_final: 0.4117 (mtm) REVERT: J 115 ARG cc_start: 0.3108 (tpp-160) cc_final: 0.2884 (tpp-160) REVERT: J 184 VAL cc_start: 0.7817 (t) cc_final: 0.7548 (p) REVERT: J 197 MET cc_start: 0.7184 (ptm) cc_final: 0.5929 (ptm) REVERT: J 397 ASN cc_start: 0.4420 (OUTLIER) cc_final: 0.3977 (t0) REVERT: B 71 ASP cc_start: 0.7536 (t0) cc_final: 0.7251 (t0) REVERT: B 101 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7317 (m-10) REVERT: B 235 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8439 (mttt) REVERT: B 300 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.7120 (tt) REVERT: B 304 TYR cc_start: 0.7868 (m-10) cc_final: 0.7167 (m-10) REVERT: H 47 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8530 (ptmt) REVERT: H 294 ILE cc_start: 0.9126 (pt) cc_final: 0.8620 (mt) REVERT: F 127 LYS cc_start: 0.5169 (tptp) cc_final: 0.4917 (tppt) REVERT: F 144 MET cc_start: 0.3617 (ttm) cc_final: 0.3395 (tpp) REVERT: K 83 ILE cc_start: 0.8585 (pp) cc_final: 0.8362 (pt) REVERT: K 120 GLN cc_start: 0.7081 (mp-120) cc_final: 0.6106 (pp30) REVERT: O 106 ILE cc_start: 0.1967 (OUTLIER) cc_final: 0.1601 (mm) REVERT: O 201 MET cc_start: 0.2989 (mmm) cc_final: -0.0933 (ppp) REVERT: O 239 MET cc_start: -0.0575 (tpp) cc_final: -0.1451 (mpp) REVERT: O 257 GLU cc_start: 0.1030 (mp0) cc_final: 0.0302 (pt0) REVERT: O 332 ASP cc_start: 0.3412 (m-30) cc_final: 0.2338 (t70) REVERT: O 412 LEU cc_start: 0.3647 (tp) cc_final: 0.3159 (pp) REVERT: L 45 MET cc_start: 0.8561 (tmm) cc_final: 0.8337 (ppp) REVERT: L 83 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8287 (pt) REVERT: P 149 LYS cc_start: 0.0558 (mttt) cc_final: 0.0120 (tptp) REVERT: P 201 MET cc_start: 0.2886 (mmm) cc_final: -0.1629 (tmm) REVERT: P 455 LYS cc_start: 0.5638 (mttm) cc_final: 0.4766 (mptt) outliers start: 141 outliers final: 97 residues processed: 491 average time/residue: 0.1885 time to fit residues: 158.0108 Evaluate side-chains 465 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 361 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain P residue 111 HIS Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 290 ASN Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 443 VAL Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 138 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 448 optimal weight: 40.0000 chunk 366 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 344 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 GLN ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.169877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130469 restraints weight = 72909.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126118 restraints weight = 67347.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127000 restraints weight = 61398.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126973 restraints weight = 44704.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127753 restraints weight = 34832.390| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37650 Z= 0.171 Angle : 0.696 10.146 50952 Z= 0.352 Chirality : 0.048 0.194 5958 Planarity : 0.005 0.054 6490 Dihedral : 5.895 69.781 5031 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.21 % Favored : 90.75 % Rotamer: Outliers : 3.45 % Allowed : 20.44 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.18 (0.12), residues: 4604 helix: -0.42 (0.13), residues: 1446 sheet: -1.83 (0.19), residues: 710 loop : -1.98 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 234 TYR 0.043 0.002 TYR L 195 PHE 0.038 0.002 PHE J 174 TRP 0.055 0.002 TRP K 132 HIS 0.007 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00400 (37650) covalent geometry : angle 0.69621 (50952) hydrogen bonds : bond 0.03159 ( 1104) hydrogen bonds : angle 4.76319 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 377 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7331 (t0) cc_final: 0.7104 (t0) REVERT: A 101 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: C 319 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8598 (tt) REVERT: C 326 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7777 (mm-40) REVERT: C 340 MET cc_start: 0.7264 (mmm) cc_final: 0.7050 (mmm) REVERT: C 349 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8020 (tm-30) REVERT: C 384 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7284 (tp-100) REVERT: C 388 ASP cc_start: 0.7967 (m-30) cc_final: 0.7736 (m-30) REVERT: C 491 MET cc_start: 0.7969 (mmm) cc_final: 0.7747 (mmm) REVERT: D 326 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7842 (mm-40) REVERT: D 384 GLN cc_start: 0.8384 (tp-100) cc_final: 0.7968 (tp-100) REVERT: D 491 MET cc_start: 0.7947 (mmm) cc_final: 0.7666 (mmm) REVERT: D 626 LYS cc_start: 0.8570 (tppp) cc_final: 0.8220 (tptt) REVERT: G 294 ILE cc_start: 0.9079 (pt) cc_final: 0.8636 (mt) REVERT: I 201 TYR cc_start: 0.6946 (t80) cc_final: 0.6474 (t80) REVERT: I 295 MET cc_start: 0.1522 (ttt) cc_final: 0.0799 (tpp) REVERT: I 389 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7739 (tm-30) REVERT: I 397 ASN cc_start: 0.4654 (OUTLIER) cc_final: 0.4154 (t0) REVERT: J 76 MET cc_start: 0.5513 (pmm) cc_final: 0.4118 (mtm) REVERT: J 184 VAL cc_start: 0.7691 (t) cc_final: 0.7447 (p) REVERT: J 197 MET cc_start: 0.7457 (ptm) cc_final: 0.6493 (ptm) REVERT: B 71 ASP cc_start: 0.7524 (t0) cc_final: 0.7219 (t0) REVERT: B 101 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: B 300 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.7191 (tt) REVERT: B 304 TYR cc_start: 0.7959 (m-10) cc_final: 0.7130 (m-10) REVERT: H 47 LYS cc_start: 0.8745 (ptpp) cc_final: 0.8463 (ptmt) REVERT: H 294 ILE cc_start: 0.9103 (pt) cc_final: 0.8601 (mt) REVERT: F 127 LYS cc_start: 0.5283 (tptp) cc_final: 0.5063 (tppt) REVERT: F 144 MET cc_start: 0.3579 (ttm) cc_final: 0.3373 (tpp) REVERT: K 120 GLN cc_start: 0.7053 (mp-120) cc_final: 0.6079 (pp30) REVERT: O 106 ILE cc_start: 0.1926 (OUTLIER) cc_final: 0.1559 (mm) REVERT: O 201 MET cc_start: 0.3051 (mmm) cc_final: -0.1171 (ppp) REVERT: O 239 MET cc_start: -0.0663 (tpp) cc_final: -0.1409 (mpp) REVERT: O 257 GLU cc_start: 0.1149 (mp0) cc_final: 0.0386 (pt0) REVERT: O 332 ASP cc_start: 0.3411 (m-30) cc_final: 0.2326 (t70) REVERT: O 412 LEU cc_start: 0.3269 (tp) cc_final: 0.2833 (pp) REVERT: P 201 MET cc_start: 0.2832 (mmm) cc_final: -0.1674 (tmm) REVERT: P 455 LYS cc_start: 0.5622 (mttm) cc_final: 0.4743 (mptt) outliers start: 144 outliers final: 101 residues processed: 482 average time/residue: 0.2021 time to fit residues: 166.5311 Evaluate side-chains 465 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 358 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 50 CYS Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain P residue 111 HIS Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 290 ASN Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 443 VAL Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 457 optimal weight: 2.9990 chunk 424 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 294 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 443 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 393 HIS ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 393 HIS ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 144 ASN ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.170229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129649 restraints weight = 73292.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126527 restraints weight = 60739.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127194 restraints weight = 49235.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126757 restraints weight = 40809.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126888 restraints weight = 34181.521| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37650 Z= 0.158 Angle : 0.696 14.861 50952 Z= 0.352 Chirality : 0.048 0.216 5958 Planarity : 0.004 0.053 6490 Dihedral : 5.854 70.002 5031 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.75 % Favored : 91.20 % Rotamer: Outliers : 3.14 % Allowed : 20.75 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.11 (0.12), residues: 4604 helix: -0.39 (0.13), residues: 1450 sheet: -1.71 (0.20), residues: 682 loop : -1.95 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 324 TYR 0.028 0.002 TYR F 362 PHE 0.052 0.002 PHE J 407 TRP 0.053 0.002 TRP K 132 HIS 0.007 0.001 HIS G 162 Details of bonding type rmsd covalent geometry : bond 0.00371 (37650) covalent geometry : angle 0.69615 (50952) hydrogen bonds : bond 0.03128 ( 1104) hydrogen bonds : angle 4.75846 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 375 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7554 (t0) cc_final: 0.7312 (t0) REVERT: A 99 GLN cc_start: 0.8557 (pm20) cc_final: 0.8135 (pm20) REVERT: A 101 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7478 (m-10) REVERT: C 319 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8661 (tt) REVERT: C 326 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7827 (mm-40) REVERT: C 349 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 384 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7385 (tp-100) REVERT: C 491 MET cc_start: 0.7976 (mmm) cc_final: 0.7735 (mmm) REVERT: D 326 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7875 (mm-40) REVERT: D 384 GLN cc_start: 0.8393 (tp-100) cc_final: 0.7944 (tp-100) REVERT: D 491 MET cc_start: 0.8004 (mmm) cc_final: 0.7730 (mmm) REVERT: D 626 LYS cc_start: 0.8479 (tppp) cc_final: 0.8156 (tptt) REVERT: G 61 GLU cc_start: 0.7759 (pm20) cc_final: 0.7262 (mp0) REVERT: G 294 ILE cc_start: 0.9102 (pt) cc_final: 0.8673 (mt) REVERT: I 295 MET cc_start: 0.1302 (ttt) cc_final: 0.0569 (tpp) REVERT: I 389 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7517 (tm-30) REVERT: I 397 ASN cc_start: 0.4546 (OUTLIER) cc_final: 0.4143 (t0) REVERT: J 184 VAL cc_start: 0.7821 (t) cc_final: 0.7554 (p) REVERT: J 197 MET cc_start: 0.7337 (ptm) cc_final: 0.6506 (ptm) REVERT: J 397 ASN cc_start: 0.4420 (OUTLIER) cc_final: 0.4056 (t0) REVERT: B 71 ASP cc_start: 0.7442 (t0) cc_final: 0.7086 (t0) REVERT: B 101 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7388 (m-10) REVERT: B 300 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.7365 (tt) REVERT: B 304 TYR cc_start: 0.7912 (m-10) cc_final: 0.7140 (m-10) REVERT: H 47 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8484 (ptmt) REVERT: H 294 ILE cc_start: 0.9139 (pt) cc_final: 0.8646 (mt) REVERT: F 127 LYS cc_start: 0.5263 (tptp) cc_final: 0.5039 (tppt) REVERT: F 144 MET cc_start: 0.3616 (ttm) cc_final: 0.3357 (tpp) REVERT: K 120 GLN cc_start: 0.6934 (mp-120) cc_final: 0.6263 (pp30) REVERT: O 106 ILE cc_start: 0.1986 (OUTLIER) cc_final: 0.1620 (mm) REVERT: O 201 MET cc_start: 0.3057 (mmm) cc_final: -0.1213 (ppp) REVERT: O 239 MET cc_start: -0.0814 (tpp) cc_final: -0.1431 (mpp) REVERT: O 257 GLU cc_start: 0.1111 (mp0) cc_final: 0.0345 (pt0) REVERT: O 332 ASP cc_start: 0.3422 (m-30) cc_final: 0.2339 (t70) REVERT: O 412 LEU cc_start: 0.3244 (tp) cc_final: 0.2841 (pp) REVERT: P 201 MET cc_start: 0.2865 (mmm) cc_final: -0.1586 (tmm) REVERT: P 455 LYS cc_start: 0.5626 (mttm) cc_final: 0.4737 (mptt) outliers start: 131 outliers final: 98 residues processed: 474 average time/residue: 0.1943 time to fit residues: 158.2413 Evaluate side-chains 465 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 360 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 50 CYS Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain P residue 111 HIS Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 443 VAL Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 229 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 412 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 chunk 132 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 458 optimal weight: 6.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN C 464 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 GLN P 232 HIS P 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.172861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132906 restraints weight = 72919.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130128 restraints weight = 60713.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130247 restraints weight = 52607.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130315 restraints weight = 39667.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.130940 restraints weight = 30667.848| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37650 Z= 0.119 Angle : 0.679 14.037 50952 Z= 0.340 Chirality : 0.047 0.412 5958 Planarity : 0.004 0.054 6490 Dihedral : 5.614 67.721 5031 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.19 % Favored : 91.77 % Rotamer: Outliers : 2.62 % Allowed : 21.43 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.12), residues: 4604 helix: -0.31 (0.14), residues: 1446 sheet: -1.66 (0.19), residues: 682 loop : -1.86 (0.13), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 234 TYR 0.029 0.001 TYR E 362 PHE 0.047 0.002 PHE J 407 TRP 0.049 0.002 TRP K 132 HIS 0.007 0.001 HIS G 162 Details of bonding type rmsd covalent geometry : bond 0.00274 (37650) covalent geometry : angle 0.67918 (50952) hydrogen bonds : bond 0.02977 ( 1104) hydrogen bonds : angle 4.67065 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9208 Ramachandran restraints generated. 4604 Oldfield, 0 Emsley, 4604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 383 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7560 (t0) cc_final: 0.7269 (t0) REVERT: A 99 GLN cc_start: 0.8567 (pm20) cc_final: 0.8206 (pm20) REVERT: C 326 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7828 (mm-40) REVERT: C 340 MET cc_start: 0.7523 (mtp) cc_final: 0.7287 (ptp) REVERT: C 349 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7996 (tm-30) REVERT: C 384 GLN cc_start: 0.8377 (tp-100) cc_final: 0.7952 (tp-100) REVERT: C 460 ASP cc_start: 0.8167 (t0) cc_final: 0.7509 (t0) REVERT: C 464 ASN cc_start: 0.7453 (m-40) cc_final: 0.7184 (m110) REVERT: C 491 MET cc_start: 0.7941 (mmm) cc_final: 0.7731 (mmm) REVERT: D 326 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7870 (mm-40) REVERT: D 349 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8354 (tm-30) REVERT: D 384 GLN cc_start: 0.8382 (tp-100) cc_final: 0.7947 (tp-100) REVERT: D 491 MET cc_start: 0.7918 (mmm) cc_final: 0.6962 (mmt) REVERT: G 61 GLU cc_start: 0.7601 (pm20) cc_final: 0.7120 (mp0) REVERT: G 294 ILE cc_start: 0.9068 (pt) cc_final: 0.8638 (mt) REVERT: I 295 MET cc_start: 0.1075 (ttt) cc_final: 0.0597 (tpt) REVERT: I 389 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7199 (tm-30) REVERT: I 397 ASN cc_start: 0.4579 (OUTLIER) cc_final: 0.4238 (t0) REVERT: J 184 VAL cc_start: 0.7816 (t) cc_final: 0.7499 (p) REVERT: J 197 MET cc_start: 0.7347 (ptm) cc_final: 0.6580 (ptm) REVERT: J 201 TYR cc_start: 0.6360 (t80) cc_final: 0.5357 (t80) REVERT: J 221 GLN cc_start: 0.6566 (mp10) cc_final: 0.6038 (tm-30) REVERT: J 392 PHE cc_start: 0.5605 (p90) cc_final: 0.5002 (p90) REVERT: J 397 ASN cc_start: 0.4459 (OUTLIER) cc_final: 0.4034 (t0) REVERT: B 71 ASP cc_start: 0.7357 (t0) cc_final: 0.7019 (t0) REVERT: B 74 MET cc_start: 0.7689 (tpt) cc_final: 0.7313 (tpt) REVERT: B 101 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7326 (m-10) REVERT: B 300 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.7170 (tt) REVERT: B 304 TYR cc_start: 0.7914 (m-10) cc_final: 0.7275 (m-10) REVERT: H 61 GLU cc_start: 0.7771 (pm20) cc_final: 0.7526 (pm20) REVERT: H 294 ILE cc_start: 0.9087 (pt) cc_final: 0.8617 (mt) REVERT: F 127 LYS cc_start: 0.5771 (tptp) cc_final: 0.5497 (tppt) REVERT: K 120 GLN cc_start: 0.6804 (mp-120) cc_final: 0.6179 (pp30) REVERT: O 106 ILE cc_start: 0.1951 (OUTLIER) cc_final: 0.1587 (mm) REVERT: O 201 MET cc_start: 0.3091 (mmm) cc_final: -0.1213 (ppp) REVERT: O 239 MET cc_start: -0.0773 (tpp) cc_final: -0.1325 (mpp) REVERT: O 257 GLU cc_start: 0.1142 (mp0) cc_final: 0.0340 (pt0) REVERT: O 332 ASP cc_start: 0.3652 (m-30) cc_final: 0.2290 (t70) REVERT: O 412 LEU cc_start: 0.3121 (tp) cc_final: 0.2635 (pp) REVERT: P 201 MET cc_start: 0.2478 (mmm) cc_final: -0.1207 (tmm) REVERT: P 455 LYS cc_start: 0.5585 (mttm) cc_final: 0.4709 (mptt) outliers start: 109 outliers final: 91 residues processed: 466 average time/residue: 0.1984 time to fit residues: 157.9169 Evaluate side-chains 458 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 362 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 50 CYS Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 242 VAL Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 414 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain O residue 400 THR Chi-restraints excluded: chain O residue 422 HIS Chi-restraints excluded: chain O residue 443 VAL Chi-restraints excluded: chain O residue 449 LYS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain P residue 111 HIS Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 224 CYS Chi-restraints excluded: chain P residue 254 MET Chi-restraints excluded: chain P residue 290 ASN Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 400 THR Chi-restraints excluded: chain P residue 443 VAL Chi-restraints excluded: chain P residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 36 optimal weight: 0.0370 chunk 406 optimal weight: 4.9990 chunk 396 optimal weight: 0.0370 chunk 364 optimal weight: 30.0000 chunk 266 optimal weight: 2.9990 chunk 397 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.173452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133251 restraints weight = 72528.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130583 restraints weight = 60643.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130750 restraints weight = 51965.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.130826 restraints weight = 40530.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131421 restraints weight = 31107.979| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37650 Z= 0.119 Angle : 0.686 14.330 50952 Z= 0.341 Chirality : 0.047 0.325 5958 Planarity : 0.004 0.083 6490 Dihedral : 5.488 65.456 5031 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.97 % Favored : 91.99 % Rotamer: Outliers : 2.83 % Allowed : 21.71 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.12), residues: 4604 helix: -0.26 (0.14), residues: 1448 sheet: -1.63 (0.19), residues: 684 loop : -1.82 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 324 TYR 0.029 0.001 TYR E 362 PHE 0.048 0.002 PHE J 407 TRP 0.047 0.002 TRP K 132 HIS 0.007 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00273 (37650) covalent geometry : angle 0.68560 (50952) hydrogen bonds : bond 0.02922 ( 1104) hydrogen bonds : angle 4.62095 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5683.32 seconds wall clock time: 99 minutes 26.53 seconds (5966.53 seconds total)