Starting phenix.real_space_refine on Sat Sep 28 21:51:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/09_2024/8umu_42384.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/09_2024/8umu_42384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/09_2024/8umu_42384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/09_2024/8umu_42384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/09_2024/8umu_42384.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/09_2024/8umu_42384.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 136 5.16 5 C 12926 2.51 5 N 3528 2.21 5 O 3917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20521 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4074 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 482} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2563 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "D" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2526 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 13, 'TRANS': 313} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.15, per 1000 atoms: 0.59 Number of scatterers: 20521 At special positions: 0 Unit cell: (117.576, 128.34, 140.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 11 15.00 Mg 3 11.99 O 3917 8.00 N 3528 7.00 C 12926 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: 5.35 Conformation dependent library (CDL) restraints added in 2.8 seconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 14 sheets defined 51.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.607A pdb=" N PHE A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.539A pdb=" N GLU A 293 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 294' Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 311 through 316 removed outlier: 4.326A pdb=" N VAL A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 441 through 453 removed outlier: 3.628A pdb=" N ILE A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.953A pdb=" N GLN A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.600A pdb=" N LEU A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 4.006A pdb=" N TYR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 Processing helix chain 'A' and resid 628 through 643 removed outlier: 4.108A pdb=" N GLY A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 654 Processing helix chain 'A' and resid 666 through 690 Processing helix chain 'A' and resid 692 through 698 removed outlier: 3.522A pdb=" N LEU A 695 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 696 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 697 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 698 - end of helix No H-bonds generated for 'chain 'A' and resid 692 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.088A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 744 removed outlier: 3.712A pdb=" N GLU A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 752 removed outlier: 3.840A pdb=" N ARG A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.996A pdb=" N GLU A 823 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 125 removed outlier: 4.727A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.523A pdb=" N SER B 145 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 146 " --> pdb=" O ALA B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.371A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 removed outlier: 3.609A pdb=" N GLN B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.604A pdb=" N ILE B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.802A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 4.147A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.643A pdb=" N GLY B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.876A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 removed outlier: 3.723A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 removed outlier: 4.048A pdb=" N THR C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 85 removed outlier: 3.630A pdb=" N SER C 85 " --> pdb=" O GLU C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 103 through 110 removed outlier: 3.554A pdb=" N SER C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.599A pdb=" N ALA C 129 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 130' Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.757A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.884A pdb=" N LEU C 186 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 209 removed outlier: 4.264A pdb=" N MET C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.543A pdb=" N GLN C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 removed outlier: 3.534A pdb=" N VAL C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.859A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 313 removed outlier: 3.699A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.581A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.871A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.509A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 3.508A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.809A pdb=" N SER D 154 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 155' Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 223 through 234 removed outlier: 4.012A pdb=" N SER D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.775A pdb=" N ALA D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.671A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.596A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 298 removed outlier: 3.584A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.531A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.672A pdb=" N GLN D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.554A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.583A pdb=" N ARG E 15 " --> pdb=" O SER E 12 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 12 through 16' Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.020A pdb=" N CYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 103 through 118 removed outlier: 4.263A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.759A pdb=" N GLN E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 127' Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.669A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 removed outlier: 3.883A pdb=" N ARG E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 removed outlier: 3.775A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.608A pdb=" N CYS E 220 " --> pdb=" O ALA E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.943A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.396A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 16 removed outlier: 3.621A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 removed outlier: 3.691A pdb=" N LEU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 190 through 194 removed outlier: 3.525A pdb=" N ALA F 194 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 219 No H-bonds generated for 'chain 'F' and resid 217 through 219' Processing helix chain 'G' and resid 9 through 18 removed outlier: 3.827A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.504A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 155 removed outlier: 4.195A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 153 removed outlier: 3.770A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 209 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.694A pdb=" N LEU A 168 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 399 removed outlier: 6.681A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 369 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 371 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.289A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.493A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 122 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.514A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.153A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN D 73 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N PHE D 197 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.449A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.232A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 104 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN G 179 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.697A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.374A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN F 177 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 179 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP H 113 " --> pdb=" O ASN F 179 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS F 181 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL H 111 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.607A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER H 172 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALA H 157 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.753A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 66 through 71 removed outlier: 7.276A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3231 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: 7.36 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5306 1.33 - 1.49: 6129 1.49 - 1.64: 9212 1.64 - 1.79: 86 1.79 - 1.95: 120 Bond restraints: 20853 Sorted by residual: bond pdb=" CA SER B 238 " pdb=" C SER B 238 " ideal model delta sigma weight residual 1.524 1.425 0.099 1.24e-02 6.50e+03 6.38e+01 bond pdb=" CA GLN B 237 " pdb=" C GLN B 237 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.24e-02 6.50e+03 4.59e+01 bond pdb=" CA ASP G 21 " pdb=" C ASP G 21 " ideal model delta sigma weight residual 1.522 1.436 0.085 1.31e-02 5.83e+03 4.25e+01 bond pdb=" N ILE G 23 " pdb=" CA ILE G 23 " ideal model delta sigma weight residual 1.460 1.527 -0.068 1.25e-02 6.40e+03 2.93e+01 bond pdb=" N LYS F 14 " pdb=" CA LYS F 14 " ideal model delta sigma weight residual 1.459 1.398 0.061 1.21e-02 6.83e+03 2.55e+01 ... (remaining 20848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 27416 2.67 - 5.33: 655 5.33 - 8.00: 113 8.00 - 10.67: 34 10.67 - 13.34: 5 Bond angle restraints: 28223 Sorted by residual: angle pdb=" N GLU F 17 " pdb=" CA GLU F 17 " pdb=" C GLU F 17 " ideal model delta sigma weight residual 113.23 100.51 12.72 1.24e+00 6.50e-01 1.05e+02 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" C LYS G 20 " ideal model delta sigma weight residual 111.71 121.98 -10.27 1.15e+00 7.56e-01 7.97e+01 angle pdb=" N ILE F 78 " pdb=" CA ILE F 78 " pdb=" C ILE F 78 " ideal model delta sigma weight residual 113.22 105.48 7.74 1.23e+00 6.61e-01 3.96e+01 angle pdb=" C GLN B 237 " pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " ideal model delta sigma weight residual 110.96 101.47 9.49 1.54e+00 4.22e-01 3.80e+01 angle pdb=" C SER B 238 " pdb=" CA SER B 238 " pdb=" CB SER B 238 " ideal model delta sigma weight residual 110.96 101.65 9.31 1.54e+00 4.22e-01 3.65e+01 ... (remaining 28218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 11661 24.53 - 49.06: 1057 49.06 - 73.59: 136 73.59 - 98.13: 22 98.13 - 122.66: 2 Dihedral angle restraints: 12878 sinusoidal: 5265 harmonic: 7613 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 177.35 122.66 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -175.46 115.45 1 2.00e+01 2.50e-03 3.43e+01 dihedral pdb=" C GLN B 237 " pdb=" N GLN B 237 " pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " ideal model delta harmonic sigma weight residual -122.60 -109.96 -12.64 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 12875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3025 0.104 - 0.207: 246 0.207 - 0.310: 15 0.310 - 0.414: 3 0.414 - 0.517: 3 Chirality restraints: 3292 Sorted by residual: chirality pdb=" CA PHE B 240 " pdb=" N PHE B 240 " pdb=" C PHE B 240 " pdb=" CB PHE B 240 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA LYS G 20 " pdb=" N LYS G 20 " pdb=" C LYS G 20 " pdb=" CB LYS G 20 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CB ILE H 241 " pdb=" CA ILE H 241 " pdb=" CG1 ILE H 241 " pdb=" CG2 ILE H 241 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 3289 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 405 " -0.083 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO A 406 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 406 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 406 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 699 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 360 " -0.051 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO A 361 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.043 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 333 2.66 - 3.22: 17654 3.22 - 3.78: 32380 3.78 - 4.34: 42928 4.34 - 4.90: 71115 Nonbonded interactions: 164410 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.104 2.170 nonbonded pdb="MG MG B 401 " pdb=" O3G AGS B 402 " model vdw 2.167 2.170 nonbonded pdb=" O THR E 168 " pdb=" OG1 THR E 168 " model vdw 2.257 3.040 nonbonded pdb=" O TYR E 254 " pdb=" OG1 THR E 258 " model vdw 2.271 3.040 nonbonded pdb=" O GLU D 259 " pdb=" OG1 THR D 263 " model vdw 2.285 3.040 ... (remaining 164405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 256) selection = (chain 'H' and resid 1 through 256) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.870 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.006 0.099 20853 Z= 0.364 Angle : 1.015 13.336 28223 Z= 0.577 Chirality : 0.059 0.517 3292 Planarity : 0.008 0.124 3607 Dihedral : 17.808 122.657 7922 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.84 % Allowed : 27.36 % Favored : 71.80 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.15), residues: 2577 helix: -1.65 (0.12), residues: 1169 sheet: -0.06 (0.22), residues: 555 loop : -1.15 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 251 HIS 0.011 0.002 HIS H 246 PHE 0.049 0.003 PHE B 223 TYR 0.040 0.002 TYR F 249 ARG 0.014 0.001 ARG A 846 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 342 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.6499 (mmm) cc_final: 0.6147 (mmm) REVERT: C 51 ASP cc_start: 0.6192 (t0) cc_final: 0.5873 (t0) REVERT: E 317 TYR cc_start: 0.8270 (t80) cc_final: 0.7417 (t80) REVERT: F 121 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7109 (tt) REVERT: G 27 CYS cc_start: 0.7266 (m) cc_final: 0.6569 (t) REVERT: H 2 PHE cc_start: 0.5988 (t80) cc_final: 0.5520 (t80) REVERT: H 133 TYR cc_start: 0.3392 (m-80) cc_final: 0.1611 (m-10) outliers start: 19 outliers final: 5 residues processed: 353 average time/residue: 0.3511 time to fit residues: 183.7643 Evaluate side-chains 292 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 286 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain H residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 182 GLN B 204 ASN B 226 GLN B 234 ASN C 55 HIS C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 194 HIS ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 ASN H 204 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20853 Z= 0.265 Angle : 0.653 11.069 28223 Z= 0.332 Chirality : 0.043 0.162 3292 Planarity : 0.006 0.074 3607 Dihedral : 7.906 105.653 2880 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.52 % Allowed : 25.21 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2577 helix: -0.25 (0.14), residues: 1191 sheet: 0.12 (0.22), residues: 560 loop : -0.77 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 307 HIS 0.009 0.001 HIS H 246 PHE 0.023 0.002 PHE B 223 TYR 0.024 0.002 TYR F 249 ARG 0.015 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 325 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 PHE cc_start: 0.5140 (t80) cc_final: 0.4614 (t80) REVERT: B 136 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7682 (mtmt) REVERT: B 145 SER cc_start: 0.8176 (OUTLIER) cc_final: 0.7782 (m) REVERT: B 229 MET cc_start: 0.7711 (tpp) cc_final: 0.7319 (tpp) REVERT: B 336 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7087 (mp10) REVERT: C 20 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6316 (mt) REVERT: C 51 ASP cc_start: 0.6576 (t0) cc_final: 0.6101 (t0) REVERT: C 91 ASN cc_start: 0.6525 (p0) cc_final: 0.6284 (p0) REVERT: C 143 GLU cc_start: 0.6074 (mt-10) cc_final: 0.5798 (mt-10) REVERT: C 311 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6309 (mtp180) REVERT: D 95 LEU cc_start: 0.4873 (tp) cc_final: 0.4342 (mt) REVERT: E 317 TYR cc_start: 0.8194 (t80) cc_final: 0.7369 (t80) REVERT: G 27 CYS cc_start: 0.7500 (m) cc_final: 0.6897 (t) REVERT: H 2 PHE cc_start: 0.6107 (t80) cc_final: 0.5407 (t80) REVERT: H 133 TYR cc_start: 0.3543 (m-80) cc_final: 0.2154 (m-10) outliers start: 80 outliers final: 37 residues processed: 382 average time/residue: 0.3332 time to fit residues: 193.2664 Evaluate side-chains 330 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 288 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 453 ASN A 509 HIS A 820 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20853 Z= 0.315 Angle : 0.667 11.954 28223 Z= 0.338 Chirality : 0.044 0.150 3292 Planarity : 0.005 0.067 3607 Dihedral : 7.520 93.328 2875 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.06 % Allowed : 24.51 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2577 helix: 0.04 (0.14), residues: 1195 sheet: 0.17 (0.22), residues: 544 loop : -0.71 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 4 HIS 0.008 0.001 HIS H 246 PHE 0.025 0.002 PHE H 207 TYR 0.029 0.002 TYR G 249 ARG 0.005 0.001 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 319 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 PHE cc_start: 0.5350 (t80) cc_final: 0.4762 (t80) REVERT: B 127 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7654 (ttpt) REVERT: B 136 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7476 (mtmt) REVERT: B 145 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7811 (m) REVERT: B 336 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: C 20 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6304 (mt) REVERT: C 85 SER cc_start: 0.7483 (m) cc_final: 0.7117 (p) REVERT: C 91 ASN cc_start: 0.6612 (p0) cc_final: 0.6351 (p0) REVERT: C 165 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7785 (tp) REVERT: D 272 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: E 317 TYR cc_start: 0.8211 (t80) cc_final: 0.7678 (t80) REVERT: H 2 PHE cc_start: 0.6054 (t80) cc_final: 0.5205 (t80) REVERT: H 8 GLN cc_start: 0.7301 (tm-30) cc_final: 0.6921 (tm-30) REVERT: H 91 ARG cc_start: 0.7267 (tmt170) cc_final: 0.7017 (tmt170) REVERT: H 133 TYR cc_start: 0.3756 (m-80) cc_final: 0.2312 (m-10) outliers start: 115 outliers final: 65 residues processed: 409 average time/residue: 0.3311 time to fit residues: 208.0150 Evaluate side-chains 363 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 291 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 347 GLN E 22 GLN E 71 HIS E 194 HIS H 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20853 Z= 0.270 Angle : 0.623 9.867 28223 Z= 0.316 Chirality : 0.043 0.144 3292 Planarity : 0.005 0.066 3607 Dihedral : 7.273 86.484 2874 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.15 % Allowed : 24.81 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2577 helix: 0.30 (0.15), residues: 1191 sheet: 0.14 (0.22), residues: 545 loop : -0.65 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 4 HIS 0.008 0.001 HIS H 246 PHE 0.019 0.002 PHE G 2 TYR 0.024 0.002 TYR G 249 ARG 0.004 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 315 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7642 (ttpt) REVERT: B 136 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7606 (mtmt) REVERT: B 145 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7793 (m) REVERT: B 216 ASP cc_start: 0.6039 (p0) cc_final: 0.5812 (p0) REVERT: B 336 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: C 20 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6300 (mt) REVERT: C 85 SER cc_start: 0.7455 (m) cc_final: 0.7159 (p) REVERT: C 91 ASN cc_start: 0.6594 (p0) cc_final: 0.6330 (p0) REVERT: C 225 MET cc_start: 0.7833 (tmm) cc_final: 0.7506 (tmm) REVERT: D 272 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: E 213 HIS cc_start: 0.6542 (t-90) cc_final: 0.6210 (m-70) REVERT: E 317 TYR cc_start: 0.8223 (t80) cc_final: 0.7571 (t80) REVERT: H 2 PHE cc_start: 0.6200 (t80) cc_final: 0.5321 (t80) REVERT: H 91 ARG cc_start: 0.7279 (tmt170) cc_final: 0.6700 (tmt170) REVERT: H 133 TYR cc_start: 0.3773 (m-80) cc_final: 0.2378 (m-10) outliers start: 117 outliers final: 76 residues processed: 405 average time/residue: 0.3437 time to fit residues: 211.8386 Evaluate side-chains 379 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 297 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 171 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS F 44 HIS F 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 20853 Z= 0.474 Angle : 0.768 11.041 28223 Z= 0.387 Chirality : 0.047 0.152 3292 Planarity : 0.006 0.102 3607 Dihedral : 7.453 72.718 2872 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.34 % Allowed : 24.77 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2577 helix: -0.13 (0.14), residues: 1199 sheet: -0.12 (0.23), residues: 532 loop : -0.85 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 4 HIS 0.010 0.001 HIS F 44 PHE 0.025 0.003 PHE G 2 TYR 0.038 0.002 TYR G 249 ARG 0.006 0.001 ARG E 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 332 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6805 (tt) REVERT: A 483 MET cc_start: 0.7145 (tpp) cc_final: 0.6883 (tpp) REVERT: A 632 PHE cc_start: 0.5629 (t80) cc_final: 0.4868 (t80) REVERT: A 806 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5860 (pp20) REVERT: B 127 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7621 (ttpt) REVERT: B 136 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7819 (mtmt) REVERT: B 228 ASP cc_start: 0.6296 (t0) cc_final: 0.5958 (t70) REVERT: B 229 MET cc_start: 0.7990 (tpp) cc_final: 0.7600 (tpp) REVERT: B 336 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: C 85 SER cc_start: 0.7553 (m) cc_final: 0.7290 (p) REVERT: C 91 ASN cc_start: 0.6804 (p0) cc_final: 0.6471 (p0) REVERT: C 225 MET cc_start: 0.7945 (tmm) cc_final: 0.7611 (tmm) REVERT: D 272 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: E 127 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6932 (ttp-110) REVERT: E 136 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: E 154 LYS cc_start: 0.8496 (ptpt) cc_final: 0.8205 (ptpt) REVERT: E 170 LYS cc_start: 0.6934 (ptpt) cc_final: 0.6589 (pttt) REVERT: E 194 HIS cc_start: 0.8260 (t-90) cc_final: 0.8010 (t-170) REVERT: E 317 TYR cc_start: 0.8324 (t80) cc_final: 0.7945 (t80) REVERT: F 8 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7127 (tp-100) REVERT: F 246 HIS cc_start: 0.6446 (OUTLIER) cc_final: 0.6117 (p-80) REVERT: H 91 ARG cc_start: 0.7364 (tmt170) cc_final: 0.6950 (tmt170) REVERT: H 162 CYS cc_start: 0.6963 (t) cc_final: 0.6660 (p) outliers start: 144 outliers final: 98 residues processed: 444 average time/residue: 0.3253 time to fit residues: 221.0013 Evaluate side-chains 410 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 303 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 246 HIS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 162 CYS Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 240 LYS Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.5980 chunk 222 optimal weight: 6.9990 chunk 48 optimal weight: 0.0570 chunk 145 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 347 GLN E 71 HIS F 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20853 Z= 0.183 Angle : 0.614 10.511 28223 Z= 0.310 Chirality : 0.043 0.205 3292 Planarity : 0.005 0.071 3607 Dihedral : 6.903 64.292 2872 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.18 % Allowed : 27.54 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2577 helix: 0.48 (0.15), residues: 1198 sheet: 0.03 (0.23), residues: 526 loop : -0.60 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 4 HIS 0.005 0.001 HIS G 246 PHE 0.027 0.002 PHE B 223 TYR 0.017 0.001 TYR G 249 ARG 0.005 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 335 time to evaluate : 2.380 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 482 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6620 (tt) REVERT: A 483 MET cc_start: 0.7028 (tpp) cc_final: 0.6669 (tpp) REVERT: A 848 ILE cc_start: 0.7560 (mt) cc_final: 0.7356 (mm) REVERT: B 136 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7541 (mtmt) REVERT: B 229 MET cc_start: 0.7864 (tpp) cc_final: 0.7513 (tpp) REVERT: C 85 SER cc_start: 0.7462 (m) cc_final: 0.7258 (p) REVERT: C 91 ASN cc_start: 0.6503 (p0) cc_final: 0.6175 (p0) REVERT: C 225 MET cc_start: 0.7900 (tmm) cc_final: 0.7558 (tmm) REVERT: C 311 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6302 (mtp180) REVERT: D 272 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: E 213 HIS cc_start: 0.6497 (t-90) cc_final: 0.6225 (m-70) REVERT: E 317 TYR cc_start: 0.8235 (t80) cc_final: 0.7980 (t80) REVERT: H 91 ARG cc_start: 0.7410 (tmt170) cc_final: 0.6989 (tmt170) REVERT: H 116 MET cc_start: 0.7050 (tpt) cc_final: 0.6402 (tpt) REVERT: H 144 PHE cc_start: 0.7807 (t80) cc_final: 0.7525 (t80) REVERT: H 162 CYS cc_start: 0.6890 (t) cc_final: 0.6605 (p) outliers start: 95 outliers final: 61 residues processed: 406 average time/residue: 0.3356 time to fit residues: 204.4937 Evaluate side-chains 376 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 311 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 255 ILE Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 246 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 71 HIS E 194 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20853 Z= 0.285 Angle : 0.654 9.738 28223 Z= 0.328 Chirality : 0.044 0.168 3292 Planarity : 0.005 0.104 3607 Dihedral : 6.804 64.375 2872 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.80 % Allowed : 27.50 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2577 helix: 0.47 (0.15), residues: 1196 sheet: 0.00 (0.23), residues: 528 loop : -0.67 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 4 HIS 0.004 0.001 HIS C 289 PHE 0.026 0.002 PHE G 2 TYR 0.031 0.002 TYR G 249 ARG 0.005 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 321 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6739 (tt) REVERT: A 483 MET cc_start: 0.7059 (tpp) cc_final: 0.6721 (tpp) REVERT: A 630 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7426 (tm-30) REVERT: A 632 PHE cc_start: 0.5619 (t80) cc_final: 0.4828 (t80) REVERT: B 127 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7606 (ttpt) REVERT: B 136 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7845 (mtmt) REVERT: B 228 ASP cc_start: 0.6024 (t0) cc_final: 0.5656 (t70) REVERT: C 85 SER cc_start: 0.7506 (m) cc_final: 0.7271 (p) REVERT: C 91 ASN cc_start: 0.6636 (p0) cc_final: 0.6331 (p0) REVERT: C 225 MET cc_start: 0.7961 (tmm) cc_final: 0.7601 (tmm) REVERT: C 311 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6448 (mtp180) REVERT: D 272 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: E 213 HIS cc_start: 0.6566 (t-90) cc_final: 0.6253 (m-70) REVERT: H 8 GLN cc_start: 0.7045 (tm-30) cc_final: 0.6766 (tm-30) REVERT: H 75 MET cc_start: 0.8079 (ppp) cc_final: 0.7565 (tmm) REVERT: H 91 ARG cc_start: 0.7433 (tmt170) cc_final: 0.7043 (tmt170) REVERT: H 116 MET cc_start: 0.7046 (tpt) cc_final: 0.6084 (tpt) REVERT: H 133 TYR cc_start: 0.3779 (m-80) cc_final: 0.2076 (m-10) REVERT: H 162 CYS cc_start: 0.6890 (t) cc_final: 0.6609 (p) outliers start: 109 outliers final: 83 residues processed: 401 average time/residue: 0.3504 time to fit residues: 212.6176 Evaluate side-chains 389 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 301 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 240 LYS Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0870 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 71 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20853 Z= 0.211 Angle : 0.631 9.638 28223 Z= 0.316 Chirality : 0.043 0.168 3292 Planarity : 0.005 0.082 3607 Dihedral : 6.589 63.172 2872 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.14 % Allowed : 28.16 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2577 helix: 0.59 (0.15), residues: 1198 sheet: 0.05 (0.23), residues: 527 loop : -0.55 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 4 HIS 0.004 0.001 HIS G 246 PHE 0.021 0.002 PHE G 2 TYR 0.024 0.001 TYR G 249 ARG 0.006 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 321 time to evaluate : 2.205 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 482 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6659 (tt) REVERT: A 483 MET cc_start: 0.7044 (tpp) cc_final: 0.6687 (tpp) REVERT: A 839 GLN cc_start: 0.8150 (mp10) cc_final: 0.7925 (mm-40) REVERT: B 132 LYS cc_start: 0.7261 (tttm) cc_final: 0.6967 (tmtt) REVERT: B 136 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: B 229 MET cc_start: 0.7896 (tpp) cc_final: 0.7643 (tpp) REVERT: C 85 SER cc_start: 0.7465 (m) cc_final: 0.7261 (p) REVERT: C 91 ASN cc_start: 0.6595 (p0) cc_final: 0.6266 (p0) REVERT: C 225 MET cc_start: 0.8036 (tmm) cc_final: 0.7677 (tmm) REVERT: C 311 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6375 (mtp180) REVERT: D 272 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: E 213 HIS cc_start: 0.6458 (t-90) cc_final: 0.6239 (m-70) REVERT: F 246 HIS cc_start: 0.6264 (OUTLIER) cc_final: 0.6053 (p-80) REVERT: G 207 PHE cc_start: 0.8217 (m-80) cc_final: 0.7984 (m-80) REVERT: H 91 ARG cc_start: 0.7419 (tmt170) cc_final: 0.7041 (tmt170) REVERT: H 116 MET cc_start: 0.7017 (tpt) cc_final: 0.6388 (tpt) REVERT: H 162 CYS cc_start: 0.6792 (t) cc_final: 0.6479 (p) REVERT: H 207 PHE cc_start: 0.7794 (m-80) cc_final: 0.7273 (m-80) outliers start: 94 outliers final: 75 residues processed: 393 average time/residue: 0.3309 time to fit residues: 196.4579 Evaluate side-chains 388 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 308 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 246 HIS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 240 LYS Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 217 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 194 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20853 Z= 0.260 Angle : 0.651 8.920 28223 Z= 0.327 Chirality : 0.044 0.166 3292 Planarity : 0.005 0.072 3607 Dihedral : 6.511 63.079 2872 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.44 % Allowed : 28.07 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 2577 helix: 0.59 (0.15), residues: 1197 sheet: -0.06 (0.23), residues: 529 loop : -0.60 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 4 HIS 0.004 0.001 HIS G 246 PHE 0.023 0.002 PHE G 2 TYR 0.029 0.002 TYR G 249 ARG 0.006 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 311 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6714 (tt) REVERT: A 483 MET cc_start: 0.7077 (tpp) cc_final: 0.6720 (tpp) REVERT: A 632 PHE cc_start: 0.5533 (t80) cc_final: 0.4761 (t80) REVERT: A 839 GLN cc_start: 0.8193 (mp10) cc_final: 0.7969 (mm-40) REVERT: B 127 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7415 (ttpt) REVERT: B 136 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7899 (mtmt) REVERT: B 229 MET cc_start: 0.7925 (tpp) cc_final: 0.7554 (tpp) REVERT: C 51 ASP cc_start: 0.6755 (t0) cc_final: 0.6417 (t0) REVERT: C 85 SER cc_start: 0.7521 (m) cc_final: 0.7281 (p) REVERT: C 91 ASN cc_start: 0.6659 (p0) cc_final: 0.6330 (p0) REVERT: C 225 MET cc_start: 0.8029 (tmm) cc_final: 0.7675 (tmm) REVERT: C 311 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6427 (mtp180) REVERT: D 272 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8079 (pt0) REVERT: E 213 HIS cc_start: 0.6534 (t-90) cc_final: 0.6294 (m-70) REVERT: H 8 GLN cc_start: 0.7046 (tm-30) cc_final: 0.6790 (tm-30) REVERT: H 91 ARG cc_start: 0.7435 (tmt170) cc_final: 0.7116 (tmt170) REVERT: H 116 MET cc_start: 0.7055 (tpt) cc_final: 0.6443 (tpt) REVERT: H 133 TYR cc_start: 0.3741 (m-80) cc_final: 0.2047 (m-10) REVERT: H 144 PHE cc_start: 0.8091 (t80) cc_final: 0.7795 (t80) REVERT: H 162 CYS cc_start: 0.6883 (t) cc_final: 0.6523 (p) REVERT: H 207 PHE cc_start: 0.7565 (m-80) cc_final: 0.7094 (m-80) outliers start: 101 outliers final: 85 residues processed: 388 average time/residue: 0.3449 time to fit residues: 203.5670 Evaluate side-chains 397 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 307 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.0970 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 156 optimal weight: 0.5980 chunk 124 optimal weight: 0.2980 chunk 161 optimal weight: 4.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 71 HIS E 302 ASN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20853 Z= 0.183 Angle : 0.617 8.879 28223 Z= 0.309 Chirality : 0.042 0.162 3292 Planarity : 0.004 0.066 3607 Dihedral : 6.296 61.317 2872 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.39 % Allowed : 29.08 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2577 helix: 0.79 (0.15), residues: 1198 sheet: 0.02 (0.23), residues: 529 loop : -0.46 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 4 HIS 0.004 0.001 HIS G 246 PHE 0.019 0.001 PHE B 223 TYR 0.019 0.001 TYR G 249 ARG 0.006 0.000 ARG H 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 327 time to evaluate : 2.425 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 482 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6609 (tt) REVERT: A 483 MET cc_start: 0.6994 (tpp) cc_final: 0.6610 (tpp) REVERT: A 848 ILE cc_start: 0.7444 (mt) cc_final: 0.7097 (mm) REVERT: B 127 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7380 (ttpt) REVERT: B 136 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7877 (mtmt) REVERT: B 229 MET cc_start: 0.7840 (tpp) cc_final: 0.7588 (tpp) REVERT: C 51 ASP cc_start: 0.6687 (t0) cc_final: 0.6357 (t0) REVERT: C 225 MET cc_start: 0.7968 (tmm) cc_final: 0.7605 (tmm) REVERT: D 62 LEU cc_start: 0.3269 (tt) cc_final: 0.2559 (pp) REVERT: D 86 SER cc_start: 0.6394 (m) cc_final: 0.6157 (p) REVERT: D 272 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: E 136 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: F 1 MET cc_start: 0.7353 (tpt) cc_final: 0.7087 (tpp) REVERT: F 72 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8104 (mt) REVERT: F 148 CYS cc_start: 0.7982 (m) cc_final: 0.7388 (t) REVERT: H 8 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6924 (tm-30) REVERT: H 91 ARG cc_start: 0.7446 (tmt170) cc_final: 0.7205 (tmt170) REVERT: H 116 MET cc_start: 0.7069 (tpt) cc_final: 0.6484 (tpt) REVERT: H 133 TYR cc_start: 0.3695 (m-80) cc_final: 0.2065 (m-10) REVERT: H 144 PHE cc_start: 0.8070 (t80) cc_final: 0.7751 (t80) REVERT: H 162 CYS cc_start: 0.6774 (t) cc_final: 0.6435 (p) REVERT: H 207 PHE cc_start: 0.7397 (m-80) cc_final: 0.6866 (m-10) outliers start: 77 outliers final: 66 residues processed: 388 average time/residue: 0.3346 time to fit residues: 196.3392 Evaluate side-chains 381 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 309 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 244 MET Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 194 HIS E 213 HIS F 8 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.200411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154466 restraints weight = 29706.971| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.62 r_work: 0.3855 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20853 Z= 0.248 Angle : 0.645 8.270 28223 Z= 0.323 Chirality : 0.043 0.202 3292 Planarity : 0.005 0.065 3607 Dihedral : 6.283 61.841 2872 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.70 % Allowed : 28.82 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2577 helix: 0.74 (0.15), residues: 1197 sheet: -0.02 (0.23), residues: 531 loop : -0.48 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 4 HIS 0.008 0.001 HIS E 213 PHE 0.022 0.002 PHE G 2 TYR 0.028 0.001 TYR G 249 ARG 0.007 0.000 ARG G 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4875.97 seconds wall clock time: 87 minutes 36.20 seconds (5256.20 seconds total)