Starting phenix.real_space_refine on Sun Jun 15 01:02:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey1_50051/06_2025/9ey1_50051.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey1_50051/06_2025/9ey1_50051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ey1_50051/06_2025/9ey1_50051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey1_50051/06_2025/9ey1_50051.map" model { file = "/net/cci-nas-00/data/ceres_data/9ey1_50051/06_2025/9ey1_50051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey1_50051/06_2025/9ey1_50051.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 Zn 1 6.06 5 P 72 5.49 5 S 86 5.16 5 C 10336 2.51 5 N 2949 2.21 5 O 3325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16769 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 5512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5512 Classifications: {'peptide': 705} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 660} Chain breaks: 2 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "T" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1461 Classifications: {'RNA': 69} Modifications used: {'rna2p': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 25, 'rna3p_pyr': 27} Link IDs: {'rna2p': 17, 'rna3p': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2345 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 13.26, per 1000 atoms: 0.79 Number of scatterers: 16769 At special positions: 0 Unit cell: (106.05, 117.16, 172.71, 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) Zn 1 29.99 S 86 16.00 P 72 15.00 O 3325 8.00 N 2949 7.00 C 10336 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: 4.68 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E1000 " - pdb=" NE2 HIS E 724 " 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3662 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 15 sheets defined 49.5% alpha, 13.6% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 6.95 Creating SS restraints... Processing helix chain 'E' and resid 37 through 42 Processing helix chain 'E' and resid 90 through 98 Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 143 through 152 removed outlier: 3.500A pdb=" N GLU E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 removed outlier: 3.829A pdb=" N LYS E 260 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 281 removed outlier: 4.171A pdb=" N ALA E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 323 through 331 removed outlier: 3.685A pdb=" N GLN E 327 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 331 " --> pdb=" O GLN E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 351 removed outlier: 3.568A pdb=" N LEU E 349 " --> pdb=" O PRO E 345 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 362 removed outlier: 3.637A pdb=" N TRP E 357 " --> pdb=" O ARG E 353 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET E 358 " --> pdb=" O TYR E 354 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 361 " --> pdb=" O TRP E 357 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY E 362 " --> pdb=" O MET E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 393 removed outlier: 4.024A pdb=" N ILE E 392 " --> pdb=" O GLN E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 removed outlier: 4.001A pdb=" N PHE E 446 " --> pdb=" O ASN E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 519 through 529 Processing helix chain 'E' and resid 531 through 538 Processing helix chain 'E' and resid 548 through 552 Processing helix chain 'E' and resid 554 through 570 Processing helix chain 'E' and resid 583 through 595 removed outlier: 4.094A pdb=" N TRP E 587 " --> pdb=" O GLN E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 600 No H-bonds generated for 'chain 'E' and resid 598 through 600' Processing helix chain 'E' and resid 608 through 611 Processing helix chain 'E' and resid 618 through 632 removed outlier: 3.818A pdb=" N LEU E 624 " --> pdb=" O ALA E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 677 Processing helix chain 'E' and resid 693 through 700 Processing helix chain 'E' and resid 704 through 716 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 763 removed outlier: 4.006A pdb=" N LYS E 762 " --> pdb=" O PRO E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 771 removed outlier: 3.513A pdb=" N LYS E 768 " --> pdb=" O ILE E 764 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 769 " --> pdb=" O PRO E 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 791 removed outlier: 3.770A pdb=" N GLU E 777 " --> pdb=" O GLY E 773 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E 786 " --> pdb=" O ARG E 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.838A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 122 removed outlier: 3.546A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.519A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.516A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.628A pdb=" N VAL A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.676A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.608A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.632A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.826A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 186 removed outlier: 4.597A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.618A pdb=" N VAL B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 121 through 137 removed outlier: 3.864A pdb=" N GLY C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.770A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.629A pdb=" N PHE C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.518A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 removed outlier: 3.556A pdb=" N LEU D 24 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.733A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 137 removed outlier: 3.679A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 165 through 186 removed outlier: 4.729A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 204 through 209 removed outlier: 4.069A pdb=" N LEU D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 removed outlier: 3.720A pdb=" N SER D 219 " --> pdb=" O ASN D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.502A pdb=" N TYR D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 removed outlier: 4.116A pdb=" N ILE F 98 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N MET F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY F 105 " --> pdb=" O TRP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.539A pdb=" N MET F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 164 removed outlier: 3.986A pdb=" N GLU F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.667A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 removed outlier: 3.543A pdb=" N MET F 215 " --> pdb=" O GLU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 237 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 removed outlier: 3.708A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 269 " --> pdb=" O TRP F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 282 Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing helix chain 'F' and resid 377 through 379 No H-bonds generated for 'chain 'F' and resid 377 through 379' Processing sheet with id=AA1, first strand: chain 'E' and resid 162 through 167 removed outlier: 6.682A pdb=" N CYS E 136 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ARG E 166 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU E 138 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP E 106 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER E 139 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE E 108 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE E 109 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU E 84 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA E 73 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 63 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL E 58 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.584A pdb=" N TYR E 173 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA E 305 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL E 340 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL E 307 " --> pdb=" O VAL E 340 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS E 342 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL E 309 " --> pdb=" O HIS E 342 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS E 367 " --> pdb=" O VAL E 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.540A pdb=" N ILE E 291 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS E 286 " --> pdb=" O ARG E 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 602 through 606 removed outlier: 5.907A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA E 540 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL E 579 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 542 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N SER E 511 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL E 542 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU E 513 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET E 750 " --> pdb=" O PHE E 485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 634 through 638 removed outlier: 6.331A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS E 685 " --> pdb=" O ASN E 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.720A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A 13 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A 40 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 15 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.585A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.563A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.582A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU D 253 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA D 197 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB5, first strand: chain 'F' and resid 272 through 273 removed outlier: 6.441A pdb=" N LEU F 205 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N CYS F 246 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE F 207 " --> pdb=" O CYS F 246 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 342 through 344 removed outlier: 6.031A pdb=" N GLN F 343 " --> pdb=" O THR F 382 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4724 1.33 - 1.45: 2999 1.45 - 1.57: 9217 1.57 - 1.69: 142 1.69 - 1.82: 136 Bond restraints: 17218 Sorted by residual: bond pdb=" C2 1MA T 9 " pdb=" N3 1MA T 9 " ideal model delta sigma weight residual 1.290 1.458 -0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N3 1MA T 9 " pdb=" C4 1MA T 9 " ideal model delta sigma weight residual 1.353 1.515 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" C5 1MA T 9 " pdb=" C6 1MA T 9 " ideal model delta sigma weight residual 1.437 1.533 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" N1 1MA T 9 " pdb=" C2 1MA T 9 " ideal model delta sigma weight residual 1.359 1.435 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" N HIS E 546 " pdb=" CA HIS E 546 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.29e-02 6.01e+03 8.20e+00 ... (remaining 17213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.86: 23626 6.86 - 13.72: 26 13.72 - 20.58: 1 20.58 - 27.44: 0 27.44 - 34.30: 2 Bond angle restraints: 23655 Sorted by residual: angle pdb=" C1' 1MA T 9 " pdb=" N9 1MA T 9 " pdb=" C8 1MA T 9 " ideal model delta sigma weight residual 127.61 93.31 34.30 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C1' 1MA T 9 " pdb=" N9 1MA T 9 " pdb=" C4 1MA T 9 " ideal model delta sigma weight residual 125.83 158.95 -33.12 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CA HIS E 702 " pdb=" C HIS E 702 " pdb=" O HIS E 702 " ideal model delta sigma weight residual 120.89 114.52 6.37 1.10e+00 8.26e-01 3.36e+01 angle pdb=" C GLY E 160 " pdb=" N ILE E 161 " pdb=" CA ILE E 161 " ideal model delta sigma weight residual 123.14 116.98 6.16 1.31e+00 5.83e-01 2.21e+01 angle pdb=" PA GTP T 201 " pdb=" O3A GTP T 201 " pdb=" PB GTP T 201 " ideal model delta sigma weight residual 120.50 134.53 -14.03 3.00e+00 1.11e-01 2.19e+01 ... (remaining 23650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 9954 34.82 - 69.64: 462 69.64 - 104.46: 60 104.46 - 139.28: 6 139.28 - 174.10: 1 Dihedral angle restraints: 10483 sinusoidal: 4784 harmonic: 5699 Sorted by residual: dihedral pdb=" O4' C T 44 " pdb=" C1' C T 44 " pdb=" N1 C T 44 " pdb=" C2 C T 44 " ideal model delta sinusoidal sigma weight residual 232.00 57.90 174.10 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O3B GTP T 201 " pdb=" O3A GTP T 201 " pdb=" PB GTP T 201 " pdb=" PA GTP T 201 " ideal model delta sinusoidal sigma weight residual -68.92 59.04 -127.96 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" O2G GTP T 201 " pdb=" O3B GTP T 201 " pdb=" PG GTP T 201 " pdb=" PB GTP T 201 " ideal model delta sinusoidal sigma weight residual 177.30 -58.66 -124.04 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 10480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2716 0.113 - 0.227: 46 0.227 - 0.340: 1 0.340 - 0.454: 2 0.454 - 0.567: 3 Chirality restraints: 2768 Sorted by residual: chirality pdb=" P U T 2 " pdb=" OP1 U T 2 " pdb=" OP2 U T 2 " pdb=" O5' U T 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" P A T 67 " pdb=" OP1 A T 67 " pdb=" OP2 A T 67 " pdb=" O5' A T 67 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" P C T 68 " pdb=" OP1 C T 68 " pdb=" OP2 C T 68 " pdb=" O5' C T 68 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 2765 not shown) Planarity restraints: 2821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 187 " -0.038 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO A 188 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 229 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO C 230 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 229 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO B 230 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " 0.026 5.00e-02 4.00e+02 ... (remaining 2818 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 207 2.63 - 3.20: 15174 3.20 - 3.77: 27790 3.77 - 4.33: 39327 4.33 - 4.90: 61678 Nonbonded interactions: 144176 Sorted by model distance: nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E1000 " model vdw 2.066 2.230 nonbonded pdb=" OD2 ASP E 550 " pdb="ZN ZN E1000 " model vdw 2.067 2.230 nonbonded pdb=" O2' 1MA T 9 " pdb=" OD1 ASN F 222 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR C 153 " pdb=" OH TYR C 233 " model vdw 2.209 3.040 nonbonded pdb=" O LEU F 290 " pdb=" O2' SAH F 501 " model vdw 2.226 3.040 ... (remaining 144171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5.430 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 54.270 Find NCS groups from input model: 0.470 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:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 0.444 17220 Z= 0.270 Angle : 0.809 34.298 23655 Z= 0.411 Chirality : 0.047 0.567 2768 Planarity : 0.005 0.058 2821 Dihedral : 18.770 174.103 6821 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 1.66 % Allowed : 20.96 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.31 (0.19), residues: 1991 helix: 0.68 (0.18), residues: 817 sheet: -0.18 (0.28), residues: 359 loop : 0.11 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 433 HIS 0.009 0.001 HIS E 546 PHE 0.014 0.001 PHE F 384 TYR 0.028 0.001 TYR F 132 ARG 0.009 0.000 ARG E 785 Details of bonding type rmsd hydrogen bonds : bond 0.23833 ( 751) hydrogen bonds : angle 8.32075 ( 2112) metal coordination : bond 0.31387 ( 2) covalent geometry : bond 0.00447 (17218) covalent geometry : angle 0.80863 (23655) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 374 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: E 138 LEU cc_start: 0.7760 (mp) cc_final: 0.7524 (mm) REVERT: E 145 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7499 (mp0) REVERT: E 181 TYR cc_start: 0.8073 (m-80) cc_final: 0.7760 (m-10) REVERT: E 249 LEU cc_start: 0.8721 (tt) cc_final: 0.8057 (mt) REVERT: E 306 PHE cc_start: 0.7928 (p90) cc_final: 0.7641 (p90) REVERT: E 309 VAL cc_start: 0.8136 (p) cc_final: 0.7859 (m) REVERT: E 310 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: E 436 ASP cc_start: 0.7968 (t0) cc_final: 0.7752 (m-30) REVERT: E 449 GLU cc_start: 0.8889 (tp30) cc_final: 0.8617 (tp30) REVERT: E 490 SER cc_start: 0.7431 (p) cc_final: 0.7206 (m) REVERT: E 524 LEU cc_start: 0.8429 (mt) cc_final: 0.8044 (mt) REVERT: E 546 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6398 (p-80) REVERT: E 588 LEU cc_start: 0.8009 (mm) cc_final: 0.7740 (mt) REVERT: E 602 ILE cc_start: 0.7915 (mm) cc_final: 0.7707 (tp) REVERT: E 682 LEU cc_start: 0.8383 (tp) cc_final: 0.8146 (tm) REVERT: E 716 ASN cc_start: 0.7938 (t0) cc_final: 0.7727 (t0) REVERT: E 760 MET cc_start: 0.7924 (mmm) cc_final: 0.7723 (mmm) REVERT: E 777 GLU cc_start: 0.8516 (tt0) cc_final: 0.8086 (tm-30) REVERT: A 28 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6496 (tt0) REVERT: A 70 ASP cc_start: 0.6734 (m-30) cc_final: 0.6137 (m-30) REVERT: A 84 ARG cc_start: 0.7312 (ptm160) cc_final: 0.7008 (ptm160) REVERT: A 105 LYS cc_start: 0.6962 (mtmt) cc_final: 0.6373 (mttm) REVERT: A 118 LEU cc_start: 0.6634 (mp) cc_final: 0.6401 (mm) REVERT: A 123 MET cc_start: 0.7130 (ttp) cc_final: 0.6646 (tmm) REVERT: A 135 GLU cc_start: 0.6445 (mm-30) cc_final: 0.6095 (mp0) REVERT: A 160 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: A 162 GLN cc_start: 0.6793 (mt0) cc_final: 0.6341 (mt0) REVERT: A 211 GLU cc_start: 0.6200 (pm20) cc_final: 0.5765 (pm20) REVERT: A 236 LEU cc_start: 0.7279 (tp) cc_final: 0.6930 (tp) REVERT: A 242 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6598 (mt-10) REVERT: B 30 LEU cc_start: 0.6208 (mt) cc_final: 0.5886 (mm) REVERT: B 41 ASP cc_start: 0.6711 (t0) cc_final: 0.6496 (t0) REVERT: B 44 ASN cc_start: 0.7233 (p0) cc_final: 0.6867 (p0) REVERT: B 48 GLU cc_start: 0.6991 (tp30) cc_final: 0.6529 (tp30) REVERT: B 52 LYS cc_start: 0.7137 (mtpt) cc_final: 0.6721 (mtpp) REVERT: B 69 LYS cc_start: 0.6733 (tptp) cc_final: 0.6445 (ttmm) REVERT: B 70 ASP cc_start: 0.6455 (m-30) cc_final: 0.6026 (m-30) REVERT: B 79 LYS cc_start: 0.6705 (tptt) cc_final: 0.6223 (ttmm) REVERT: B 96 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6582 (p) REVERT: B 99 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6849 (mtpp) REVERT: B 112 GLU cc_start: 0.6842 (mp0) cc_final: 0.6331 (mm-30) REVERT: B 140 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6929 (tp30) REVERT: B 143 GLN cc_start: 0.6587 (pm20) cc_final: 0.6005 (mp10) REVERT: B 159 PHE cc_start: 0.5220 (m-80) cc_final: 0.4308 (t80) REVERT: B 160 GLU cc_start: 0.6037 (mp0) cc_final: 0.5570 (mt-10) REVERT: B 162 GLN cc_start: 0.6799 (mt0) cc_final: 0.6497 (mt0) REVERT: B 194 MET cc_start: 0.6670 (mmm) cc_final: 0.6453 (mmm) REVERT: B 242 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6433 (mp0) REVERT: B 257 ILE cc_start: 0.7463 (tt) cc_final: 0.7181 (tp) REVERT: B 260 GLN cc_start: 0.7534 (mm110) cc_final: 0.7289 (tp40) REVERT: C 41 ASP cc_start: 0.7104 (t0) cc_final: 0.6896 (t70) REVERT: C 48 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6990 (tp30) REVERT: C 52 LYS cc_start: 0.7337 (tppt) cc_final: 0.7084 (tppt) REVERT: C 53 LYS cc_start: 0.7429 (ttpp) cc_final: 0.6905 (ttpp) REVERT: C 69 LYS cc_start: 0.8271 (tppt) cc_final: 0.7390 (mtmm) REVERT: C 104 LYS cc_start: 0.7308 (tttt) cc_final: 0.7042 (ttmt) REVERT: C 107 GLN cc_start: 0.6390 (tt0) cc_final: 0.6033 (mt0) REVERT: C 112 GLU cc_start: 0.6745 (mp0) cc_final: 0.6531 (mp0) REVERT: C 120 VAL cc_start: 0.7247 (t) cc_final: 0.7039 (t) REVERT: C 135 GLU cc_start: 0.6540 (tp30) cc_final: 0.6297 (mm-30) REVERT: C 189 ILE cc_start: 0.6778 (mt) cc_final: 0.6556 (mt) REVERT: C 212 LYS cc_start: 0.7284 (mtmm) cc_final: 0.6952 (mttt) REVERT: C 242 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6459 (mt-10) REVERT: C 251 ILE cc_start: 0.7919 (mt) cc_final: 0.7711 (mm) REVERT: C 259 MET cc_start: 0.6775 (mmm) cc_final: 0.6471 (mmm) REVERT: D 24 LEU cc_start: 0.7243 (tp) cc_final: 0.7018 (tp) REVERT: D 48 GLU cc_start: 0.6550 (pm20) cc_final: 0.6187 (mp0) REVERT: D 56 ASN cc_start: 0.7576 (p0) cc_final: 0.7312 (p0) REVERT: D 79 LYS cc_start: 0.6797 (mmmm) cc_final: 0.6229 (tppt) REVERT: D 81 LYS cc_start: 0.7273 (tmtm) cc_final: 0.6939 (tmtt) REVERT: D 84 ARG cc_start: 0.6854 (ptm-80) cc_final: 0.6466 (ptp-110) REVERT: D 86 ASP cc_start: 0.6642 (m-30) cc_final: 0.6330 (m-30) REVERT: D 123 MET cc_start: 0.6644 (tmm) cc_final: 0.6150 (tmm) REVERT: D 138 GLN cc_start: 0.7611 (mm110) cc_final: 0.7408 (mm-40) REVERT: D 159 PHE cc_start: 0.6043 (m-80) cc_final: 0.5362 (m-80) REVERT: D 179 THR cc_start: 0.6332 (t) cc_final: 0.6113 (m) REVERT: D 194 MET cc_start: 0.7302 (mmm) cc_final: 0.6836 (mmm) REVERT: D 205 LEU cc_start: 0.5786 (tp) cc_final: 0.5332 (mt) REVERT: D 226 ARG cc_start: 0.6729 (ptt90) cc_final: 0.5713 (ppt170) REVERT: D 232 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5918 (mt-10) REVERT: F 116 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F 130 LYS cc_start: 0.8160 (tttt) cc_final: 0.7550 (tttm) REVERT: F 178 LEU cc_start: 0.7449 (tp) cc_final: 0.7247 (tp) REVERT: F 191 MET cc_start: 0.7251 (mtm) cc_final: 0.6984 (mtp) REVERT: F 209 MET cc_start: 0.7609 (mmt) cc_final: 0.7033 (mmt) REVERT: F 214 TYR cc_start: 0.7170 (m-80) cc_final: 0.6725 (m-10) REVERT: F 250 ILE cc_start: 0.7028 (mt) cc_final: 0.6609 (tp) REVERT: F 276 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7796 (mppt) REVERT: F 327 LYS cc_start: 0.7880 (mttm) cc_final: 0.7656 (mmpt) REVERT: F 336 LEU cc_start: 0.7561 (mt) cc_final: 0.7361 (mt) REVERT: F 356 MET cc_start: 0.7626 (mmm) cc_final: 0.7238 (mmm) REVERT: F 360 LEU cc_start: 0.7882 (mt) cc_final: 0.7659 (mt) outliers start: 27 outliers final: 13 residues processed: 398 average time/residue: 1.2791 time to fit residues: 566.2307 Evaluate side-chains 260 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 702 HIS Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 455 ASN B 107 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 143 GLN F 200 GLN F 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.117349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.088046 restraints weight = 29540.267| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.25 r_work: 0.3081 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17220 Z= 0.164 Angle : 0.661 8.085 23655 Z= 0.333 Chirality : 0.044 0.164 2768 Planarity : 0.005 0.052 2821 Dihedral : 15.586 177.349 3218 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.61 % Allowed : 20.22 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.43 (0.19), residues: 1991 helix: 1.00 (0.18), residues: 853 sheet: -0.33 (0.26), residues: 348 loop : -0.05 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 183 HIS 0.005 0.001 HIS F 278 PHE 0.016 0.002 PHE E 521 TYR 0.015 0.002 TYR E 729 ARG 0.006 0.001 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 751) hydrogen bonds : angle 5.56528 ( 2112) metal coordination : bond 0.00647 ( 2) covalent geometry : bond 0.00361 (17218) covalent geometry : angle 0.66144 (23655) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 248 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8545 (tt) cc_final: 0.7921 (mt) REVERT: E 262 MET cc_start: 0.8571 (mmm) cc_final: 0.8256 (mpm) REVERT: E 479 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6727 (tm130) REVERT: E 524 LEU cc_start: 0.8165 (mt) cc_final: 0.7940 (mt) REVERT: E 588 LEU cc_start: 0.7694 (mm) cc_final: 0.7405 (mt) REVERT: E 715 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5216 (mtp) REVERT: E 720 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7800 (mp) REVERT: E 760 MET cc_start: 0.7803 (mmm) cc_final: 0.7309 (mmm) REVERT: E 778 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6876 (mtp) REVERT: A 28 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6857 (tt0) REVERT: A 40 LEU cc_start: 0.7805 (tt) cc_final: 0.7548 (tm) REVERT: A 102 ASN cc_start: 0.7832 (t0) cc_final: 0.7483 (t0) REVERT: A 112 GLU cc_start: 0.6766 (mp0) cc_final: 0.6337 (mm-30) REVERT: A 140 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7212 (tp30) REVERT: A 213 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.7411 (t) REVERT: A 232 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6684 (mp0) REVERT: A 242 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6597 (mt-10) REVERT: B 48 GLU cc_start: 0.7422 (tp30) cc_final: 0.7123 (tp30) REVERT: B 52 LYS cc_start: 0.7374 (mtpt) cc_final: 0.7150 (mtpp) REVERT: B 143 GLN cc_start: 0.6523 (pm20) cc_final: 0.6227 (mp10) REVERT: C 53 LYS cc_start: 0.7962 (ttpp) cc_final: 0.7722 (ttpt) REVERT: C 69 LYS cc_start: 0.7824 (tppt) cc_final: 0.7513 (mtmm) REVERT: C 118 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7076 (mp) REVERT: C 147 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7801 (mtt90) REVERT: C 212 LYS cc_start: 0.7604 (mtmm) cc_final: 0.7374 (mttt) REVERT: D 48 GLU cc_start: 0.6716 (pm20) cc_final: 0.6411 (mp0) REVERT: D 56 ASN cc_start: 0.7686 (p0) cc_final: 0.7451 (p0) REVERT: D 81 LYS cc_start: 0.7293 (tmtm) cc_final: 0.7076 (tmtt) REVERT: D 84 ARG cc_start: 0.7075 (ptm-80) cc_final: 0.6640 (ptp90) REVERT: D 110 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7405 (p) REVERT: D 123 MET cc_start: 0.7271 (tmm) cc_final: 0.7001 (tmm) REVERT: D 159 PHE cc_start: 0.6399 (m-80) cc_final: 0.5871 (m-80) REVERT: D 236 LEU cc_start: 0.7742 (tp) cc_final: 0.7503 (tp) REVERT: D 260 GLN cc_start: 0.6116 (OUTLIER) cc_final: 0.5584 (pm20) REVERT: F 104 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8249 (tm) REVERT: F 120 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8544 (mt) REVERT: F 130 LYS cc_start: 0.8056 (tttt) cc_final: 0.7686 (tttm) REVERT: F 191 MET cc_start: 0.7303 (mtm) cc_final: 0.6950 (mtp) REVERT: F 209 MET cc_start: 0.7597 (mmt) cc_final: 0.7172 (mmt) REVERT: F 214 TYR cc_start: 0.7202 (m-80) cc_final: 0.6773 (m-10) REVERT: F 217 ARG cc_start: 0.7105 (tpt-90) cc_final: 0.6880 (tmt-80) REVERT: F 221 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6585 (tp40) outliers start: 75 outliers final: 19 residues processed: 301 average time/residue: 1.2788 time to fit residues: 435.6719 Evaluate side-chains 222 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 623 ARG Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 727 GLN Chi-restraints excluded: chain E residue 778 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 14 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 75 optimal weight: 0.0040 chunk 88 optimal weight: 0.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 379 ASN E 461 GLN B 107 GLN C 44 ASN C 162 GLN C 220 GLN D 102 ASN F 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.117132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.086721 restraints weight = 29624.564| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.32 r_work: 0.3081 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17220 Z= 0.221 Angle : 0.707 8.976 23655 Z= 0.357 Chirality : 0.047 0.323 2768 Planarity : 0.006 0.049 2821 Dihedral : 15.478 179.724 3193 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.84 % Allowed : 19.73 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.01 (0.18), residues: 1991 helix: 0.77 (0.18), residues: 861 sheet: -0.58 (0.26), residues: 333 loop : -0.43 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 233 HIS 0.007 0.002 HIS F 278 PHE 0.019 0.002 PHE A 223 TYR 0.017 0.002 TYR F 137 ARG 0.006 0.001 ARG F 236 Details of bonding type rmsd hydrogen bonds : bond 0.05664 ( 751) hydrogen bonds : angle 5.52091 ( 2112) metal coordination : bond 0.00421 ( 2) covalent geometry : bond 0.00507 (17218) covalent geometry : angle 0.70738 (23655) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 205 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 MET cc_start: 0.7834 (ttm) cc_final: 0.7601 (ttm) REVERT: E 249 LEU cc_start: 0.8653 (tt) cc_final: 0.8051 (mt) REVERT: E 479 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: E 715 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5224 (mtp) REVERT: E 720 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7798 (mp) REVERT: E 760 MET cc_start: 0.7997 (mmm) cc_final: 0.7531 (mmm) REVERT: A 28 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6999 (tt0) REVERT: A 69 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6776 (ttpp) REVERT: A 102 ASN cc_start: 0.7868 (t0) cc_final: 0.7516 (t0) REVERT: A 112 GLU cc_start: 0.6698 (mp0) cc_final: 0.6309 (mm-30) REVERT: A 232 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6798 (mp0) REVERT: A 241 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7849 (mp) REVERT: A 242 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6920 (mt-10) REVERT: B 79 LYS cc_start: 0.7238 (tptt) cc_final: 0.6643 (ttmm) REVERT: B 104 LYS cc_start: 0.7328 (mtmm) cc_final: 0.6719 (mmmm) REVERT: B 142 ASP cc_start: 0.6389 (p0) cc_final: 0.5975 (p0) REVERT: B 143 GLN cc_start: 0.6560 (pm20) cc_final: 0.6339 (mp10) REVERT: C 69 LYS cc_start: 0.7865 (tppt) cc_final: 0.7563 (mppt) REVERT: C 118 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7091 (mp) REVERT: C 147 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7647 (mtt90) REVERT: C 212 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7251 (mttt) REVERT: D 53 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7893 (ttmm) REVERT: D 81 LYS cc_start: 0.7392 (tmtm) cc_final: 0.7158 (tmtt) REVERT: D 110 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7413 (p) REVERT: D 123 MET cc_start: 0.7397 (tmm) cc_final: 0.7124 (tmm) REVERT: D 260 GLN cc_start: 0.6182 (OUTLIER) cc_final: 0.5695 (pm20) REVERT: F 104 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8250 (tm) REVERT: F 115 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: F 130 LYS cc_start: 0.8077 (tttt) cc_final: 0.7648 (tttm) REVERT: F 191 MET cc_start: 0.7268 (mtm) cc_final: 0.6951 (mtp) REVERT: F 209 MET cc_start: 0.7554 (mmt) cc_final: 0.7098 (mmt) REVERT: F 214 TYR cc_start: 0.7259 (m-80) cc_final: 0.6757 (m-10) REVERT: F 217 ARG cc_start: 0.7050 (tpt-90) cc_final: 0.6849 (tpt90) REVERT: F 330 ASN cc_start: 0.6838 (m-40) cc_final: 0.6511 (m-40) outliers start: 95 outliers final: 42 residues processed: 273 average time/residue: 1.4535 time to fit residues: 444.0104 Evaluate side-chains 239 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 623 ARG Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 119 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 116 optimal weight: 0.0070 chunk 189 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 505 ASN C 44 ASN F 162 ASN F 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.118622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088768 restraints weight = 29527.937| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.34 r_work: 0.3105 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17220 Z= 0.137 Angle : 0.608 8.318 23655 Z= 0.304 Chirality : 0.042 0.153 2768 Planarity : 0.005 0.051 2821 Dihedral : 15.179 179.041 3193 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.12 % Allowed : 21.70 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.25 (0.19), residues: 1991 helix: 1.09 (0.18), residues: 855 sheet: -0.65 (0.25), residues: 341 loop : -0.35 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 659 HIS 0.003 0.001 HIS D 109 PHE 0.019 0.002 PHE D 159 TYR 0.022 0.002 TYR F 137 ARG 0.006 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 751) hydrogen bonds : angle 5.15474 ( 2112) metal coordination : bond 0.00130 ( 2) covalent geometry : bond 0.00306 (17218) covalent geometry : angle 0.60837 (23655) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.7856 (ttm) cc_final: 0.7576 (ttm) REVERT: E 249 LEU cc_start: 0.8647 (tt) cc_final: 0.8040 (mt) REVERT: E 262 MET cc_start: 0.8375 (mmm) cc_final: 0.7842 (mpm) REVERT: E 588 LEU cc_start: 0.7759 (mm) cc_final: 0.7550 (mt) REVERT: E 715 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.4929 (mtp) REVERT: E 720 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7837 (mp) REVERT: E 760 MET cc_start: 0.7801 (mmm) cc_final: 0.7306 (mmm) REVERT: A 28 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7020 (tt0) REVERT: A 69 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6700 (ttpp) REVERT: A 70 ASP cc_start: 0.7234 (m-30) cc_final: 0.6754 (m-30) REVERT: A 102 ASN cc_start: 0.7878 (t0) cc_final: 0.7562 (t0) REVERT: A 112 GLU cc_start: 0.6675 (mp0) cc_final: 0.6296 (mm-30) REVERT: A 123 MET cc_start: 0.7328 (tmm) cc_final: 0.7084 (tmm) REVERT: A 140 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7239 (tp30) REVERT: A 232 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6819 (mp0) REVERT: A 242 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6846 (mt-10) REVERT: B 79 LYS cc_start: 0.7226 (tptt) cc_final: 0.6633 (ttmm) REVERT: B 104 LYS cc_start: 0.7382 (mtmm) cc_final: 0.6899 (mmmm) REVERT: B 142 ASP cc_start: 0.6238 (p0) cc_final: 0.5785 (p0) REVERT: B 143 GLN cc_start: 0.6529 (pm20) cc_final: 0.6283 (mp10) REVERT: B 226 ARG cc_start: 0.7321 (ptt90) cc_final: 0.7046 (ptm-80) REVERT: B 242 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: C 69 LYS cc_start: 0.7801 (tppt) cc_final: 0.7452 (mtmm) REVERT: C 118 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7069 (mp) REVERT: C 147 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7802 (mtt90) REVERT: D 48 GLU cc_start: 0.6409 (pm20) cc_final: 0.6054 (mp0) REVERT: D 53 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: D 81 LYS cc_start: 0.7330 (tmtm) cc_final: 0.7092 (tmtt) REVERT: D 110 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7402 (p) REVERT: D 123 MET cc_start: 0.7316 (tmm) cc_final: 0.7039 (tmm) REVERT: F 104 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8228 (tm) REVERT: F 130 LYS cc_start: 0.8131 (tttt) cc_final: 0.7701 (mttt) REVERT: F 133 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7676 (mm) REVERT: F 144 LYS cc_start: 0.8359 (mmmm) cc_final: 0.7669 (mmtm) REVERT: F 148 ILE cc_start: 0.8564 (mp) cc_final: 0.8258 (pp) REVERT: F 191 MET cc_start: 0.7220 (mtm) cc_final: 0.6938 (mtp) REVERT: F 214 TYR cc_start: 0.7265 (m-80) cc_final: 0.6811 (m-10) REVERT: F 330 ASN cc_start: 0.6792 (m-40) cc_final: 0.6424 (m-40) outliers start: 67 outliers final: 27 residues processed: 257 average time/residue: 1.2534 time to fit residues: 361.6334 Evaluate side-chains 224 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 78 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN C 44 ASN D 56 ASN F 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.118355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.088112 restraints weight = 29882.153| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.31 r_work: 0.3103 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17220 Z= 0.167 Angle : 0.635 8.533 23655 Z= 0.319 Chirality : 0.043 0.152 2768 Planarity : 0.005 0.049 2821 Dihedral : 15.113 179.601 3192 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.67 % Allowed : 21.45 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.13 (0.19), residues: 1991 helix: 1.01 (0.18), residues: 855 sheet: -0.81 (0.25), residues: 333 loop : -0.39 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 101 HIS 0.006 0.001 HIS F 278 PHE 0.017 0.002 PHE E 154 TYR 0.025 0.002 TYR E 729 ARG 0.005 0.001 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 751) hydrogen bonds : angle 5.16240 ( 2112) metal coordination : bond 0.00195 ( 2) covalent geometry : bond 0.00381 (17218) covalent geometry : angle 0.63463 (23655) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 207 time to evaluate : 1.826 Fit side-chains REVERT: E 95 MET cc_start: 0.7776 (ttm) cc_final: 0.7449 (ttm) REVERT: E 99 LYS cc_start: 0.8374 (tppt) cc_final: 0.8099 (tppt) REVERT: E 249 LEU cc_start: 0.8651 (tt) cc_final: 0.8043 (mt) REVERT: E 262 MET cc_start: 0.8438 (mmm) cc_final: 0.8064 (mpm) REVERT: E 479 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: E 588 LEU cc_start: 0.7719 (mm) cc_final: 0.7500 (mt) REVERT: E 610 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7238 (mm) REVERT: E 720 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7912 (mp) REVERT: E 729 TYR cc_start: 0.5359 (m-80) cc_final: 0.5130 (m-10) REVERT: E 760 MET cc_start: 0.7885 (mmm) cc_final: 0.7458 (mmm) REVERT: A 28 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7150 (tt0) REVERT: A 64 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6684 (t0) REVERT: A 69 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6737 (ttpp) REVERT: A 102 ASN cc_start: 0.7848 (t0) cc_final: 0.7554 (t0) REVERT: A 123 MET cc_start: 0.7428 (tmm) cc_final: 0.7200 (tmm) REVERT: A 140 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7156 (tp30) REVERT: A 232 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6812 (mp0) REVERT: B 79 LYS cc_start: 0.7222 (tptt) cc_final: 0.6572 (ttmm) REVERT: B 104 LYS cc_start: 0.7309 (mtmm) cc_final: 0.6860 (mmmm) REVERT: B 142 ASP cc_start: 0.6169 (p0) cc_final: 0.5814 (p0) REVERT: B 143 GLN cc_start: 0.6508 (pm20) cc_final: 0.6302 (mp10) REVERT: B 226 ARG cc_start: 0.7339 (ptt90) cc_final: 0.7055 (ptm-80) REVERT: B 242 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: C 69 LYS cc_start: 0.7918 (tppt) cc_final: 0.7619 (mppt) REVERT: C 118 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7023 (mp) REVERT: C 147 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7701 (mtt90) REVERT: D 48 GLU cc_start: 0.6366 (pm20) cc_final: 0.6056 (mp0) REVERT: D 53 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7899 (ttmm) REVERT: D 123 MET cc_start: 0.7334 (tmm) cc_final: 0.7069 (tmm) REVERT: D 143 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: D 260 GLN cc_start: 0.6204 (OUTLIER) cc_final: 0.5763 (pm20) REVERT: F 104 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8278 (tm) REVERT: F 115 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: F 130 LYS cc_start: 0.8159 (tttt) cc_final: 0.7720 (mttm) REVERT: F 133 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7697 (mm) REVERT: F 144 LYS cc_start: 0.8336 (mmmm) cc_final: 0.7672 (mmtm) REVERT: F 148 ILE cc_start: 0.8589 (mp) cc_final: 0.8292 (pp) REVERT: F 191 MET cc_start: 0.7193 (mtm) cc_final: 0.6920 (mtp) REVERT: F 214 TYR cc_start: 0.7156 (m-80) cc_final: 0.6685 (m-10) REVERT: F 330 ASN cc_start: 0.6841 (m-40) cc_final: 0.6488 (m-40) outliers start: 76 outliers final: 38 residues processed: 262 average time/residue: 1.1809 time to fit residues: 348.2447 Evaluate side-chains 239 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 203 optimal weight: 0.2980 chunk 192 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 164 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 ASN F 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088902 restraints weight = 29814.761| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.27 r_work: 0.3119 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17220 Z= 0.139 Angle : 0.600 8.474 23655 Z= 0.301 Chirality : 0.042 0.161 2768 Planarity : 0.005 0.050 2821 Dihedral : 15.009 178.696 3192 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.06 % Allowed : 22.86 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.20 (0.19), residues: 1991 helix: 1.13 (0.18), residues: 860 sheet: -0.79 (0.25), residues: 333 loop : -0.43 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 101 HIS 0.004 0.001 HIS D 109 PHE 0.018 0.002 PHE D 159 TYR 0.026 0.002 TYR F 137 ARG 0.004 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 751) hydrogen bonds : angle 5.04021 ( 2112) metal coordination : bond 0.00142 ( 2) covalent geometry : bond 0.00316 (17218) covalent geometry : angle 0.60003 (23655) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 195 time to evaluate : 1.720 Fit side-chains REVERT: E 86 ASN cc_start: 0.7177 (m-40) cc_final: 0.6899 (m-40) REVERT: E 95 MET cc_start: 0.7743 (ttm) cc_final: 0.7408 (ttm) REVERT: E 249 LEU cc_start: 0.8622 (tt) cc_final: 0.8039 (mt) REVERT: E 479 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: E 588 LEU cc_start: 0.7722 (mm) cc_final: 0.7488 (mt) REVERT: E 610 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7235 (mm) REVERT: A 28 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7211 (tt0) REVERT: A 64 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6588 (t0) REVERT: A 70 ASP cc_start: 0.7180 (m-30) cc_final: 0.6656 (m-30) REVERT: A 102 ASN cc_start: 0.7862 (t0) cc_final: 0.7563 (t0) REVERT: A 123 MET cc_start: 0.7445 (tmm) cc_final: 0.7182 (tmm) REVERT: A 140 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7132 (tp30) REVERT: A 232 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6833 (mp0) REVERT: B 79 LYS cc_start: 0.7220 (tptt) cc_final: 0.6564 (ttmm) REVERT: B 104 LYS cc_start: 0.7355 (mtmm) cc_final: 0.6867 (mmmm) REVERT: B 142 ASP cc_start: 0.6175 (p0) cc_final: 0.5821 (p0) REVERT: B 205 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.4939 (tt) REVERT: B 226 ARG cc_start: 0.7410 (ptt90) cc_final: 0.7172 (ptm-80) REVERT: B 242 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6816 (mt-10) REVERT: C 69 LYS cc_start: 0.7860 (tppt) cc_final: 0.7604 (mppt) REVERT: C 118 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6991 (mp) REVERT: C 147 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7754 (mtt90) REVERT: D 48 GLU cc_start: 0.6320 (pm20) cc_final: 0.6034 (mp0) REVERT: D 53 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7876 (ttmm) REVERT: D 123 MET cc_start: 0.7340 (tmm) cc_final: 0.7074 (tmm) REVERT: D 143 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: D 260 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5750 (pm20) REVERT: F 104 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8255 (tm) REVERT: F 115 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: F 130 LYS cc_start: 0.8216 (tttt) cc_final: 0.7643 (tttm) REVERT: F 144 LYS cc_start: 0.8410 (mmmm) cc_final: 0.7842 (mmtm) REVERT: F 191 MET cc_start: 0.7193 (mtm) cc_final: 0.6893 (mtp) REVERT: F 209 MET cc_start: 0.7540 (mmt) cc_final: 0.7130 (mmt) REVERT: F 214 TYR cc_start: 0.7143 (m-80) cc_final: 0.6680 (m-10) REVERT: F 330 ASN cc_start: 0.6820 (m-40) cc_final: 0.6445 (m-40) outliers start: 66 outliers final: 34 residues processed: 246 average time/residue: 1.1239 time to fit residues: 313.4293 Evaluate side-chains 232 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 0.3980 chunk 184 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 137 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN D 56 ASN F 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088834 restraints weight = 29670.867| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.30 r_work: 0.3117 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17220 Z= 0.144 Angle : 0.620 9.500 23655 Z= 0.309 Chirality : 0.043 0.342 2768 Planarity : 0.005 0.049 2821 Dihedral : 14.979 178.437 3192 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.55 % Allowed : 22.99 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.21 (0.19), residues: 1991 helix: 1.15 (0.18), residues: 860 sheet: -0.77 (0.25), residues: 333 loop : -0.46 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 659 HIS 0.004 0.001 HIS D 109 PHE 0.019 0.002 PHE D 159 TYR 0.018 0.002 TYR E 729 ARG 0.004 0.000 ARG E 623 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 751) hydrogen bonds : angle 5.02777 ( 2112) metal coordination : bond 0.00160 ( 2) covalent geometry : bond 0.00328 (17218) covalent geometry : angle 0.61993 (23655) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 1.851 Fit side-chains REVERT: E 86 ASN cc_start: 0.7169 (m-40) cc_final: 0.6891 (m-40) REVERT: E 95 MET cc_start: 0.7739 (ttm) cc_final: 0.7394 (ttm) REVERT: E 99 LYS cc_start: 0.8398 (tppt) cc_final: 0.8157 (tppt) REVERT: E 249 LEU cc_start: 0.8674 (tt) cc_final: 0.8021 (mt) REVERT: E 262 MET cc_start: 0.8415 (mmm) cc_final: 0.7806 (mpm) REVERT: E 479 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6633 (tm130) REVERT: E 588 LEU cc_start: 0.7744 (mm) cc_final: 0.7517 (mt) REVERT: E 734 LEU cc_start: 0.5864 (tm) cc_final: 0.5275 (mt) REVERT: A 28 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7171 (tt0) REVERT: A 64 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6599 (t0) REVERT: A 69 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6666 (ttpp) REVERT: A 70 ASP cc_start: 0.7184 (m-30) cc_final: 0.6666 (m-30) REVERT: A 102 ASN cc_start: 0.7863 (t0) cc_final: 0.7565 (t0) REVERT: A 123 MET cc_start: 0.7457 (tmm) cc_final: 0.7217 (tmm) REVERT: A 140 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7179 (tp30) REVERT: A 232 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6897 (mp0) REVERT: B 79 LYS cc_start: 0.7248 (tptt) cc_final: 0.6580 (ttmm) REVERT: B 104 LYS cc_start: 0.7330 (mtmm) cc_final: 0.6848 (mmmm) REVERT: B 205 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.4841 (tt) REVERT: B 242 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: C 69 LYS cc_start: 0.7892 (tppt) cc_final: 0.7633 (mppt) REVERT: C 118 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7044 (mp) REVERT: C 147 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7655 (mtt90) REVERT: D 48 GLU cc_start: 0.6304 (pm20) cc_final: 0.6031 (mp0) REVERT: D 53 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7872 (ttmm) REVERT: D 123 MET cc_start: 0.7344 (tmm) cc_final: 0.6742 (tmm) REVERT: D 260 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.5727 (pm20) REVERT: F 104 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8277 (tm) REVERT: F 115 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: F 130 LYS cc_start: 0.8208 (tttt) cc_final: 0.7692 (mttm) REVERT: F 142 VAL cc_start: 0.7442 (t) cc_final: 0.7135 (p) REVERT: F 144 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7801 (mmtm) REVERT: F 148 ILE cc_start: 0.8590 (mp) cc_final: 0.8306 (pp) REVERT: F 191 MET cc_start: 0.7188 (mtm) cc_final: 0.6893 (mtp) REVERT: F 209 MET cc_start: 0.7573 (mmt) cc_final: 0.7153 (mmt) REVERT: F 214 TYR cc_start: 0.7236 (m-80) cc_final: 0.6782 (m-10) REVERT: F 330 ASN cc_start: 0.6841 (m-40) cc_final: 0.6487 (m-40) outliers start: 74 outliers final: 40 residues processed: 259 average time/residue: 1.1436 time to fit residues: 335.0192 Evaluate side-chains 234 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 162 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 138 optimal weight: 0.0870 chunk 139 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 727 GLN B 107 GLN D 56 ASN F 221 GLN F 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090457 restraints weight = 29509.676| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.24 r_work: 0.3124 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17220 Z= 0.134 Angle : 0.613 9.421 23655 Z= 0.305 Chirality : 0.042 0.164 2768 Planarity : 0.005 0.050 2821 Dihedral : 14.914 177.827 3192 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.36 % Allowed : 23.36 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.28 (0.19), residues: 1991 helix: 1.21 (0.18), residues: 862 sheet: -0.72 (0.25), residues: 348 loop : -0.41 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 659 HIS 0.003 0.001 HIS E 546 PHE 0.019 0.001 PHE D 159 TYR 0.023 0.002 TYR F 137 ARG 0.004 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 751) hydrogen bonds : angle 4.97051 ( 2112) metal coordination : bond 0.00121 ( 2) covalent geometry : bond 0.00307 (17218) covalent geometry : angle 0.61278 (23655) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 193 time to evaluate : 1.687 Fit side-chains REVERT: E 86 ASN cc_start: 0.7054 (m-40) cc_final: 0.6807 (m-40) REVERT: E 95 MET cc_start: 0.7747 (ttm) cc_final: 0.7387 (ttm) REVERT: E 249 LEU cc_start: 0.8699 (tt) cc_final: 0.8063 (mt) REVERT: E 262 MET cc_start: 0.8476 (mmm) cc_final: 0.7794 (mpm) REVERT: E 297 CYS cc_start: 0.7275 (t) cc_final: 0.6822 (t) REVERT: E 479 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: E 558 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7914 (mm) REVERT: E 588 LEU cc_start: 0.7766 (mm) cc_final: 0.7544 (mt) REVERT: A 28 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7210 (tt0) REVERT: A 64 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6581 (t0) REVERT: A 69 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6669 (ttpp) REVERT: A 70 ASP cc_start: 0.7184 (m-30) cc_final: 0.6756 (m-30) REVERT: A 102 ASN cc_start: 0.7885 (t0) cc_final: 0.7593 (t0) REVERT: A 123 MET cc_start: 0.7386 (tmm) cc_final: 0.7139 (tmm) REVERT: A 140 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7198 (tp30) REVERT: A 232 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6883 (mp0) REVERT: B 79 LYS cc_start: 0.7211 (tptt) cc_final: 0.6560 (ttmm) REVERT: B 104 LYS cc_start: 0.7389 (mtmm) cc_final: 0.6898 (mmmm) REVERT: B 242 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: C 69 LYS cc_start: 0.7914 (tppt) cc_final: 0.7637 (mppt) REVERT: C 118 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7154 (mp) REVERT: C 147 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7752 (mtt90) REVERT: D 48 GLU cc_start: 0.6324 (pm20) cc_final: 0.6041 (mp0) REVERT: D 53 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7857 (ttmm) REVERT: D 123 MET cc_start: 0.7354 (tmm) cc_final: 0.6755 (tmm) REVERT: D 260 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5756 (pm20) REVERT: F 101 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.7314 (m100) REVERT: F 104 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8258 (tm) REVERT: F 130 LYS cc_start: 0.8259 (tttt) cc_final: 0.7613 (tttm) REVERT: F 137 TYR cc_start: 0.8062 (t80) cc_final: 0.7860 (t80) REVERT: F 142 VAL cc_start: 0.7491 (t) cc_final: 0.7209 (p) REVERT: F 144 LYS cc_start: 0.8333 (mmmm) cc_final: 0.7793 (mmtm) REVERT: F 148 ILE cc_start: 0.8592 (mp) cc_final: 0.8310 (pp) REVERT: F 191 MET cc_start: 0.7211 (mtm) cc_final: 0.6970 (mtp) REVERT: F 209 MET cc_start: 0.7600 (mmt) cc_final: 0.7184 (mmt) REVERT: F 214 TYR cc_start: 0.7192 (m-80) cc_final: 0.6741 (m-10) REVERT: F 330 ASN cc_start: 0.6774 (m-40) cc_final: 0.6437 (m-40) outliers start: 71 outliers final: 44 residues processed: 252 average time/residue: 1.1459 time to fit residues: 325.6373 Evaluate side-chains 239 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 177 optimal weight: 0.9980 chunk 164 optimal weight: 0.0270 chunk 50 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 GLN E 727 GLN B 107 GLN D 56 ASN F 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.119191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090066 restraints weight = 29794.304| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.30 r_work: 0.3121 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17220 Z= 0.148 Angle : 0.634 9.761 23655 Z= 0.317 Chirality : 0.043 0.160 2768 Planarity : 0.005 0.055 2821 Dihedral : 14.931 177.998 3192 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.49 % Allowed : 23.29 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.25 (0.19), residues: 1991 helix: 1.18 (0.18), residues: 863 sheet: -0.72 (0.26), residues: 348 loop : -0.43 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 659 HIS 0.004 0.001 HIS F 278 PHE 0.019 0.002 PHE D 159 TYR 0.019 0.002 TYR F 137 ARG 0.003 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 751) hydrogen bonds : angle 5.05432 ( 2112) metal coordination : bond 0.00153 ( 2) covalent geometry : bond 0.00340 (17218) covalent geometry : angle 0.63411 (23655) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 185 time to evaluate : 1.774 Fit side-chains REVERT: E 86 ASN cc_start: 0.6996 (m-40) cc_final: 0.6737 (m-40) REVERT: E 95 MET cc_start: 0.7693 (ttm) cc_final: 0.7356 (ttm) REVERT: E 249 LEU cc_start: 0.8653 (tt) cc_final: 0.8015 (mt) REVERT: E 262 MET cc_start: 0.8479 (mmm) cc_final: 0.7907 (mpm) REVERT: E 297 CYS cc_start: 0.7233 (t) cc_final: 0.6832 (t) REVERT: E 479 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6656 (tm130) REVERT: E 588 LEU cc_start: 0.7752 (mm) cc_final: 0.7528 (mt) REVERT: E 715 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.4929 (mtp) REVERT: A 28 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7235 (tt0) REVERT: A 64 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6602 (t0) REVERT: A 69 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6669 (ttpp) REVERT: A 70 ASP cc_start: 0.7218 (m-30) cc_final: 0.6748 (m-30) REVERT: A 102 ASN cc_start: 0.7876 (t0) cc_final: 0.7586 (t0) REVERT: A 123 MET cc_start: 0.7458 (tmm) cc_final: 0.7204 (tmm) REVERT: A 140 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7225 (tp30) REVERT: A 232 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6823 (mp0) REVERT: B 79 LYS cc_start: 0.7207 (tptt) cc_final: 0.6552 (ttmm) REVERT: B 104 LYS cc_start: 0.7377 (mtmm) cc_final: 0.6897 (mmmm) REVERT: B 159 PHE cc_start: 0.6388 (m-80) cc_final: 0.5531 (t80) REVERT: B 242 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6816 (mt-10) REVERT: C 69 LYS cc_start: 0.7927 (tppt) cc_final: 0.7653 (mppt) REVERT: C 118 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6980 (mp) REVERT: C 147 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7660 (mtt90) REVERT: D 48 GLU cc_start: 0.6272 (pm20) cc_final: 0.6005 (mp0) REVERT: D 53 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7869 (ttmm) REVERT: D 123 MET cc_start: 0.7350 (tmm) cc_final: 0.6747 (tmm) REVERT: D 260 GLN cc_start: 0.6203 (OUTLIER) cc_final: 0.5746 (pm20) REVERT: F 101 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.7352 (m100) REVERT: F 104 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8305 (tm) REVERT: F 115 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: F 130 LYS cc_start: 0.8250 (tttt) cc_final: 0.7603 (tttm) REVERT: F 142 VAL cc_start: 0.7499 (t) cc_final: 0.7224 (p) REVERT: F 144 LYS cc_start: 0.8343 (mmmm) cc_final: 0.7793 (mmtm) REVERT: F 148 ILE cc_start: 0.8583 (mp) cc_final: 0.8294 (pp) REVERT: F 191 MET cc_start: 0.7194 (mtm) cc_final: 0.6927 (mtp) REVERT: F 209 MET cc_start: 0.7621 (mmt) cc_final: 0.7186 (mmt) REVERT: F 214 TYR cc_start: 0.7189 (m-80) cc_final: 0.6740 (m-10) outliers start: 73 outliers final: 48 residues processed: 243 average time/residue: 1.2131 time to fit residues: 334.4323 Evaluate side-chains 240 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 157 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 727 GLN B 107 GLN D 56 ASN F 221 GLN F 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.090184 restraints weight = 29713.986| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.31 r_work: 0.3122 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17220 Z= 0.155 Angle : 0.648 9.666 23655 Z= 0.323 Chirality : 0.043 0.168 2768 Planarity : 0.005 0.052 2821 Dihedral : 14.929 178.194 3192 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.24 % Allowed : 23.85 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.20 (0.19), residues: 1991 helix: 1.14 (0.18), residues: 863 sheet: -0.74 (0.26), residues: 343 loop : -0.46 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 659 HIS 0.004 0.001 HIS F 278 PHE 0.019 0.002 PHE D 159 TYR 0.038 0.002 TYR E 729 ARG 0.003 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 751) hydrogen bonds : angle 5.08392 ( 2112) metal coordination : bond 0.00261 ( 2) covalent geometry : bond 0.00357 (17218) covalent geometry : angle 0.64776 (23655) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 179 time to evaluate : 1.807 Fit side-chains REVERT: E 86 ASN cc_start: 0.6990 (m-40) cc_final: 0.6741 (m-40) REVERT: E 95 MET cc_start: 0.7644 (ttm) cc_final: 0.7282 (ttm) REVERT: E 249 LEU cc_start: 0.8670 (tt) cc_final: 0.8060 (mt) REVERT: E 262 MET cc_start: 0.8557 (mmm) cc_final: 0.8058 (mpm) REVERT: E 297 CYS cc_start: 0.7275 (t) cc_final: 0.6864 (t) REVERT: E 479 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6665 (tm130) REVERT: E 588 LEU cc_start: 0.7786 (mm) cc_final: 0.7562 (mt) REVERT: E 715 MET cc_start: 0.5492 (OUTLIER) cc_final: 0.4848 (mtp) REVERT: A 28 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7093 (tt0) REVERT: A 64 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6589 (t0) REVERT: A 69 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6666 (ttpp) REVERT: A 70 ASP cc_start: 0.7191 (m-30) cc_final: 0.6693 (m-30) REVERT: A 102 ASN cc_start: 0.7880 (t0) cc_final: 0.7588 (t0) REVERT: A 123 MET cc_start: 0.7461 (tmm) cc_final: 0.7201 (tmm) REVERT: A 232 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6850 (mp0) REVERT: B 79 LYS cc_start: 0.7201 (tptt) cc_final: 0.6545 (ttmm) REVERT: B 104 LYS cc_start: 0.7350 (mtmm) cc_final: 0.6910 (mmmm) REVERT: B 159 PHE cc_start: 0.6363 (m-80) cc_final: 0.5522 (t80) REVERT: B 242 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: C 69 LYS cc_start: 0.7950 (tppt) cc_final: 0.7661 (mppt) REVERT: C 118 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6978 (mp) REVERT: C 147 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7688 (mtt90) REVERT: D 48 GLU cc_start: 0.6293 (pm20) cc_final: 0.6020 (mp0) REVERT: D 53 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7858 (ttmm) REVERT: D 123 MET cc_start: 0.7328 (tmm) cc_final: 0.6721 (tmm) REVERT: D 260 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.5791 (pm20) REVERT: F 104 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8069 (mm) REVERT: F 115 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: F 130 LYS cc_start: 0.8243 (tttt) cc_final: 0.7580 (mttm) REVERT: F 142 VAL cc_start: 0.7449 (t) cc_final: 0.7153 (p) REVERT: F 144 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7778 (mmtm) REVERT: F 148 ILE cc_start: 0.8614 (mp) cc_final: 0.8311 (pp) REVERT: F 191 MET cc_start: 0.7202 (mtm) cc_final: 0.6905 (mtp) REVERT: F 209 MET cc_start: 0.7617 (mmt) cc_final: 0.7167 (mmt) REVERT: F 214 TYR cc_start: 0.7169 (m-80) cc_final: 0.6726 (m-10) outliers start: 69 outliers final: 43 residues processed: 234 average time/residue: 1.1209 time to fit residues: 297.2439 Evaluate side-chains 234 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 143 optimal weight: 0.5980 chunk 92 optimal weight: 0.0970 chunk 155 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 195 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 390 ASN E 727 GLN B 107 GLN D 56 ASN F 221 GLN F 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.119509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.091015 restraints weight = 29723.195| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.28 r_work: 0.3134 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17220 Z= 0.140 Angle : 0.626 10.975 23655 Z= 0.311 Chirality : 0.043 0.169 2768 Planarity : 0.005 0.051 2821 Dihedral : 14.849 177.960 3192 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.75 % Allowed : 24.46 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.30 (0.19), residues: 1991 helix: 1.23 (0.18), residues: 863 sheet: -0.75 (0.26), residues: 348 loop : -0.40 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 659 HIS 0.003 0.001 HIS E 546 PHE 0.019 0.001 PHE D 159 TYR 0.024 0.002 TYR E 729 ARG 0.003 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 751) hydrogen bonds : angle 4.97126 ( 2112) metal coordination : bond 0.00121 ( 2) covalent geometry : bond 0.00322 (17218) covalent geometry : angle 0.62629 (23655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12535.12 seconds wall clock time: 216 minutes 1.22 seconds (12961.22 seconds total)