Starting phenix.real_space_refine on Sun Jun 30 17:59:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/06_2024/8umw_42386_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/06_2024/8umw_42386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/06_2024/8umw_42386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/06_2024/8umw_42386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/06_2024/8umw_42386_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/06_2024/8umw_42386_updated.pdb" } resolution = 2.93 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= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 61 5.49 5 Mg 4 5.21 5 S 138 5.16 5 C 13599 2.51 5 N 3772 2.21 5 O 4286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E GLU 348": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 256": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 21860 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4319 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 512} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2591 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2541 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.59, per 1000 atoms: 0.53 Number of scatterers: 21860 At special positions: 0 Unit cell: (118.404, 127.512, 139.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 61 15.00 Mg 4 11.99 O 4286 8.00 N 3772 7.00 C 13599 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 - 3.50 Amino acid : False - 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: 8.36 Conformation dependent library (CDL) restraints added in 3.7 seconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 16 sheets defined 44.4% alpha, 14.3% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 9.09 Creating SS restraints... Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 298 through 311 removed outlier: 4.137A pdb=" N TRP A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.672A pdb=" N ALA A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 667 through 688 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 698 through 708 Proline residue: A 702 - end of helix Processing helix chain 'A' and resid 722 through 743 removed outlier: 3.756A pdb=" N GLY A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 749 No H-bonds generated for 'chain 'A' and resid 746 through 749' Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 783 through 798 Processing helix chain 'A' and resid 822 through 825 No H-bonds generated for 'chain 'A' and resid 822 through 825' Processing helix chain 'A' and resid 838 through 862 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 82 through 97 Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 113 through 116 No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 163 removed outlier: 3.684A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.571A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 260 through 271 removed outlier: 4.187A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 310 through 329 removed outlier: 3.581A pdb=" N LYS B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.681A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 83 through 86 No H-bonds generated for 'chain 'C' and resid 83 through 86' Processing helix chain 'C' and resid 98 through 101 No H-bonds generated for 'chain 'C' and resid 98 through 101' Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.798A pdb=" N ARG C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.594A pdb=" N VAL C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 277 through 290 removed outlier: 3.980A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 313 removed outlier: 4.109A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 330 removed outlier: 3.932A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'D' and resid 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.569A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 104 No H-bonds generated for 'chain 'D' and resid 101 through 104' Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.828A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.683A pdb=" N LEU D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 188 through 193 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 265 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.596A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 97 through 116 removed outlier: 6.812A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG E 105 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN E 109 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU E 110 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET E 111 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU E 112 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS E 113 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 114 " --> pdb=" O MET E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 142 through 154 removed outlier: 3.852A pdb=" N ARG E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG E 150 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 209 through 218 Processing helix chain 'E' and resid 223 through 236 Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 288 through 301 removed outlier: 4.240A pdb=" N HIS E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 324 Processing helix chain 'E' and resid 328 through 348 Processing helix chain 'F' and resid 9 through 18 Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 72 through 79 removed outlier: 3.653A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 removed outlier: 3.674A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 221 removed outlier: 4.845A pdb=" N ALA F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR F 219 " --> pdb=" O PHE F 215 " (cutoff:3.500A) Proline residue: F 220 - end of helix Processing helix chain 'G' and resid 10 through 18 Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.027A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.784A pdb=" N LYS G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 15 No H-bonds generated for 'chain 'H' and resid 12 through 15' Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 73 through 81 removed outlier: 3.686A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 removed outlier: 3.623A pdb=" N SER H 152 " --> pdb=" O CYS H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 209 through 218 removed outlier: 4.369A pdb=" N ALA H 218 " --> pdb=" O PHE H 214 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 177 through 181 Processing sheet with id= B, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.809A pdb=" N ILE A 486 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU A 372 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS A 488 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 803 through 806 Processing sheet with id= D, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.082A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 170 through 174 removed outlier: 3.502A pdb=" N GLY C 60 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 195 through 199 removed outlier: 3.652A pdb=" N GLY D 78 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 179 through 183 removed outlier: 6.479A pdb=" N HIS E 37 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL E 182 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 60 through 62 Processing sheet with id= I, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.149A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 136 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 204 through 208 removed outlier: 5.902A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 2 through 6 Processing sheet with id= L, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.652A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 203 through 208 removed outlier: 6.335A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 60 through 62 Processing sheet with id= O, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.704A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 203 through 208 936 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 9.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7236 1.36 - 1.50: 5710 1.50 - 1.65: 9155 1.65 - 1.80: 103 1.80 - 1.95: 105 Bond restraints: 22309 Sorted by residual: bond pdb=" C HIS B 259 " pdb=" N PRO B 260 " ideal model delta sigma weight residual 1.336 1.398 -0.062 1.25e-02 6.40e+03 2.50e+01 bond pdb=" C TYR E 238 " pdb=" N PRO E 239 " ideal model delta sigma weight residual 1.333 1.374 -0.040 1.01e-02 9.80e+03 1.58e+01 bond pdb=" N VAL A 776 " pdb=" CA VAL A 776 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N ILE D 326 " pdb=" CA ILE D 326 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.50e+00 bond pdb=" CA ALA C 216 " pdb=" CB ALA C 216 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.63e-02 3.76e+03 9.41e+00 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.37: 883 106.37 - 113.70: 12673 113.70 - 121.03: 10499 121.03 - 128.36: 6195 128.36 - 135.69: 148 Bond angle restraints: 30398 Sorted by residual: angle pdb=" C MET C 182 " pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 120.33 124.42 -4.09 8.00e-01 1.56e+00 2.61e+01 angle pdb=" C PRO B 258 " pdb=" N HIS B 259 " pdb=" CA HIS B 259 " ideal model delta sigma weight residual 120.26 126.94 -6.68 1.34e+00 5.57e-01 2.49e+01 angle pdb=" O LYS G 181 " pdb=" C LYS G 181 " pdb=" N LEU G 182 " ideal model delta sigma weight residual 123.31 128.45 -5.14 1.17e+00 7.31e-01 1.93e+01 angle pdb=" N VAL B 115 " pdb=" CA VAL B 115 " pdb=" C VAL B 115 " ideal model delta sigma weight residual 112.96 108.69 4.27 1.00e+00 1.00e+00 1.83e+01 angle pdb=" C ASP B 110 " pdb=" N ARG B 111 " pdb=" CA ARG B 111 " ideal model delta sigma weight residual 122.46 128.22 -5.76 1.41e+00 5.03e-01 1.67e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 12945 28.46 - 56.91: 642 56.91 - 85.37: 43 85.37 - 113.82: 2 113.82 - 142.28: 3 Dihedral angle restraints: 13635 sinusoidal: 5895 harmonic: 7740 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 157.72 142.28 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" CA GLU A 818 " pdb=" C GLU A 818 " pdb=" N PRO A 819 " pdb=" CA PRO A 819 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LEU F 79 " pdb=" C LEU F 79 " pdb=" N LYS F 80 " pdb=" CA LYS F 80 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3127 0.069 - 0.137: 376 0.137 - 0.206: 30 0.206 - 0.274: 2 0.274 - 0.343: 1 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CA LEU G 182 " pdb=" N LEU G 182 " pdb=" C LEU G 182 " pdb=" CB LEU G 182 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA ILE D 326 " pdb=" N ILE D 326 " pdb=" C ILE D 326 " pdb=" CB ILE D 326 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ARG A 696 " pdb=" N ARG A 696 " pdb=" C ARG A 696 " pdb=" CB ARG A 696 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3533 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 699 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " -0.047 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO E 174 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " -0.233 9.50e-02 1.11e+02 1.04e-01 6.69e+00 pdb=" NE ARG E 160 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.008 2.00e-02 2.50e+03 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 223 2.62 - 3.19: 17310 3.19 - 3.76: 34385 3.76 - 4.33: 48028 4.33 - 4.90: 79298 Nonbonded interactions: 179244 Sorted by model distance: nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR C 67 " pdb="MG MG C 401 " model vdw 2.058 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.058 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G AGS B 402 " model vdw 2.062 2.170 ... (remaining 179239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 258) selection = (chain 'H' and resid 1 through 258) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.490 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 61.700 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.110 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.004 0.065 22309 Z= 0.248 Angle : 0.688 12.063 30398 Z= 0.403 Chirality : 0.046 0.343 3536 Planarity : 0.007 0.104 3723 Dihedral : 15.129 142.281 8597 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.90 % Allowed : 8.83 % Favored : 89.26 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 2623 helix: -1.36 (0.12), residues: 1250 sheet: -0.23 (0.23), residues: 512 loop : -1.04 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 251 HIS 0.004 0.001 HIS E 331 PHE 0.019 0.002 PHE A 632 TYR 0.015 0.002 TYR D 77 ARG 0.003 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 514 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 531 MET cc_start: 0.6518 (mmt) cc_final: 0.6039 (mmt) REVERT: A 767 ASP cc_start: 0.7412 (t70) cc_final: 0.7180 (t0) REVERT: C 89 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7371 (tm-30) REVERT: C 307 ASP cc_start: 0.8311 (m-30) cc_final: 0.8033 (m-30) REVERT: D 209 GLN cc_start: 0.8151 (tt0) cc_final: 0.7890 (mt0) REVERT: D 221 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8302 (mttt) REVERT: E 11 CYS cc_start: 0.7786 (m) cc_final: 0.7571 (p) REVERT: E 191 ASP cc_start: 0.7367 (m-30) cc_final: 0.7157 (m-30) REVERT: F 71 ASN cc_start: 0.8259 (t0) cc_final: 0.7958 (t0) REVERT: F 114 TYR cc_start: 0.0312 (m-80) cc_final: 0.0061 (m-80) REVERT: F 240 LYS cc_start: 0.8005 (tppp) cc_final: 0.7802 (mtmp) REVERT: F 248 LYS cc_start: 0.8313 (mttt) cc_final: 0.7597 (mtpt) REVERT: G 147 ILE cc_start: 0.8716 (tt) cc_final: 0.8339 (mt) REVERT: G 222 SER cc_start: 0.8099 (m) cc_final: 0.7647 (t) REVERT: H 160 ILE cc_start: 0.8901 (mm) cc_final: 0.8694 (mm) REVERT: H 196 THR cc_start: 0.8618 (p) cc_final: 0.8361 (t) REVERT: H 214 PHE cc_start: 0.8507 (m-10) cc_final: 0.8118 (m-80) REVERT: H 219 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.6929 (t) REVERT: H 230 SER cc_start: 0.8621 (t) cc_final: 0.8398 (m) outliers start: 44 outliers final: 14 residues processed: 538 average time/residue: 1.3155 time to fit residues: 802.8795 Evaluate side-chains 334 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 319 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 6.9990 chunk 200 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN A 723 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN B 125 GLN B 226 GLN B 268 GLN B 269 HIS B 346 GLN C 29 GLN C 37 HIS C 257 GLN C 317 ASN C 330 GLN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN E 120 GLN E 124 ASN E 194 HIS F 8 GLN F 44 HIS G 108 GLN H 36 ASN H 38 GLN H 44 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22309 Z= 0.258 Angle : 0.563 9.471 30398 Z= 0.292 Chirality : 0.041 0.171 3536 Planarity : 0.005 0.080 3723 Dihedral : 14.571 145.463 3480 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.59 % Allowed : 16.36 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2623 helix: -0.04 (0.14), residues: 1259 sheet: -0.27 (0.22), residues: 518 loop : -0.61 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 253 HIS 0.009 0.001 HIS F 44 PHE 0.023 0.002 PHE H 144 TYR 0.016 0.002 TYR A 838 ARG 0.009 0.001 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 334 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7851 (tm-30) REVERT: A 354 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7335 (ttm) REVERT: A 531 MET cc_start: 0.6406 (mmt) cc_final: 0.6017 (mmt) REVERT: A 560 TYR cc_start: 0.7785 (m-80) cc_final: 0.7224 (m-80) REVERT: B 104 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: B 207 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: B 336 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: C 86 MET cc_start: 0.8879 (mmm) cc_final: 0.8562 (mmm) REVERT: C 307 ASP cc_start: 0.8289 (m-30) cc_final: 0.8041 (m-30) REVERT: D 165 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8530 (tpt90) REVERT: D 209 GLN cc_start: 0.8149 (tt0) cc_final: 0.7885 (mt0) REVERT: D 221 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8388 (mttm) REVERT: D 290 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: E 11 CYS cc_start: 0.7898 (m) cc_final: 0.7642 (p) REVERT: E 83 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7033 (tp30) REVERT: E 298 GLU cc_start: 0.7967 (tp30) cc_final: 0.7761 (tp30) REVERT: F 1 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7136 (tpt) REVERT: F 17 GLU cc_start: 0.7569 (tp30) cc_final: 0.7274 (tp30) REVERT: F 21 ASP cc_start: 0.6974 (t0) cc_final: 0.6749 (t0) REVERT: F 61 ARG cc_start: 0.7623 (ttt180) cc_final: 0.7419 (ttt90) REVERT: F 64 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7722 (mtm110) REVERT: F 71 ASN cc_start: 0.8177 (t0) cc_final: 0.7772 (t0) REVERT: F 72 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8433 (tm) REVERT: F 87 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7158 (tt) REVERT: F 168 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6811 (mmtm) REVERT: F 240 LYS cc_start: 0.8175 (tppp) cc_final: 0.7895 (mtmp) REVERT: F 248 LYS cc_start: 0.8380 (mttt) cc_final: 0.7580 (mtpt) REVERT: G 61 ARG cc_start: 0.7971 (ptt180) cc_final: 0.7591 (ptt-90) REVERT: G 91 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7679 (mtm-85) REVERT: G 147 ILE cc_start: 0.8804 (tt) cc_final: 0.8550 (mt) REVERT: G 199 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6260 (mpt) REVERT: G 222 SER cc_start: 0.8190 (m) cc_final: 0.7643 (t) REVERT: G 240 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7649 (tptp) REVERT: G 250 TYR cc_start: 0.8687 (m-80) cc_final: 0.7655 (m-80) REVERT: H 98 THR cc_start: 0.6045 (OUTLIER) cc_final: 0.5732 (m) REVERT: H 162 CYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7043 (t) REVERT: H 196 THR cc_start: 0.8789 (p) cc_final: 0.8486 (t) REVERT: H 219 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7242 (t) outliers start: 83 outliers final: 35 residues processed: 383 average time/residue: 1.2701 time to fit residues: 554.1860 Evaluate side-chains 350 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 300 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 213 optimal weight: 0.2980 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN C 37 HIS ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 194 HIS F 8 GLN H 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22309 Z= 0.268 Angle : 0.549 8.877 30398 Z= 0.282 Chirality : 0.041 0.167 3536 Planarity : 0.004 0.075 3723 Dihedral : 14.437 148.512 3467 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.94 % Allowed : 17.14 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2623 helix: 0.45 (0.14), residues: 1269 sheet: -0.24 (0.23), residues: 507 loop : -0.50 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 251 HIS 0.007 0.001 HIS E 194 PHE 0.014 0.001 PHE H 144 TYR 0.016 0.002 TYR H 133 ARG 0.009 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 321 time to evaluate : 2.391 Fit side-chains revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 354 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7492 (ttm) REVERT: A 387 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 531 MET cc_start: 0.6572 (mmt) cc_final: 0.6151 (mmt) REVERT: A 560 TYR cc_start: 0.7845 (m-80) cc_final: 0.7358 (m-80) REVERT: A 740 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7942 (tp) REVERT: B 104 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: B 207 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: B 336 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8299 (mp10) REVERT: C 50 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: C 80 ASP cc_start: 0.7145 (p0) cc_final: 0.6683 (p0) REVERT: C 86 MET cc_start: 0.8882 (mmm) cc_final: 0.8501 (mmm) REVERT: C 130 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8795 (mtp) REVERT: C 307 ASP cc_start: 0.8309 (m-30) cc_final: 0.8077 (m-30) REVERT: D 209 GLN cc_start: 0.8181 (tt0) cc_final: 0.7896 (mt0) REVERT: D 290 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: E 11 CYS cc_start: 0.7940 (m) cc_final: 0.7705 (p) REVERT: E 83 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6930 (tp30) REVERT: E 111 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8332 (tmt) REVERT: E 139 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8464 (mtpt) REVERT: F 1 MET cc_start: 0.7831 (tpp) cc_final: 0.7360 (tpt) REVERT: F 17 GLU cc_start: 0.7560 (tp30) cc_final: 0.7317 (tp30) REVERT: F 21 ASP cc_start: 0.7047 (t70) cc_final: 0.6785 (t0) REVERT: F 64 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7722 (mtm110) REVERT: F 71 ASN cc_start: 0.8429 (t0) cc_final: 0.8170 (t0) REVERT: F 72 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8500 (tm) REVERT: F 87 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7260 (pp) REVERT: F 240 LYS cc_start: 0.8269 (tppp) cc_final: 0.7930 (mtmp) REVERT: F 248 LYS cc_start: 0.8386 (mttt) cc_final: 0.7581 (mtpt) REVERT: G 61 ARG cc_start: 0.8003 (ptt180) cc_final: 0.7571 (ptt-90) REVERT: G 77 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8163 (ptpt) REVERT: G 147 ILE cc_start: 0.8814 (tt) cc_final: 0.8561 (mt) REVERT: G 222 SER cc_start: 0.8200 (m) cc_final: 0.7666 (t) REVERT: G 250 TYR cc_start: 0.8700 (m-80) cc_final: 0.7608 (m-80) REVERT: H 196 THR cc_start: 0.8878 (p) cc_final: 0.8569 (t) REVERT: H 219 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7410 (t) outliers start: 114 outliers final: 47 residues processed: 392 average time/residue: 1.2320 time to fit residues: 553.4670 Evaluate side-chains 353 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 291 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 241 optimal weight: 0.0270 chunk 255 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 166 ASN E 194 HIS F 8 GLN H 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22309 Z= 0.334 Angle : 0.585 8.612 30398 Z= 0.300 Chirality : 0.042 0.170 3536 Planarity : 0.005 0.075 3723 Dihedral : 14.465 158.369 3467 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.71 % Allowed : 17.79 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 2623 helix: 0.59 (0.15), residues: 1272 sheet: -0.37 (0.22), residues: 515 loop : -0.43 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 28 HIS 0.007 0.001 HIS E 194 PHE 0.015 0.002 PHE F 169 TYR 0.015 0.002 TYR E 317 ARG 0.008 0.001 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 321 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 354 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7366 (ttp) REVERT: A 387 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8203 (mp) REVERT: A 507 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 531 MET cc_start: 0.6654 (mmt) cc_final: 0.6141 (mmt) REVERT: A 560 TYR cc_start: 0.7844 (m-80) cc_final: 0.7401 (m-80) REVERT: A 758 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 853 MET cc_start: 0.7398 (ppp) cc_final: 0.6727 (mmm) REVERT: B 104 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: B 110 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: B 207 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: B 336 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: B 348 THR cc_start: 0.9000 (m) cc_final: 0.8662 (p) REVERT: C 50 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: C 86 MET cc_start: 0.8841 (mmm) cc_final: 0.8522 (mmm) REVERT: C 130 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8775 (mtp) REVERT: C 200 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7695 (p0) REVERT: C 307 ASP cc_start: 0.8276 (m-30) cc_final: 0.8035 (m-30) REVERT: D 209 GLN cc_start: 0.8225 (tt0) cc_final: 0.7924 (mt0) REVERT: D 290 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: E 11 CYS cc_start: 0.7995 (m) cc_final: 0.7786 (p) REVERT: E 83 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: E 111 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8301 (tmt) REVERT: E 139 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8475 (mtpt) REVERT: F 1 MET cc_start: 0.7846 (tpp) cc_final: 0.7341 (tpt) REVERT: F 17 GLU cc_start: 0.7605 (tp30) cc_final: 0.7294 (tp30) REVERT: F 21 ASP cc_start: 0.7017 (t70) cc_final: 0.6661 (t0) REVERT: F 64 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7753 (mtm110) REVERT: F 71 ASN cc_start: 0.8511 (t0) cc_final: 0.8292 (t0) REVERT: F 72 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8636 (tm) REVERT: F 87 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7318 (pp) REVERT: F 144 PHE cc_start: 0.8539 (t80) cc_final: 0.8287 (t80) REVERT: F 182 LEU cc_start: 0.3608 (OUTLIER) cc_final: 0.3375 (tp) REVERT: F 240 LYS cc_start: 0.8370 (tppp) cc_final: 0.7922 (mtmp) REVERT: F 248 LYS cc_start: 0.8397 (mttt) cc_final: 0.7566 (mtpt) REVERT: G 61 ARG cc_start: 0.7994 (ptt180) cc_final: 0.7652 (ptt-90) REVERT: G 77 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8323 (ptpt) REVERT: G 80 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7445 (mtpt) REVERT: G 116 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7897 (mmm) REVERT: G 147 ILE cc_start: 0.8883 (tt) cc_final: 0.8621 (mt) REVERT: G 222 SER cc_start: 0.8192 (m) cc_final: 0.7659 (t) REVERT: H 196 THR cc_start: 0.8903 (p) cc_final: 0.8539 (t) outliers start: 132 outliers final: 63 residues processed: 400 average time/residue: 1.1985 time to fit residues: 552.2320 Evaluate side-chains 372 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 289 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS C 317 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 194 HIS F 8 GLN F 213 ASN H 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22309 Z= 0.218 Angle : 0.526 7.357 30398 Z= 0.270 Chirality : 0.040 0.184 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.331 160.273 3464 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 5.02 % Allowed : 18.96 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2623 helix: 0.83 (0.15), residues: 1274 sheet: -0.32 (0.22), residues: 513 loop : -0.35 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 28 HIS 0.006 0.001 HIS E 194 PHE 0.011 0.001 PHE H 144 TYR 0.016 0.001 TYR H 133 ARG 0.008 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 302 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 354 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7501 (ttp) REVERT: A 387 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 507 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8565 (tp) REVERT: A 531 MET cc_start: 0.6639 (mmt) cc_final: 0.6202 (mmt) REVERT: A 560 TYR cc_start: 0.7855 (m-80) cc_final: 0.7453 (m-80) REVERT: A 740 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7963 (tp) REVERT: A 758 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 806 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.5927 (mt-10) REVERT: A 852 LYS cc_start: 0.7846 (tppt) cc_final: 0.7535 (tttt) REVERT: A 853 MET cc_start: 0.7293 (ppp) cc_final: 0.6670 (mmm) REVERT: B 104 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: B 207 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: B 249 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: B 336 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: B 348 THR cc_start: 0.8977 (m) cc_final: 0.8669 (p) REVERT: C 50 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: C 86 MET cc_start: 0.8823 (mmm) cc_final: 0.8505 (mmm) REVERT: C 130 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8725 (mtp) REVERT: C 257 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: C 307 ASP cc_start: 0.8260 (m-30) cc_final: 0.8040 (m-30) REVERT: D 209 GLN cc_start: 0.8172 (tt0) cc_final: 0.7878 (mt0) REVERT: D 290 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: E 11 CYS cc_start: 0.8020 (m) cc_final: 0.7790 (p) REVERT: E 83 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: E 111 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8289 (tmt) REVERT: E 139 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8479 (mtpt) REVERT: F 1 MET cc_start: 0.7788 (tpp) cc_final: 0.7364 (tpt) REVERT: F 17 GLU cc_start: 0.7553 (tp30) cc_final: 0.7049 (tp30) REVERT: F 21 ASP cc_start: 0.6928 (t70) cc_final: 0.6597 (t0) REVERT: F 87 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7264 (pp) REVERT: F 91 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7724 (ttp-110) REVERT: F 144 PHE cc_start: 0.8526 (t80) cc_final: 0.8279 (t80) REVERT: F 182 LEU cc_start: 0.3900 (OUTLIER) cc_final: 0.3626 (tp) REVERT: F 240 LYS cc_start: 0.8349 (tppp) cc_final: 0.7897 (mtmp) REVERT: F 248 LYS cc_start: 0.8407 (mttt) cc_final: 0.7578 (mtpt) REVERT: G 61 ARG cc_start: 0.7973 (ptt180) cc_final: 0.7557 (ptt-90) REVERT: G 77 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8295 (ptpt) REVERT: G 80 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7745 (tptm) REVERT: G 116 MET cc_start: 0.8156 (mmp) cc_final: 0.7805 (mmm) REVERT: G 132 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: G 147 ILE cc_start: 0.8837 (tt) cc_final: 0.8578 (mt) REVERT: G 222 SER cc_start: 0.8245 (m) cc_final: 0.7705 (t) REVERT: G 250 TYR cc_start: 0.8690 (m-80) cc_final: 0.7665 (m-80) REVERT: H 16 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8598 (tm) REVERT: H 75 MET cc_start: 0.7358 (ttt) cc_final: 0.7019 (ttt) REVERT: H 196 THR cc_start: 0.8912 (p) cc_final: 0.8543 (t) outliers start: 116 outliers final: 56 residues processed: 375 average time/residue: 1.2418 time to fit residues: 534.3551 Evaluate side-chains 359 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 282 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 0.2980 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN F 8 GLN F 71 ASN F 213 ASN H 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22309 Z= 0.257 Angle : 0.555 9.531 30398 Z= 0.282 Chirality : 0.041 0.197 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.253 161.361 3460 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.06 % Allowed : 19.87 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2623 helix: 0.88 (0.15), residues: 1272 sheet: -0.43 (0.22), residues: 522 loop : -0.34 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 28 HIS 0.005 0.001 HIS E 331 PHE 0.012 0.001 PHE A 632 TYR 0.015 0.002 TYR A 291 ARG 0.009 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 292 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 354 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7494 (ttp) REVERT: A 387 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8203 (mp) REVERT: A 507 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8569 (tp) REVERT: A 531 MET cc_start: 0.6631 (mmt) cc_final: 0.6167 (mmt) REVERT: A 560 TYR cc_start: 0.7842 (m-80) cc_final: 0.7492 (m-80) REVERT: A 758 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (tp) REVERT: A 853 MET cc_start: 0.7236 (ppp) cc_final: 0.6632 (mmm) REVERT: B 104 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: B 110 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: B 207 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: B 336 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: B 348 THR cc_start: 0.8996 (m) cc_final: 0.8669 (p) REVERT: C 50 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: C 86 MET cc_start: 0.8806 (mmm) cc_final: 0.8531 (mmm) REVERT: C 130 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8744 (mtp) REVERT: C 200 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7591 (p0) REVERT: C 307 ASP cc_start: 0.8237 (m-30) cc_final: 0.8029 (m-30) REVERT: D 113 GLU cc_start: 0.7036 (mp0) cc_final: 0.6751 (mp0) REVERT: D 209 GLN cc_start: 0.8211 (tt0) cc_final: 0.7913 (mt0) REVERT: D 290 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: E 11 CYS cc_start: 0.8029 (m) cc_final: 0.7818 (p) REVERT: E 83 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: E 111 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8281 (tmt) REVERT: E 139 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8478 (mtpt) REVERT: F 1 MET cc_start: 0.7788 (tpp) cc_final: 0.7366 (tpt) REVERT: F 17 GLU cc_start: 0.7532 (tp30) cc_final: 0.7024 (tp30) REVERT: F 21 ASP cc_start: 0.6970 (t70) cc_final: 0.6610 (t0) REVERT: F 71 ASN cc_start: 0.8311 (t0) cc_final: 0.8022 (t0) REVERT: F 87 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7263 (pp) REVERT: F 182 LEU cc_start: 0.4169 (OUTLIER) cc_final: 0.3858 (tp) REVERT: F 214 PHE cc_start: 0.8566 (m-10) cc_final: 0.8230 (m-10) REVERT: F 248 LYS cc_start: 0.8418 (mttt) cc_final: 0.7552 (mtpt) REVERT: G 61 ARG cc_start: 0.7981 (ptt180) cc_final: 0.7620 (ptt-90) REVERT: G 77 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8294 (ptpt) REVERT: G 78 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8589 (mp) REVERT: G 80 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7740 (tptm) REVERT: G 116 MET cc_start: 0.8173 (mmp) cc_final: 0.7900 (mmm) REVERT: G 132 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7127 (pp20) REVERT: G 147 ILE cc_start: 0.8865 (tt) cc_final: 0.8614 (mt) REVERT: G 222 SER cc_start: 0.8243 (m) cc_final: 0.7730 (t) REVERT: G 250 TYR cc_start: 0.8698 (m-80) cc_final: 0.7635 (m-80) REVERT: H 257 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.6241 (t70) outliers start: 117 outliers final: 67 residues processed: 372 average time/residue: 1.2153 time to fit residues: 518.1583 Evaluate side-chains 367 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 280 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 244 MET Chi-restraints excluded: chain H residue 257 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS F 8 GLN F 38 GLN H 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22309 Z= 0.325 Angle : 0.595 9.661 30398 Z= 0.301 Chirality : 0.042 0.172 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.302 161.732 3459 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.15 % Allowed : 20.35 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2623 helix: 0.83 (0.15), residues: 1272 sheet: -0.49 (0.22), residues: 530 loop : -0.36 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 28 HIS 0.006 0.001 HIS E 194 PHE 0.022 0.002 PHE F 144 TYR 0.021 0.002 TYR A 815 ARG 0.008 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 293 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 354 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7436 (ttp) REVERT: A 387 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 419 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8115 (mpp) REVERT: A 507 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 531 MET cc_start: 0.6586 (mmt) cc_final: 0.6057 (mmt) REVERT: A 560 TYR cc_start: 0.7888 (m-80) cc_final: 0.7499 (m-80) REVERT: A 758 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 852 LYS cc_start: 0.7868 (tppt) cc_final: 0.7526 (tttt) REVERT: A 853 MET cc_start: 0.7219 (ppp) cc_final: 0.6657 (mmm) REVERT: B 104 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: B 110 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: B 207 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: B 336 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: B 348 THR cc_start: 0.9006 (m) cc_final: 0.8658 (p) REVERT: C 50 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: C 86 MET cc_start: 0.8797 (mmm) cc_final: 0.8538 (mmm) REVERT: C 130 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8754 (mtp) REVERT: C 200 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7616 (p0) REVERT: C 307 ASP cc_start: 0.8254 (m-30) cc_final: 0.8047 (m-30) REVERT: D 209 GLN cc_start: 0.8210 (tt0) cc_final: 0.7906 (mt0) REVERT: D 290 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: E 83 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6961 (tp30) REVERT: E 111 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8240 (tmt) REVERT: E 139 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8482 (mtpt) REVERT: F 1 MET cc_start: 0.7726 (tpp) cc_final: 0.7306 (tpt) REVERT: F 17 GLU cc_start: 0.7522 (tp30) cc_final: 0.7036 (tp30) REVERT: F 21 ASP cc_start: 0.6973 (t70) cc_final: 0.6591 (t0) REVERT: F 53 ARG cc_start: 0.8260 (mpp80) cc_final: 0.7819 (mpp80) REVERT: F 87 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7288 (pp) REVERT: F 144 PHE cc_start: 0.8494 (t80) cc_final: 0.8228 (t80) REVERT: F 182 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.4181 (tp) REVERT: F 248 LYS cc_start: 0.8422 (mttt) cc_final: 0.7579 (mtpt) REVERT: G 61 ARG cc_start: 0.8018 (ptt180) cc_final: 0.7704 (ptt-90) REVERT: G 77 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8428 (ptmt) REVERT: G 80 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7822 (tptm) REVERT: G 116 MET cc_start: 0.8215 (mmp) cc_final: 0.7942 (mmm) REVERT: G 132 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: G 147 ILE cc_start: 0.8894 (tt) cc_final: 0.8643 (mt) REVERT: G 199 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6727 (mpt) REVERT: G 222 SER cc_start: 0.8229 (m) cc_final: 0.7740 (t) REVERT: G 238 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6334 (mt-10) outliers start: 119 outliers final: 71 residues processed: 372 average time/residue: 1.2158 time to fit residues: 522.1374 Evaluate side-chains 366 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 274 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 233 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 0.0070 chunk 125 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 0.4980 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS F 8 GLN F 38 GLN H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22309 Z= 0.245 Angle : 0.570 11.240 30398 Z= 0.288 Chirality : 0.041 0.214 3536 Planarity : 0.004 0.072 3723 Dihedral : 14.238 161.972 3459 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.76 % Allowed : 21.52 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2623 helix: 0.96 (0.15), residues: 1270 sheet: -0.46 (0.22), residues: 529 loop : -0.31 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.007 0.001 HIS E 194 PHE 0.019 0.001 PHE F 144 TYR 0.023 0.002 TYR A 291 ARG 0.008 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 295 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7544 (ttp) REVERT: A 387 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8227 (mp) REVERT: A 507 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8575 (tp) REVERT: A 531 MET cc_start: 0.6558 (mmt) cc_final: 0.6040 (mmt) REVERT: A 560 TYR cc_start: 0.7861 (m-80) cc_final: 0.7492 (m-80) REVERT: A 758 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8313 (tp) REVERT: A 853 MET cc_start: 0.7182 (ppp) cc_final: 0.6625 (mmm) REVERT: B 104 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: B 110 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: B 207 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: B 336 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: B 348 THR cc_start: 0.8989 (m) cc_final: 0.8656 (p) REVERT: C 50 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: C 86 MET cc_start: 0.8791 (mmm) cc_final: 0.8533 (mmm) REVERT: C 130 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8747 (mtp) REVERT: C 200 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7602 (p0) REVERT: D 209 GLN cc_start: 0.8196 (tt0) cc_final: 0.7902 (mt0) REVERT: D 290 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: E 83 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: E 111 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8233 (tmt) REVERT: E 139 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8473 (mtpt) REVERT: F 1 MET cc_start: 0.7704 (tpp) cc_final: 0.7286 (tpt) REVERT: F 21 ASP cc_start: 0.6988 (t70) cc_final: 0.6584 (t0) REVERT: F 53 ARG cc_start: 0.8234 (mpp80) cc_final: 0.7839 (mpp80) REVERT: F 144 PHE cc_start: 0.8501 (t80) cc_final: 0.8260 (t80) REVERT: F 182 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.4228 (tp) REVERT: F 248 LYS cc_start: 0.8410 (mttt) cc_final: 0.7547 (mtpt) REVERT: G 61 ARG cc_start: 0.7993 (ptt180) cc_final: 0.7682 (ptt-90) REVERT: G 77 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8312 (ptmt) REVERT: G 78 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8552 (mp) REVERT: G 80 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7793 (tptm) REVERT: G 116 MET cc_start: 0.8230 (mmp) cc_final: 0.7964 (mmm) REVERT: G 132 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: G 147 ILE cc_start: 0.8880 (tt) cc_final: 0.8633 (mt) REVERT: G 199 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6738 (mpt) REVERT: G 222 SER cc_start: 0.8236 (m) cc_final: 0.7764 (t) outliers start: 110 outliers final: 73 residues processed: 368 average time/residue: 1.1609 time to fit residues: 492.7163 Evaluate side-chains 365 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 273 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 244 MET Chi-restraints excluded: chain H residue 257 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 237 optimal weight: 0.0870 chunk 142 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS C 257 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS F 8 GLN H 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22309 Z= 0.239 Angle : 0.569 11.784 30398 Z= 0.288 Chirality : 0.041 0.227 3536 Planarity : 0.004 0.072 3723 Dihedral : 14.195 162.013 3459 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.42 % Allowed : 22.25 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2623 helix: 1.03 (0.15), residues: 1265 sheet: -0.35 (0.22), residues: 514 loop : -0.32 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 28 HIS 0.007 0.001 HIS E 194 PHE 0.022 0.001 PHE F 144 TYR 0.022 0.002 TYR A 291 ARG 0.009 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 284 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7594 (ttp) REVERT: A 387 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 507 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8561 (tp) REVERT: A 531 MET cc_start: 0.6582 (mmt) cc_final: 0.6042 (mmt) REVERT: A 560 TYR cc_start: 0.7861 (m-80) cc_final: 0.7504 (m-80) REVERT: A 758 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8307 (tp) REVERT: A 852 LYS cc_start: 0.7888 (tppt) cc_final: 0.7541 (tttt) REVERT: A 853 MET cc_start: 0.7188 (ppp) cc_final: 0.6620 (mmm) REVERT: B 104 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: B 110 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: B 207 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: B 336 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8315 (mp10) REVERT: B 348 THR cc_start: 0.9000 (m) cc_final: 0.8668 (p) REVERT: C 50 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: C 86 MET cc_start: 0.8784 (mmm) cc_final: 0.8542 (mmm) REVERT: C 130 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8747 (mtp) REVERT: C 200 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7590 (p0) REVERT: D 209 GLN cc_start: 0.8194 (tt0) cc_final: 0.7901 (mt0) REVERT: D 290 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: E 83 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: E 111 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8228 (tmt) REVERT: E 139 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8475 (mtpt) REVERT: F 1 MET cc_start: 0.7648 (tpp) cc_final: 0.7149 (tpt) REVERT: F 17 GLU cc_start: 0.7398 (tp30) cc_final: 0.6970 (tp30) REVERT: F 21 ASP cc_start: 0.7020 (t70) cc_final: 0.6610 (t0) REVERT: F 53 ARG cc_start: 0.8241 (mpp80) cc_final: 0.7882 (mpp80) REVERT: F 61 ARG cc_start: 0.7792 (ttt180) cc_final: 0.7588 (ttt90) REVERT: F 71 ASN cc_start: 0.8257 (t0) cc_final: 0.8000 (t0) REVERT: F 87 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7265 (pp) REVERT: F 144 PHE cc_start: 0.8494 (t80) cc_final: 0.8268 (t80) REVERT: F 182 LEU cc_start: 0.4617 (OUTLIER) cc_final: 0.4256 (tp) REVERT: F 248 LYS cc_start: 0.8413 (mttt) cc_final: 0.7538 (mtpt) REVERT: G 61 ARG cc_start: 0.7984 (ptt180) cc_final: 0.7674 (ptt-90) REVERT: G 77 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8304 (ptmt) REVERT: G 80 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7784 (tptm) REVERT: G 132 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7171 (pp20) REVERT: G 147 ILE cc_start: 0.8874 (tt) cc_final: 0.8624 (mt) REVERT: G 199 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6777 (mpt) REVERT: G 222 SER cc_start: 0.8246 (m) cc_final: 0.7789 (t) REVERT: G 238 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6280 (mt-10) outliers start: 102 outliers final: 68 residues processed: 353 average time/residue: 1.2559 time to fit residues: 507.3147 Evaluate side-chains 357 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 269 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 118 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 161 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN E 194 HIS E 313 GLN F 8 GLN H 38 GLN H 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22309 Z= 0.157 Angle : 0.552 11.715 30398 Z= 0.279 Chirality : 0.039 0.246 3536 Planarity : 0.004 0.072 3723 Dihedral : 14.028 160.861 3459 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.12 % Allowed : 24.11 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2623 helix: 1.22 (0.15), residues: 1266 sheet: -0.27 (0.23), residues: 502 loop : -0.23 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.007 0.001 HIS E 194 PHE 0.019 0.001 PHE F 144 TYR 0.020 0.001 TYR A 291 ARG 0.009 0.000 ARG C 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 296 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7612 (ttp) REVERT: A 387 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 507 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8563 (tp) REVERT: A 531 MET cc_start: 0.6524 (mmt) cc_final: 0.6125 (mmt) REVERT: A 560 TYR cc_start: 0.7821 (m-80) cc_final: 0.7525 (m-80) REVERT: A 758 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8253 (tp) REVERT: A 822 GLU cc_start: 0.7768 (pt0) cc_final: 0.7481 (pp20) REVERT: A 852 LYS cc_start: 0.7871 (tppt) cc_final: 0.7506 (tttt) REVERT: A 853 MET cc_start: 0.7103 (ppp) cc_final: 0.6574 (mmm) REVERT: B 104 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: B 110 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: B 336 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: C 86 MET cc_start: 0.8769 (mmm) cc_final: 0.8518 (mmm) REVERT: C 130 MET cc_start: 0.9067 (mtm) cc_final: 0.8743 (mtp) REVERT: D 209 GLN cc_start: 0.8163 (tt0) cc_final: 0.7888 (mt0) REVERT: D 290 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: E 111 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8253 (tmt) REVERT: E 139 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8451 (mtpt) REVERT: F 1 MET cc_start: 0.7563 (tpp) cc_final: 0.7057 (tpt) REVERT: F 17 GLU cc_start: 0.7282 (tp30) cc_final: 0.6858 (tp30) REVERT: F 21 ASP cc_start: 0.7040 (t70) cc_final: 0.6632 (t0) REVERT: F 53 ARG cc_start: 0.8244 (mpp80) cc_final: 0.7940 (mpp80) REVERT: F 87 ILE cc_start: 0.7632 (mp) cc_final: 0.7327 (pp) REVERT: F 144 PHE cc_start: 0.8506 (t80) cc_final: 0.8293 (t80) REVERT: F 182 LEU cc_start: 0.4569 (OUTLIER) cc_final: 0.4231 (tp) REVERT: F 214 PHE cc_start: 0.8602 (m-10) cc_final: 0.8371 (m-10) REVERT: F 248 LYS cc_start: 0.8392 (mttt) cc_final: 0.7527 (mtpt) REVERT: G 61 ARG cc_start: 0.7970 (ptt180) cc_final: 0.7653 (ptt-90) REVERT: G 77 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8376 (ptmt) REVERT: G 132 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7163 (pp20) REVERT: G 147 ILE cc_start: 0.8799 (tt) cc_final: 0.8546 (mt) REVERT: G 199 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6674 (mpt) REVERT: G 222 SER cc_start: 0.8290 (m) cc_final: 0.7808 (t) REVERT: G 250 TYR cc_start: 0.8662 (m-80) cc_final: 0.7606 (m-80) REVERT: H 240 LYS cc_start: 0.8041 (mppt) cc_final: 0.7637 (ttpt) outliers start: 72 outliers final: 39 residues processed: 339 average time/residue: 1.2353 time to fit residues: 482.0010 Evaluate side-chains 333 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 281 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 193 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN E 313 GLN F 8 GLN H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122379 restraints weight = 27061.516| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.31 r_work: 0.3317 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22309 Z= 0.187 Angle : 0.551 11.158 30398 Z= 0.278 Chirality : 0.040 0.259 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.999 161.589 3459 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.77 % Allowed : 24.50 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.71 (0.17), residues: 2623 helix: 1.31 (0.15), residues: 1260 sheet: -0.22 (0.23), residues: 513 loop : -0.19 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.004 0.001 HIS C 37 PHE 0.018 0.001 PHE F 144 TYR 0.019 0.001 TYR A 291 ARG 0.009 0.000 ARG C 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8738.18 seconds wall clock time: 152 minutes 53.37 seconds (9173.37 seconds total)