Starting phenix.real_space_refine on Tue Jul 23 07:52:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/07_2024/8umw_42386_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/07_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_42386/07_2024/8umw_42386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/07_2024/8umw_42386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/07_2024/8umw_42386_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umw_42386/07_2024/8umw_42386_neut.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 12.13, per 1000 atoms: 0.55 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: 8.37 Conformation dependent library (CDL) restraints added in 3.5 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... Secondary structure from input PDB file: 121 helices and 14 sheets defined 51.8% alpha, 14.4% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 6.91 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.797A pdb=" N GLU A 293 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 294' Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 418 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 440 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.768A pdb=" N SER A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.691A pdb=" N VAL A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 627 through 643 removed outlier: 3.552A pdb=" N ARG A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 656 Processing helix chain 'A' and resid 666 through 690 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.694A pdb=" N LEU A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.687A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 742 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.646A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 762 through 770 Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.715A pdb=" N TYR A 799 " --> pdb=" O THR A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.629A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.674A pdb=" N ARG B 117 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 147 through 161 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) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.571A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.554A pdb=" N GLN B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 259 through 272 removed outlier: 4.187A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.510A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.854A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.581A pdb=" N LYS B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 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 21 through 26 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.502A pdb=" N MET C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 131 through 145 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) removed outlier: 3.532A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.555A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 178 through 192 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 198 through 210 removed outlier: 4.061A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.533A pdb=" N ALA C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.600A pdb=" N GLN C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 291 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 294 through 312 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.612A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.520A pdb=" N VAL D 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 83 through 97 removed outlier: 3.569A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 115 through 128 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 156 through 162 Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.923A pdb=" N GLU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.821A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.581A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 362 removed outlier: 4.077A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.069A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.872A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 30 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 removed outlier: 4.206A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 removed outlier: 6.812A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 117 removed outlier: 3.589A pdb=" N VAL E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 115 " --> pdb=" O MET E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 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) removed outlier: 3.647A pdb=" N TYR E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.656A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.688A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.516A pdb=" N VAL E 253 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.584A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.178A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.477A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 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 155 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 217 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.740A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' 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 153 removed outlier: 3.740A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 82 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) removed outlier: 3.656A pdb=" N ALA H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.877A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA H 194 " --> pdb=" O GLU H 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 190 through 194' Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 398 removed outlier: 6.107A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 370 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N CYS A 490 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 372 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 369 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU A 371 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 806 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 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) removed outlier: 6.290A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.238A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.350A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.914A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (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) 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) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 62 removed outlier: 3.736A pdb=" N VAL G 167 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 5.496A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (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) Processing sheet with id=AB1, first strand: chain 'F' and resid 177 through 179 removed outlier: 4.759A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 61 through 62 removed outlier: 4.663A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, first strand: chain 'H' and resid 60 through 61 Processing sheet with id=AB5, 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) removed outlier: 3.592A pdb=" N THR H 196 " --> pdb=" O LYS H 138 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3126 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: 7.56 Time building geometry restraints manager: 9.21 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: 17235 3.19 - 3.76: 34257 3.76 - 4.33: 47702 4.33 - 4.90: 79243 Nonbonded interactions: 178660 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 178655 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: 1.870 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: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 61.180 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.730 ------------------------------------------------------------------------------- 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= 0.245 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 : 2.480 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: 1.3221 time to fit residues: 806.9060 Evaluate side-chains 334 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 319 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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: 0.9980 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS 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 732 GLN 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 218 ASN 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 F 184 GLN G 108 GLN H 36 ASN H 38 GLN H 44 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22309 Z= 0.190 Angle : 0.545 10.238 30398 Z= 0.283 Chirality : 0.040 0.180 3536 Planarity : 0.005 0.079 3723 Dihedral : 14.521 143.194 3480 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.42 % Allowed : 16.23 % Favored : 80.35 % 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: -0.34 (0.16), residues: 2623 helix: 0.20 (0.14), residues: 1268 sheet: -0.24 (0.23), residues: 507 loop : -0.60 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 28 HIS 0.009 0.001 HIS F 44 PHE 0.022 0.001 PHE H 144 TYR 0.014 0.001 TYR A 838 ARG 0.009 0.000 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 416 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 337 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 354 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7371 (ttm) REVERT: A 531 MET cc_start: 0.6346 (mmt) cc_final: 0.5999 (mmt) REVERT: A 560 TYR cc_start: 0.7752 (m-80) cc_final: 0.7160 (m-80) REVERT: B 104 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: B 207 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: B 348 THR cc_start: 0.8983 (m) cc_final: 0.8672 (p) REVERT: C 50 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: C 86 MET cc_start: 0.8886 (mmm) cc_final: 0.8541 (mmm) REVERT: C 307 ASP cc_start: 0.8254 (m-30) cc_final: 0.8015 (m-30) REVERT: D 209 GLN cc_start: 0.8132 (tt0) cc_final: 0.7889 (mt0) REVERT: D 290 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: E 11 CYS cc_start: 0.7867 (m) cc_final: 0.7615 (p) REVERT: F 1 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7099 (tpt) REVERT: F 17 GLU cc_start: 0.7529 (tp30) cc_final: 0.7213 (tp30) REVERT: F 61 ARG cc_start: 0.7582 (ttt180) cc_final: 0.7378 (ttt90) REVERT: F 64 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7681 (mtm110) REVERT: F 72 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8363 (tm) REVERT: F 168 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6807 (mmtm) REVERT: F 240 LYS cc_start: 0.8118 (tppp) cc_final: 0.7898 (mtmp) REVERT: F 248 LYS cc_start: 0.8352 (mttt) cc_final: 0.7528 (mtpt) REVERT: G 61 ARG cc_start: 0.7853 (ptt180) cc_final: 0.7584 (ptt-90) REVERT: G 147 ILE cc_start: 0.8701 (tt) cc_final: 0.8440 (mt) REVERT: G 199 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6235 (mpt) REVERT: G 222 SER cc_start: 0.8141 (m) cc_final: 0.7613 (t) REVERT: G 250 TYR cc_start: 0.8627 (m-80) cc_final: 0.7756 (m-80) REVERT: H 98 THR cc_start: 0.5894 (OUTLIER) cc_final: 0.5596 (m) REVERT: H 162 CYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7030 (t) REVERT: H 196 THR cc_start: 0.8658 (p) cc_final: 0.8456 (t) REVERT: H 219 THR cc_start: 0.7401 (OUTLIER) cc_final: 0.7067 (t) REVERT: H 230 SER cc_start: 0.8664 (t) cc_final: 0.8450 (m) outliers start: 79 outliers final: 30 residues processed: 383 average time/residue: 1.3088 time to fit residues: 571.3421 Evaluate side-chains 349 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 307 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 72 ILE 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 C residue 50 GLU 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 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 16 LEU 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 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 24 ASN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 199 MET 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: 1.9990 chunk 74 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 F 71 ASN H 38 GLN H 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22309 Z= 0.211 Angle : 0.523 9.219 30398 Z= 0.270 Chirality : 0.039 0.161 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.338 144.017 3465 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.90 % Allowed : 17.62 % Favored : 78.48 % 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: 0.84 (0.15), residues: 1264 sheet: -0.30 (0.22), residues: 524 loop : -0.36 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 251 HIS 0.006 0.001 HIS E 194 PHE 0.015 0.001 PHE H 144 TYR 0.016 0.001 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 417 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 327 time to evaluate : 2.536 Fit side-chains revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 354 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7472 (ttm) REVERT: A 387 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 531 MET cc_start: 0.6389 (mmt) cc_final: 0.6066 (mmt) REVERT: A 560 TYR cc_start: 0.7777 (m-80) cc_final: 0.7257 (m-80) REVERT: A 713 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.6912 (m-70) REVERT: A 740 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7857 (tp) REVERT: A 822 GLU cc_start: 0.7596 (pt0) cc_final: 0.7280 (pp20) REVERT: A 853 MET cc_start: 0.7474 (ppp) cc_final: 0.6789 (mmm) REVERT: B 104 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: B 207 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: B 336 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: B 348 THR cc_start: 0.8997 (m) cc_final: 0.8665 (p) REVERT: C 50 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: C 86 MET cc_start: 0.8838 (mmm) cc_final: 0.8549 (mmm) REVERT: C 130 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8587 (mtp) REVERT: C 307 ASP cc_start: 0.8271 (m-30) cc_final: 0.8034 (m-30) REVERT: D 113 GLU cc_start: 0.6861 (mp0) cc_final: 0.6481 (mp0) REVERT: D 205 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8134 (ptmm) REVERT: D 209 GLN cc_start: 0.8151 (tt0) cc_final: 0.7897 (mt0) REVERT: D 290 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: E 11 CYS cc_start: 0.7854 (m) cc_final: 0.7623 (p) REVERT: E 83 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: E 139 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8517 (mtpt) REVERT: F 1 MET cc_start: 0.7831 (tpp) cc_final: 0.7201 (tpt) REVERT: F 17 GLU cc_start: 0.7539 (tp30) cc_final: 0.7054 (tp30) REVERT: F 21 ASP cc_start: 0.6980 (t0) cc_final: 0.6720 (t0) REVERT: F 61 ARG cc_start: 0.7606 (ttt180) cc_final: 0.7398 (ttt90) REVERT: F 64 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7723 (mtm110) REVERT: F 71 ASN cc_start: 0.8002 (t0) cc_final: 0.7745 (t0) REVERT: F 72 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8429 (tm) REVERT: F 87 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7102 (tt) REVERT: F 168 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6917 (mmtm) REVERT: F 214 PHE cc_start: 0.8579 (m-10) cc_final: 0.8193 (m-10) REVERT: F 240 LYS cc_start: 0.8214 (tppp) cc_final: 0.7955 (mtmp) REVERT: F 248 LYS cc_start: 0.8373 (mttt) cc_final: 0.7576 (mtpt) REVERT: G 61 ARG cc_start: 0.7904 (ptt180) cc_final: 0.7611 (ptt-90) REVERT: G 77 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8117 (ptpt) REVERT: G 147 ILE cc_start: 0.8713 (tt) cc_final: 0.8458 (mt) REVERT: G 222 SER cc_start: 0.8144 (m) cc_final: 0.7654 (t) REVERT: G 240 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7631 (tptp) REVERT: G 250 TYR cc_start: 0.8666 (m-80) cc_final: 0.7672 (m-80) REVERT: H 98 THR cc_start: 0.6040 (m) cc_final: 0.5833 (m) REVERT: H 196 THR cc_start: 0.8625 (p) cc_final: 0.8422 (t) REVERT: H 219 THR cc_start: 0.7395 (OUTLIER) cc_final: 0.7099 (t) outliers start: 90 outliers final: 36 residues processed: 378 average time/residue: 1.2998 time to fit residues: 563.1956 Evaluate side-chains 349 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 295 time to evaluate : 2.501 ------------------------------------------------------------------------------- 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 373 CYS 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 713 HIS Chi-restraints excluded: chain A residue 740 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 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 130 MET Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 205 LYS 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 115 VAL Chi-restraints excluded: chain E residue 143 ASP 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 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 243 ASP 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 219 THR Chi-restraints excluded: chain H residue 233 VAL 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: 7.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN C 37 HIS C 257 GLN C 285 HIS ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 166 ASN F 8 GLN F 36 ASN F 38 GLN F 213 ASN G 71 ASN H 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 22309 Z= 0.447 Angle : 0.651 8.918 30398 Z= 0.333 Chirality : 0.045 0.188 3536 Planarity : 0.005 0.071 3723 Dihedral : 14.521 153.453 3463 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.80 % Allowed : 17.36 % Favored : 76.84 % 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: 0.75 (0.14), residues: 1271 sheet: -0.47 (0.22), residues: 513 loop : -0.43 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 253 HIS 0.029 0.002 HIS A 713 PHE 0.016 0.002 PHE D 76 TYR 0.019 0.002 TYR B 279 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 449 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 315 time to evaluate : 2.680 Fit side-chains REVERT: A 353 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 387 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 531 MET cc_start: 0.6646 (mmt) cc_final: 0.6131 (mmt) REVERT: A 534 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6655 (p0) REVERT: A 560 TYR cc_start: 0.7875 (m-80) cc_final: 0.7420 (m-80) REVERT: A 758 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8252 (tp) REVERT: A 806 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.5989 (mm-30) REVERT: A 822 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: A 853 MET cc_start: 0.7449 (ppp) cc_final: 0.6780 (mmm) REVERT: B 104 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: B 207 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: B 249 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: B 315 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 336 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: C 50 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: C 86 MET cc_start: 0.8845 (mmm) cc_final: 0.8528 (mmm) REVERT: C 130 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8645 (mtp) REVERT: C 307 ASP cc_start: 0.8276 (m-30) cc_final: 0.8045 (m-30) REVERT: D 47 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8214 (mmtm) REVERT: D 209 GLN cc_start: 0.8189 (tt0) cc_final: 0.7900 (mt0) REVERT: D 288 LYS cc_start: 0.8623 (mptt) cc_final: 0.8410 (mptp) REVERT: D 290 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: D 316 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5516 (mp0) REVERT: E 11 CYS cc_start: 0.7985 (m) cc_final: 0.7769 (p) REVERT: E 83 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: E 139 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8518 (mtpt) REVERT: F 1 MET cc_start: 0.7882 (tpp) cc_final: 0.7467 (tpt) REVERT: F 17 GLU cc_start: 0.7646 (tp30) cc_final: 0.7372 (tp30) REVERT: F 21 ASP cc_start: 0.6993 (t0) cc_final: 0.6761 (t0) REVERT: F 72 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8637 (tm) REVERT: F 87 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7282 (pp) REVERT: F 144 PHE cc_start: 0.8558 (t80) cc_final: 0.8215 (t80) REVERT: F 240 LYS cc_start: 0.8352 (tppp) cc_final: 0.7936 (mtmp) REVERT: F 248 LYS cc_start: 0.8435 (mttt) cc_final: 0.7590 (mtpt) REVERT: G 61 ARG cc_start: 0.7947 (ptt180) cc_final: 0.7567 (ptt-90) REVERT: G 77 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8333 (ptpt) REVERT: G 116 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: G 147 ILE cc_start: 0.8862 (tt) cc_final: 0.8599 (mt) REVERT: G 199 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6636 (mpt) REVERT: G 222 SER cc_start: 0.8229 (m) cc_final: 0.7688 (t) REVERT: H 219 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7373 (t) outliers start: 134 outliers final: 54 residues processed: 403 average time/residue: 1.2972 time to fit residues: 598.0414 Evaluate side-chains 372 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 297 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS 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 534 ASP 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 806 GLU 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 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 249 GLU Chi-restraints excluded: chain B residue 315 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 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 191 THR 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 D residue 316 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 115 VAL 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 333 GLU Chi-restraints excluded: chain F residue 19 LEU 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 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 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 116 MET Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET 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 99 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN C 37 HIS C 317 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN F 8 GLN F 213 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22309 Z= 0.180 Angle : 0.522 8.124 30398 Z= 0.270 Chirality : 0.039 0.169 3536 Planarity : 0.004 0.071 3723 Dihedral : 14.340 158.916 3463 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.90 % Allowed : 20.56 % Favored : 75.54 % 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: 0.48 (0.17), residues: 2623 helix: 1.13 (0.15), residues: 1269 sheet: -0.35 (0.22), residues: 502 loop : -0.32 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.005 0.001 HIS A 713 PHE 0.012 0.001 PHE A 632 TYR 0.016 0.001 TYR H 133 ARG 0.007 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 396 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 306 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 354 MET cc_start: 0.7731 (mtm) cc_final: 0.7274 (ttp) REVERT: A 387 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8158 (mp) REVERT: A 531 MET cc_start: 0.6693 (mmt) cc_final: 0.6306 (mmt) REVERT: A 560 TYR cc_start: 0.7796 (m-80) cc_final: 0.7407 (m-80) REVERT: A 740 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7946 (tp) REVERT: A 758 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8228 (tp) REVERT: A 822 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: A 847 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7722 (tt0) REVERT: A 852 LYS cc_start: 0.7860 (tppt) cc_final: 0.7554 (tttt) REVERT: A 853 MET cc_start: 0.7318 (ppp) cc_final: 0.6687 (mmm) REVERT: B 104 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: B 315 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: B 336 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: B 348 THR cc_start: 0.8982 (m) cc_final: 0.8669 (p) REVERT: C 50 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: C 86 MET cc_start: 0.8794 (mmm) cc_final: 0.8475 (mmm) REVERT: C 126 GLU cc_start: 0.8529 (mp0) cc_final: 0.8309 (mp0) REVERT: C 130 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8582 (mtp) REVERT: C 307 ASP cc_start: 0.8246 (m-30) cc_final: 0.8017 (m-30) REVERT: D 205 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8218 (ptmt) REVERT: D 209 GLN cc_start: 0.8160 (tt0) cc_final: 0.7880 (mt0) REVERT: D 290 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: D 316 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5336 (mp0) REVERT: E 11 CYS cc_start: 0.8010 (m) cc_final: 0.7790 (p) REVERT: E 83 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6854 (tp30) REVERT: E 139 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8521 (mtpt) REVERT: E 217 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: F 1 MET cc_start: 0.7805 (tpp) cc_final: 0.7384 (tpt) REVERT: F 17 GLU cc_start: 0.7508 (tp30) cc_final: 0.7011 (tp30) REVERT: F 21 ASP cc_start: 0.7048 (t0) cc_final: 0.6717 (t0) REVERT: F 87 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7254 (pp) REVERT: F 182 LEU cc_start: 0.3293 (OUTLIER) cc_final: 0.3070 (tp) REVERT: F 240 LYS cc_start: 0.8339 (tppp) cc_final: 0.7902 (mtmp) REVERT: F 248 LYS cc_start: 0.8412 (mttt) cc_final: 0.7546 (mtpt) REVERT: G 61 ARG cc_start: 0.7911 (ptt180) cc_final: 0.7613 (ptt-90) REVERT: G 77 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8258 (ptpt) REVERT: G 116 MET cc_start: 0.8143 (mmp) cc_final: 0.7813 (mmm) REVERT: G 132 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7087 (pp20) REVERT: G 147 ILE cc_start: 0.8819 (tt) cc_final: 0.8550 (mt) REVERT: G 222 SER cc_start: 0.8225 (m) cc_final: 0.7689 (t) REVERT: G 250 TYR cc_start: 0.8674 (m-80) cc_final: 0.7594 (m-80) outliers start: 90 outliers final: 34 residues processed: 364 average time/residue: 1.2873 time to fit residues: 536.2450 Evaluate side-chains 339 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 287 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE 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 822 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 315 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 D residue 38 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 217 GLU 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 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE 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 64 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 243 ASP 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 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: 2.9990 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN F 8 GLN F 38 GLN F 213 ASN H 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2700 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= 0.233 Angle : 0.539 7.776 30398 Z= 0.277 Chirality : 0.040 0.166 3536 Planarity : 0.004 0.071 3723 Dihedral : 14.214 160.920 3458 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.89 % Allowed : 19.83 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2623 helix: 1.26 (0.15), residues: 1271 sheet: -0.41 (0.22), residues: 514 loop : -0.24 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.006 0.001 HIS A 713 PHE 0.022 0.001 PHE F 144 TYR 0.014 0.001 TYR A 291 ARG 0.010 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 415 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 302 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 387 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 531 MET cc_start: 0.6679 (mmt) cc_final: 0.6204 (mmt) REVERT: A 534 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6566 (p0) REVERT: A 560 TYR cc_start: 0.7830 (m-80) cc_final: 0.7448 (m-80) REVERT: A 758 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8242 (tp) REVERT: A 806 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5822 (mm-30) REVERT: A 822 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: A 853 MET cc_start: 0.7295 (ppp) cc_final: 0.6696 (mmm) REVERT: B 104 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: B 315 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: B 336 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: B 348 THR cc_start: 0.8983 (m) cc_final: 0.8643 (p) REVERT: C 50 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: C 86 MET cc_start: 0.8805 (mmm) cc_final: 0.8517 (mmm) REVERT: C 126 GLU cc_start: 0.8534 (mp0) cc_final: 0.8290 (mp0) REVERT: C 130 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8596 (mtp) REVERT: C 307 ASP cc_start: 0.8257 (m-30) cc_final: 0.8025 (m-30) REVERT: D 205 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8276 (ptmt) REVERT: D 209 GLN cc_start: 0.8171 (tt0) cc_final: 0.7884 (mt0) REVERT: D 290 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: D 316 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5395 (mp0) REVERT: E 11 CYS cc_start: 0.7968 (m) cc_final: 0.7767 (p) REVERT: E 83 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6891 (tp30) REVERT: E 139 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8512 (mttt) REVERT: F 1 MET cc_start: 0.7742 (tpp) cc_final: 0.7325 (tpt) REVERT: F 17 GLU cc_start: 0.7482 (tp30) cc_final: 0.7176 (tp30) REVERT: F 21 ASP cc_start: 0.7016 (t0) cc_final: 0.6657 (t0) REVERT: F 53 ARG cc_start: 0.8089 (mpp80) cc_final: 0.7738 (mpp80) REVERT: F 87 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7316 (pp) REVERT: F 144 PHE cc_start: 0.8445 (t80) cc_final: 0.8170 (t80) REVERT: F 182 LEU cc_start: 0.3762 (OUTLIER) cc_final: 0.3508 (tp) REVERT: F 240 LYS cc_start: 0.8330 (tppp) cc_final: 0.7888 (mtmp) REVERT: F 248 LYS cc_start: 0.8408 (mttt) cc_final: 0.7536 (mtpt) REVERT: G 61 ARG cc_start: 0.7934 (ptt180) cc_final: 0.7610 (ptt-90) REVERT: G 77 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8306 (ptpt) REVERT: G 80 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7729 (tptm) REVERT: G 116 MET cc_start: 0.8162 (mmp) cc_final: 0.7924 (mmm) REVERT: G 132 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7097 (pp20) REVERT: G 147 ILE cc_start: 0.8828 (tt) cc_final: 0.8558 (mt) REVERT: G 222 SER cc_start: 0.8258 (m) cc_final: 0.7722 (t) REVERT: G 250 TYR cc_start: 0.8681 (m-80) cc_final: 0.7598 (m-80) REVERT: H 257 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6305 (t70) outliers start: 113 outliers final: 54 residues processed: 376 average time/residue: 1.3105 time to fit residues: 562.5886 Evaluate side-chains 363 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 290 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS 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 534 ASP 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 758 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 822 GLU 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 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 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 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 137 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 115 VAL 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 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 159 VAL Chi-restraints excluded: chain F residue 170 SER 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 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 235 LEU Chi-restraints excluded: chain G residue 243 ASP 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 196 THR 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: 6.9990 chunk 28 optimal weight: 0.0670 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 215 optimal weight: 0.3980 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 155 optimal weight: 0.0870 chunk 117 optimal weight: 5.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 257 GLN C 317 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN F 8 GLN F 213 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22309 Z= 0.163 Angle : 0.521 9.277 30398 Z= 0.267 Chirality : 0.039 0.192 3536 Planarity : 0.004 0.070 3723 Dihedral : 14.081 160.782 3458 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.98 % Allowed : 21.47 % Favored : 74.55 % 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: 0.79 (0.17), residues: 2623 helix: 1.44 (0.15), residues: 1271 sheet: -0.33 (0.22), residues: 511 loop : -0.17 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.006 0.001 HIS A 713 PHE 0.016 0.001 PHE F 144 TYR 0.015 0.001 TYR A 291 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 405 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 313 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 531 MET cc_start: 0.6636 (mmt) cc_final: 0.6173 (mmt) REVERT: A 534 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6568 (p0) REVERT: A 560 TYR cc_start: 0.7802 (m-80) cc_final: 0.7439 (m-80) REVERT: A 822 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7462 (pp20) REVERT: A 852 LYS cc_start: 0.7808 (tppt) cc_final: 0.7491 (tttt) REVERT: A 853 MET cc_start: 0.7221 (ppp) cc_final: 0.6645 (mmm) REVERT: B 104 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: B 207 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: B 315 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 336 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: B 348 THR cc_start: 0.8959 (m) cc_final: 0.8646 (p) REVERT: C 50 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: C 86 MET cc_start: 0.8781 (mmm) cc_final: 0.8489 (mmm) REVERT: C 126 GLU cc_start: 0.8557 (mp0) cc_final: 0.8254 (mp0) REVERT: C 130 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8583 (mtp) REVERT: C 307 ASP cc_start: 0.8244 (m-30) cc_final: 0.8018 (m-30) REVERT: D 209 GLN cc_start: 0.8144 (tt0) cc_final: 0.7870 (mt0) REVERT: D 290 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: D 329 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: E 11 CYS cc_start: 0.7992 (m) cc_final: 0.7773 (p) REVERT: E 83 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6853 (tp30) REVERT: E 139 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8502 (mttt) REVERT: F 1 MET cc_start: 0.7696 (tpp) cc_final: 0.7182 (tpt) REVERT: F 17 GLU cc_start: 0.7358 (tp30) cc_final: 0.7094 (tp30) REVERT: F 21 ASP cc_start: 0.7048 (t0) cc_final: 0.6796 (t0) REVERT: F 53 ARG cc_start: 0.8080 (mpp80) cc_final: 0.7767 (mpp80) REVERT: F 64 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7776 (mtm110) REVERT: F 87 ILE cc_start: 0.7569 (mp) cc_final: 0.7252 (pp) REVERT: F 182 LEU cc_start: 0.3708 (OUTLIER) cc_final: 0.3449 (tp) REVERT: F 214 PHE cc_start: 0.8553 (m-10) cc_final: 0.7661 (m-10) REVERT: F 240 LYS cc_start: 0.8322 (tppp) cc_final: 0.7858 (mtmp) REVERT: F 248 LYS cc_start: 0.8385 (mttt) cc_final: 0.7530 (mtpt) REVERT: G 61 ARG cc_start: 0.7933 (ptt180) cc_final: 0.7638 (ptt-90) REVERT: G 77 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8381 (ptmt) REVERT: G 78 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8406 (mp) REVERT: G 80 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7706 (tptm) REVERT: G 116 MET cc_start: 0.8160 (mmp) cc_final: 0.7875 (mmm) REVERT: G 132 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: G 147 ILE cc_start: 0.8802 (tt) cc_final: 0.8525 (mt) REVERT: G 175 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8218 (mt) REVERT: G 222 SER cc_start: 0.8256 (m) cc_final: 0.7767 (t) REVERT: G 250 TYR cc_start: 0.8650 (m-80) cc_final: 0.7598 (m-80) REVERT: H 16 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8595 (tm) outliers start: 92 outliers final: 47 residues processed: 372 average time/residue: 1.2745 time to fit residues: 542.5611 Evaluate side-chains 356 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 291 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS 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 508 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 822 GLU 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 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 315 GLU 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 178 THR Chi-restraints excluded: chain C residue 288 VAL 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 137 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 30 ILE 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 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 170 SER 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 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 175 LEU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 8.9990 chunk 101 optimal weight: 0.0060 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 161 optimal weight: 0.3980 chunk 173 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- 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 ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN F 8 GLN F 213 ASN H 38 GLN H 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22309 Z= 0.188 Angle : 0.537 11.052 30398 Z= 0.272 Chirality : 0.040 0.186 3536 Planarity : 0.004 0.068 3723 Dihedral : 14.032 161.289 3458 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.16 % Allowed : 21.82 % Favored : 74.03 % 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: 0.84 (0.17), residues: 2623 helix: 1.48 (0.15), residues: 1268 sheet: -0.27 (0.22), residues: 512 loop : -0.15 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.006 0.001 HIS A 713 PHE 0.012 0.001 PHE A 632 TYR 0.015 0.001 TYR A 291 ARG 0.008 0.000 ARG C 264 *********************** 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 390 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 294 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7630 (mtm) cc_final: 0.7291 (ttp) REVERT: A 387 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 419 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7971 (mpp) REVERT: A 531 MET cc_start: 0.6672 (mmt) cc_final: 0.6171 (mmt) REVERT: A 534 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6571 (p0) REVERT: A 560 TYR cc_start: 0.7803 (m-80) cc_final: 0.7433 (m-80) REVERT: A 807 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.5420 (mmt180) REVERT: A 822 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7436 (pp20) REVERT: A 852 LYS cc_start: 0.7895 (tppt) cc_final: 0.7576 (tttt) REVERT: A 853 MET cc_start: 0.7168 (ppp) cc_final: 0.6595 (mmm) REVERT: B 104 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: B 110 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: B 207 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: B 315 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: B 336 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: B 348 THR cc_start: 0.8966 (m) cc_final: 0.8637 (p) REVERT: C 50 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: C 86 MET cc_start: 0.8776 (mmm) cc_final: 0.8499 (mmm) REVERT: C 126 GLU cc_start: 0.8568 (mp0) cc_final: 0.8261 (mp0) REVERT: C 130 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8593 (mtp) REVERT: C 307 ASP cc_start: 0.8248 (m-30) cc_final: 0.8022 (m-30) REVERT: D 209 GLN cc_start: 0.8154 (tt0) cc_final: 0.7870 (mt0) REVERT: D 290 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: D 316 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5118 (mp0) REVERT: E 11 CYS cc_start: 0.8017 (m) cc_final: 0.7805 (p) REVERT: E 83 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6877 (tp30) REVERT: E 139 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8496 (mttt) REVERT: F 1 MET cc_start: 0.7598 (tpp) cc_final: 0.7202 (tpt) REVERT: F 17 GLU cc_start: 0.7328 (tp30) cc_final: 0.6879 (tp30) REVERT: F 21 ASP cc_start: 0.7050 (t0) cc_final: 0.6679 (t0) REVERT: F 53 ARG cc_start: 0.8131 (mpp80) cc_final: 0.7835 (mpp80) REVERT: F 87 ILE cc_start: 0.7601 (mp) cc_final: 0.7291 (pp) REVERT: F 182 LEU cc_start: 0.3751 (OUTLIER) cc_final: 0.3471 (tp) REVERT: F 240 LYS cc_start: 0.8337 (tppp) cc_final: 0.7810 (mtmp) REVERT: F 248 LYS cc_start: 0.8394 (mttt) cc_final: 0.7520 (mtpt) REVERT: G 61 ARG cc_start: 0.7941 (ptt180) cc_final: 0.7618 (ptt-90) REVERT: G 77 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8333 (ptpt) REVERT: G 78 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8443 (mp) REVERT: G 116 MET cc_start: 0.8189 (mmp) cc_final: 0.7946 (mmm) REVERT: G 132 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7115 (pp20) REVERT: G 147 ILE cc_start: 0.8785 (tt) cc_final: 0.8510 (mt) REVERT: G 222 SER cc_start: 0.8272 (m) cc_final: 0.7786 (t) REVERT: G 250 TYR cc_start: 0.8660 (m-80) cc_final: 0.7597 (m-80) REVERT: H 257 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.6174 (t70) outliers start: 96 outliers final: 52 residues processed: 356 average time/residue: 1.3059 time to fit residues: 531.6423 Evaluate side-chains 357 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 285 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ASP 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 807 ARG Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 822 GLU 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 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 315 GLU 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 157 TYR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 288 VAL 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 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 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 115 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 30 ILE 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 121 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 170 SER 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 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 180 ILE 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 196 THR Chi-restraints excluded: chain H residue 233 VAL 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: 8.9990 chunk 222 optimal weight: 0.5980 chunk 237 optimal weight: 0.2980 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN F 8 GLN H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22309 Z= 0.179 Angle : 0.539 10.368 30398 Z= 0.274 Chirality : 0.039 0.206 3536 Planarity : 0.004 0.068 3723 Dihedral : 13.954 161.293 3455 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.29 % Allowed : 22.81 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2623 helix: 1.53 (0.15), residues: 1269 sheet: -0.27 (0.22), residues: 513 loop : -0.11 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.006 0.001 HIS A 713 PHE 0.038 0.001 PHE F 144 TYR 0.016 0.001 TYR H 133 ARG 0.008 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 373 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 297 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7680 (mtm) cc_final: 0.7333 (ttp) REVERT: A 387 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 531 MET cc_start: 0.6666 (mmt) cc_final: 0.6152 (mmt) REVERT: A 534 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6557 (p0) REVERT: A 560 TYR cc_start: 0.7803 (m-80) cc_final: 0.7438 (m-80) REVERT: A 807 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.5304 (mmt180) REVERT: A 822 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7437 (pp20) REVERT: A 853 MET cc_start: 0.7160 (ppp) cc_final: 0.6594 (mmm) REVERT: B 104 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: B 315 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: B 336 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: B 348 THR cc_start: 0.8955 (m) cc_final: 0.8633 (p) REVERT: C 50 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: C 86 MET cc_start: 0.8760 (mmm) cc_final: 0.8486 (mmm) REVERT: C 126 GLU cc_start: 0.8567 (mp0) cc_final: 0.8261 (mp0) REVERT: C 130 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8587 (mtp) REVERT: C 307 ASP cc_start: 0.8245 (m-30) cc_final: 0.8022 (m-30) REVERT: D 113 GLU cc_start: 0.6976 (mp0) cc_final: 0.6479 (mp0) REVERT: D 209 GLN cc_start: 0.8148 (tt0) cc_final: 0.7865 (mt0) REVERT: D 290 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: D 316 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5080 (mp0) REVERT: D 329 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: E 11 CYS cc_start: 0.8014 (m) cc_final: 0.7790 (p) REVERT: E 83 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: E 139 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8496 (mttt) REVERT: F 1 MET cc_start: 0.7492 (tpp) cc_final: 0.7220 (tpt) REVERT: F 17 GLU cc_start: 0.7298 (tp30) cc_final: 0.6850 (tp30) REVERT: F 21 ASP cc_start: 0.7068 (t0) cc_final: 0.6738 (t0) REVERT: F 53 ARG cc_start: 0.8117 (mpp80) cc_final: 0.7851 (mpp80) REVERT: F 87 ILE cc_start: 0.7594 (mp) cc_final: 0.7286 (pp) REVERT: F 91 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7695 (ttp-110) REVERT: F 182 LEU cc_start: 0.3784 (OUTLIER) cc_final: 0.3502 (tp) REVERT: F 214 PHE cc_start: 0.8564 (m-10) cc_final: 0.8114 (m-10) REVERT: F 240 LYS cc_start: 0.8333 (tppp) cc_final: 0.7808 (mtmp) REVERT: F 248 LYS cc_start: 0.8386 (mttt) cc_final: 0.7537 (mtpt) REVERT: G 61 ARG cc_start: 0.7937 (ptt180) cc_final: 0.7614 (ptt-90) REVERT: G 77 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8378 (ptmt) REVERT: G 78 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8453 (mp) REVERT: G 116 MET cc_start: 0.8166 (mmp) cc_final: 0.7930 (mmm) REVERT: G 132 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7139 (pp20) REVERT: G 147 ILE cc_start: 0.8779 (tt) cc_final: 0.8501 (mt) REVERT: G 222 SER cc_start: 0.8263 (m) cc_final: 0.7776 (t) REVERT: G 250 TYR cc_start: 0.8652 (m-80) cc_final: 0.7558 (m-80) REVERT: H 257 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.6221 (t70) outliers start: 76 outliers final: 50 residues processed: 350 average time/residue: 1.2804 time to fit residues: 511.8184 Evaluate side-chains 354 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 286 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ASP 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 807 ARG Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 822 GLU 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 219 GLU Chi-restraints excluded: chain B residue 315 GLU 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 157 TYR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 288 VAL 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 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 30 ILE 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 121 LEU 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 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 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 H residue 66 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 257 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 29 GLN C 317 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN F 8 GLN H 38 GLN H 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22309 Z= 0.237 Angle : 0.569 11.142 30398 Z= 0.288 Chirality : 0.041 0.222 3536 Planarity : 0.004 0.068 3723 Dihedral : 14.003 161.657 3455 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.64 % Allowed : 22.51 % Favored : 73.85 % 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: 0.83 (0.17), residues: 2623 helix: 1.46 (0.15), residues: 1268 sheet: -0.28 (0.22), residues: 509 loop : -0.16 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.006 0.001 HIS C 37 PHE 0.012 0.001 PHE A 632 TYR 0.015 0.001 TYR A 291 ARG 0.008 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 373 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 289 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ASP cc_start: 0.7439 (t0) cc_final: 0.7003 (t0) REVERT: A 354 MET cc_start: 0.7670 (mtm) cc_final: 0.7323 (ttp) REVERT: A 387 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8203 (mp) REVERT: A 419 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8026 (mpp) REVERT: A 531 MET cc_start: 0.6633 (mmt) cc_final: 0.6093 (mmt) REVERT: A 534 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6538 (p0) REVERT: A 560 TYR cc_start: 0.7829 (m-80) cc_final: 0.7472 (m-80) REVERT: A 822 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7479 (pp20) REVERT: A 852 LYS cc_start: 0.7820 (tppt) cc_final: 0.7453 (tttt) REVERT: A 853 MET cc_start: 0.7196 (ppp) cc_final: 0.6620 (mmm) REVERT: B 104 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: B 110 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: B 315 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: B 336 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: B 348 THR cc_start: 0.8968 (m) cc_final: 0.8631 (p) REVERT: C 86 MET cc_start: 0.8752 (mmm) cc_final: 0.8508 (mmm) REVERT: C 126 GLU cc_start: 0.8576 (mp0) cc_final: 0.8294 (mp0) REVERT: C 130 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8596 (mtp) REVERT: C 307 ASP cc_start: 0.8265 (m-30) cc_final: 0.8056 (m-30) REVERT: D 209 GLN cc_start: 0.8153 (tt0) cc_final: 0.7862 (mt0) REVERT: D 290 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: D 316 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5223 (mp0) REVERT: E 83 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6887 (tp30) REVERT: E 139 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8498 (mttt) REVERT: F 1 MET cc_start: 0.7448 (tpp) cc_final: 0.7169 (tpt) REVERT: F 17 GLU cc_start: 0.7379 (tp30) cc_final: 0.6918 (tp30) REVERT: F 21 ASP cc_start: 0.7062 (t0) cc_final: 0.6728 (t0) REVERT: F 53 ARG cc_start: 0.8130 (mpp80) cc_final: 0.7872 (mpp80) REVERT: F 87 ILE cc_start: 0.7625 (mp) cc_final: 0.7308 (pp) REVERT: F 182 LEU cc_start: 0.3991 (OUTLIER) cc_final: 0.3670 (tp) REVERT: F 214 PHE cc_start: 0.8535 (m-10) cc_final: 0.8053 (m-10) REVERT: F 240 LYS cc_start: 0.8391 (tppp) cc_final: 0.7829 (mtmp) REVERT: F 248 LYS cc_start: 0.8407 (mttt) cc_final: 0.7540 (mtpt) REVERT: G 61 ARG cc_start: 0.7964 (ptt180) cc_final: 0.7633 (ptt-90) REVERT: G 77 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8382 (ptmt) REVERT: G 116 MET cc_start: 0.8185 (mmp) cc_final: 0.7954 (mmm) REVERT: G 132 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: G 147 ILE cc_start: 0.8843 (tt) cc_final: 0.8569 (mt) REVERT: G 222 SER cc_start: 0.8279 (m) cc_final: 0.7773 (t) REVERT: G 250 TYR cc_start: 0.8666 (m-80) cc_final: 0.7588 (m-80) outliers start: 84 outliers final: 51 residues processed: 342 average time/residue: 1.2636 time to fit residues: 497.2540 Evaluate side-chains 343 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 277 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ASP 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 A residue 822 GLU 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 191 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 257 GLN 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 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 316 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 115 VAL 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 70 VAL Chi-restraints excluded: chain F residue 73 THR 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 170 SER 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 235 LEU Chi-restraints excluded: chain H residue 66 LEU 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 196 THR 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: 0.9990 chunk 64 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 257 GLN C 317 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN F 8 GLN H 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.160677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122480 restraints weight = 27103.319| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.32 r_work: 0.3318 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22309 Z= 0.212 Angle : 0.555 10.971 30398 Z= 0.282 Chirality : 0.040 0.237 3536 Planarity : 0.004 0.069 3723 Dihedral : 13.980 161.738 3455 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.29 % Allowed : 22.99 % 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: 0.86 (0.17), residues: 2623 helix: 1.48 (0.15), residues: 1270 sheet: -0.28 (0.22), residues: 512 loop : -0.11 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 28 HIS 0.006 0.001 HIS C 37 PHE 0.041 0.001 PHE F 144 TYR 0.016 0.001 TYR H 133 ARG 0.008 0.000 ARG C 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8900.10 seconds wall clock time: 155 minutes 54.71 seconds (9354.71 seconds total)