Starting phenix.real_space_refine on Tue Jul 23 09:33:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umv_42385/07_2024/8umv_42385_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umv_42385/07_2024/8umv_42385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umv_42385/07_2024/8umv_42385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umv_42385/07_2024/8umv_42385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umv_42385/07_2024/8umv_42385_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umv_42385/07_2024/8umv_42385_neut.cif" } resolution = 2.75 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= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 329 atoms to isotropic. 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 "E ARG 57": "NH1" <-> "NH2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "G TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 256": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-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: 11.41, per 1000 atoms: 0.52 Number of scatterers: 21860 At special positions: 0 Unit cell: (116.748, 128.34, 138.276, 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: 8.49 Conformation dependent library (CDL) restraints added in 3.9 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: 120 helices and 14 sheets defined 52.3% alpha, 14.4% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 7.08 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.690A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.646A pdb=" N LEU A 351 " --> pdb=" O HIS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.508A pdb=" N ARG A 410 " --> pdb=" O PRO A 406 " (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 removed outlier: 4.093A pdb=" N GLN A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.911A pdb=" N SER A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.699A 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: 4.056A 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 698 removed outlier: 3.686A pdb=" N LEU A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A 696 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 697 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 698 - end of helix Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.652A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 744 removed outlier: 3.617A pdb=" N GLY A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.565A 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 769 Processing helix chain 'A' and resid 777 through 781 Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.841A 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: 3.545A 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 119 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.686A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.587A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 255 removed outlier: 3.925A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 272 removed outlier: 4.230A pdb=" N LEU B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.901A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.555A pdb=" N LYS B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.591A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.698A 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: 3.517A 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 103 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: 3.749A pdb=" N ARG C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.546A 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 194 removed outlier: 3.554A 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: 3.993A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.592A 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 289 removed outlier: 3.897A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.514A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 83 through 97 removed outlier: 3.596A 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: 3.802A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.473A 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: 3.855A 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 Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.519A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.641A 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: 4.204A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.927A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.839A 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: 3.894A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 6.920A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 118 removed outlier: 3.812A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 115 " --> pdb=" O MET E 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 removed outlier: 3.792A pdb=" N ARG E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG E 150 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.796A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.547A 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: 3.551A pdb=" N VAL E 253 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 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: 4.119A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.516A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 removed outlier: 3.671A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.774A 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: 3.721A 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 72 through 81 removed outlier: 4.040A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.710A 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 74 through 82 removed outlier: 3.655A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 152 through 154 No H-bonds generated for 'chain 'H' and resid 152 through 154' Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.625A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.689A 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 222 Proline residue: H 220 - end of helix No H-bonds generated for 'chain 'H' and resid 217 through 222' 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 397 removed outlier: 6.130A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.251A 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: 6.113A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.174A 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: 6.184A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.377A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 5.989A 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: 6.758A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS E 37 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL E 182 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 57 through 62 removed outlier: 6.558A pdb=" N ARG F 5 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR F 60 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU F 3 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL G 167 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.307A 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: 6.909A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.085A 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 180 removed outlier: 3.507A pdb=" N ILE F 180 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE F 169 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.148A 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: 3.806A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.790A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 59 through 62 removed outlier: 4.102A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 67 through 71 removed outlier: 6.809A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3174 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: 7.92 Time building geometry restraints manager: 9.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7147 1.35 - 1.50: 5639 1.50 - 1.65: 9315 1.65 - 1.80: 85 1.80 - 1.95: 123 Bond restraints: 22309 Sorted by residual: bond pdb=" N LEU H 247 " pdb=" CA LEU H 247 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.25e-02 6.40e+03 9.23e+00 bond pdb=" N VAL G 123 " pdb=" CA VAL G 123 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.46e+00 bond pdb=" C VAL G 158 " pdb=" O VAL G 158 " ideal model delta sigma weight residual 1.238 1.207 0.031 1.10e-02 8.26e+03 7.79e+00 bond pdb=" N LEU F 118 " pdb=" CA LEU F 118 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.37e-02 5.33e+03 7.72e+00 bond pdb=" N MET F 244 " pdb=" CA MET F 244 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.27e-02 6.20e+03 7.58e+00 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.81: 735 105.81 - 113.33: 12510 113.33 - 120.85: 10075 120.85 - 128.37: 6933 128.37 - 135.89: 145 Bond angle restraints: 30398 Sorted by residual: angle pdb=" N MET F 119 " pdb=" CA MET F 119 " pdb=" C MET F 119 " ideal model delta sigma weight residual 109.95 100.50 9.45 1.59e+00 3.96e-01 3.53e+01 angle pdb=" N ARG E 234 " pdb=" CA ARG E 234 " pdb=" C ARG E 234 " ideal model delta sigma weight residual 111.36 105.24 6.12 1.09e+00 8.42e-01 3.16e+01 angle pdb=" N PRO A 819 " pdb=" CA PRO A 819 " pdb=" C PRO A 819 " ideal model delta sigma weight residual 112.47 100.94 11.53 2.06e+00 2.36e-01 3.13e+01 angle pdb=" N VAL G 158 " pdb=" CA VAL G 158 " pdb=" C VAL G 158 " ideal model delta sigma weight residual 107.75 114.37 -6.62 1.46e+00 4.69e-01 2.06e+01 angle pdb=" N GLU F 124 " pdb=" CA GLU F 124 " pdb=" C GLU F 124 " ideal model delta sigma weight residual 110.32 103.18 7.14 1.59e+00 3.96e-01 2.01e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.73: 13010 30.73 - 61.45: 601 61.45 - 92.18: 21 92.18 - 122.91: 1 122.91 - 153.63: 2 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 300.00 146.37 153.63 1 2.00e+01 2.50e-03 4.55e+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 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET G 199 " pdb=" C MET G 199 " pdb=" N ASN G 200 " pdb=" CA ASN G 200 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2624 0.044 - 0.088: 666 0.088 - 0.133: 205 0.133 - 0.177: 32 0.177 - 0.221: 9 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CA MET F 119 " pdb=" N MET F 119 " pdb=" C MET F 119 " pdb=" CB MET F 119 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU H 247 " pdb=" N LEU H 247 " pdb=" C LEU H 247 " pdb=" CB LEU H 247 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+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 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3533 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.067 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO A 699 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 162 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C CYS F 162 " 0.061 2.00e-02 2.50e+03 pdb=" O CYS F 162 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA F 163 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 119 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C MET F 119 " 0.055 2.00e-02 2.50e+03 pdb=" O MET F 119 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP F 120 " -0.019 2.00e-02 2.50e+03 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 219 2.63 - 3.20: 17570 3.20 - 3.76: 34742 3.76 - 4.33: 48344 4.33 - 4.90: 79185 Nonbonded interactions: 180060 Sorted by model distance: nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.062 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.071 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.082 2.170 nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.084 2.170 nonbonded pdb=" OG1 THR C 67 " pdb="MG MG C 401 " model vdw 2.090 2.170 ... (remaining 180055 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 61.030 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.003 0.059 22309 Z= 0.228 Angle : 0.685 11.525 30398 Z= 0.401 Chirality : 0.045 0.221 3536 Planarity : 0.007 0.122 3723 Dihedral : 15.432 153.633 8597 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.69 % Allowed : 9.22 % Favored : 89.09 % 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: -1.56 (0.15), residues: 2623 helix: -1.15 (0.12), residues: 1249 sheet: -0.46 (0.22), residues: 540 loop : -0.85 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 253 HIS 0.003 0.001 HIS E 331 PHE 0.015 0.002 PHE A 409 TYR 0.017 0.002 TYR E 279 ARG 0.006 0.000 ARG D 193 *********************** 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 475 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 436 time to evaluate : 2.382 Fit side-chains REVERT: A 644 GLU cc_start: 0.6576 (mp0) cc_final: 0.6370 (mp0) REVERT: B 66 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 99 LYS cc_start: 0.8446 (mttt) cc_final: 0.8237 (mmtt) REVERT: B 307 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7443 (tm-30) REVERT: C 51 ASP cc_start: 0.7092 (t0) cc_final: 0.6816 (t0) REVERT: C 133 ASP cc_start: 0.7616 (m-30) cc_final: 0.7309 (m-30) REVERT: C 182 MET cc_start: 0.8468 (ttt) cc_final: 0.8216 (ttt) REVERT: D 56 GLU cc_start: 0.7840 (mp0) cc_final: 0.7537 (mp0) REVERT: D 275 ASP cc_start: 0.7523 (m-30) cc_final: 0.7226 (m-30) REVERT: D 294 LYS cc_start: 0.8134 (mttt) cc_final: 0.7892 (tttp) REVERT: D 356 MET cc_start: 0.8586 (ttp) cc_final: 0.8284 (ttp) REVERT: E 9 ARG cc_start: 0.8551 (ttp-170) cc_final: 0.8262 (ttt180) REVERT: E 31 GLN cc_start: 0.7410 (mt0) cc_final: 0.7084 (pt0) REVERT: F 150 ASP cc_start: 0.7626 (m-30) cc_final: 0.7396 (m-30) REVERT: F 199 MET cc_start: 0.7025 (ppp) cc_final: 0.6791 (ppp) REVERT: F 209 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6885 (mt) REVERT: F 213 ASN cc_start: 0.6575 (m-40) cc_final: 0.6356 (m-40) REVERT: F 215 PHE cc_start: 0.8227 (m-10) cc_final: 0.7929 (m-80) REVERT: F 248 LYS cc_start: 0.8103 (mttt) cc_final: 0.7605 (mptt) REVERT: G 23 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8124 (mm) REVERT: H 116 MET cc_start: 0.6385 (mtm) cc_final: 0.6173 (mtt) REVERT: H 196 THR cc_start: 0.7450 (p) cc_final: 0.7178 (t) outliers start: 39 outliers final: 9 residues processed: 460 average time/residue: 1.4253 time to fit residues: 738.0008 Evaluate side-chains 325 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 314 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 4.9990 chunk 200 optimal weight: 0.0470 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 595 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN B 268 GLN B 298 ASN C 285 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 194 HIS F 65 ASN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22309 Z= 0.309 Angle : 0.583 8.281 30398 Z= 0.303 Chirality : 0.042 0.186 3536 Planarity : 0.005 0.079 3723 Dihedral : 14.586 152.299 3470 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.94 % Allowed : 14.68 % Favored : 81.39 % 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: -0.23 (0.16), residues: 2623 helix: 0.34 (0.14), residues: 1266 sheet: -0.49 (0.21), residues: 538 loop : -0.41 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 28 HIS 0.007 0.001 HIS E 331 PHE 0.018 0.002 PHE A 632 TYR 0.015 0.002 TYR B 279 ARG 0.008 0.001 ARG G 149 *********************** 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: 91 poor density : 325 time to evaluate : 2.734 Fit side-chains revert: symmetry clash REVERT: A 487 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8025 (mt) REVERT: A 507 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8402 (tt) REVERT: A 591 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7886 (tm130) REVERT: A 830 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7638 (mm) REVERT: B 66 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 72 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8591 (tp) REVERT: B 99 LYS cc_start: 0.8458 (mttt) cc_final: 0.8143 (mmtt) REVERT: B 307 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 51 ASP cc_start: 0.7185 (t0) cc_final: 0.6898 (t0) REVERT: C 133 ASP cc_start: 0.7590 (m-30) cc_final: 0.7346 (m-30) REVERT: D 56 GLU cc_start: 0.7934 (mp0) cc_final: 0.7639 (mp0) REVERT: D 94 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: D 107 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: D 209 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: D 275 ASP cc_start: 0.7668 (m-30) cc_final: 0.7422 (m-30) REVERT: D 294 LYS cc_start: 0.8122 (mttt) cc_final: 0.7818 (tttp) REVERT: D 356 MET cc_start: 0.8667 (ttp) cc_final: 0.8432 (ttp) REVERT: E 9 ARG cc_start: 0.8618 (ttp-170) cc_final: 0.8245 (ttt180) REVERT: F 68 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7731 (mpp) REVERT: F 209 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7222 (mt) REVERT: F 211 TYR cc_start: 0.8421 (m-80) cc_final: 0.8038 (m-80) REVERT: F 214 PHE cc_start: 0.7439 (m-10) cc_final: 0.7168 (m-80) REVERT: F 215 PHE cc_start: 0.8396 (m-10) cc_final: 0.8033 (m-80) REVERT: F 248 LYS cc_start: 0.8017 (mttt) cc_final: 0.7457 (mptt) REVERT: G 23 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8062 (mm) REVERT: G 214 PHE cc_start: 0.8358 (m-10) cc_final: 0.8132 (m-10) REVERT: G 244 MET cc_start: 0.7108 (mpt) cc_final: 0.6806 (tpp) REVERT: G 248 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8114 (mmtt) REVERT: H 248 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7274 (tttp) outliers start: 91 outliers final: 39 residues processed: 381 average time/residue: 1.3697 time to fit residues: 592.2259 Evaluate side-chains 359 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 308 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 246 HIS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 240 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS F 38 GLN F 65 ASN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN G 246 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22309 Z= 0.275 Angle : 0.550 6.659 30398 Z= 0.286 Chirality : 0.041 0.181 3536 Planarity : 0.005 0.074 3723 Dihedral : 14.464 150.245 3465 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.37 % Allowed : 16.10 % Favored : 79.52 % 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: 0.20 (0.16), residues: 2623 helix: 0.83 (0.14), residues: 1269 sheet: -0.55 (0.21), residues: 548 loop : -0.23 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 28 HIS 0.005 0.001 HIS E 331 PHE 0.015 0.002 PHE A 632 TYR 0.014 0.002 TYR D 229 ARG 0.006 0.000 ARG H 149 *********************** 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 421 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 320 time to evaluate : 2.358 Fit side-chains revert: symmetry clash REVERT: A 487 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8078 (mt) REVERT: A 507 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8523 (tt) REVERT: A 630 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8059 (mm-40) REVERT: A 830 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7657 (mm) REVERT: A 839 GLN cc_start: 0.7593 (pm20) cc_final: 0.7362 (pm20) REVERT: B 66 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 72 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8571 (tp) REVERT: B 99 LYS cc_start: 0.8448 (mttt) cc_final: 0.8147 (mmtt) REVERT: B 307 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 51 ASP cc_start: 0.7156 (t0) cc_final: 0.6836 (t0) REVERT: C 75 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7853 (mtmt) REVERT: C 133 ASP cc_start: 0.7627 (m-30) cc_final: 0.7400 (m-30) REVERT: C 196 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7276 (p0) REVERT: D 56 GLU cc_start: 0.7951 (mp0) cc_final: 0.7629 (mp0) REVERT: D 121 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: D 209 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: D 275 ASP cc_start: 0.7714 (m-30) cc_final: 0.7452 (m-30) REVERT: D 294 LYS cc_start: 0.8115 (mttt) cc_final: 0.7857 (tttp) REVERT: D 356 MET cc_start: 0.8668 (ttp) cc_final: 0.8464 (ttp) REVERT: E 9 ARG cc_start: 0.8622 (ttp-170) cc_final: 0.8224 (ttt180) REVERT: E 205 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8154 (mt) REVERT: F 68 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7691 (mpp) REVERT: F 209 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7092 (mt) REVERT: F 211 TYR cc_start: 0.8436 (m-80) cc_final: 0.8121 (m-80) REVERT: F 214 PHE cc_start: 0.7406 (m-10) cc_final: 0.7071 (m-80) REVERT: F 248 LYS cc_start: 0.7989 (mttt) cc_final: 0.7455 (mptt) REVERT: G 214 PHE cc_start: 0.8402 (m-10) cc_final: 0.8192 (m-10) REVERT: H 88 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6741 (mm) outliers start: 101 outliers final: 41 residues processed: 387 average time/residue: 1.3427 time to fit residues: 589.6385 Evaluate side-chains 353 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 299 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 757 LEU 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 175 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 81 CYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 246 HIS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN A 595 GLN A 727 GLN B 235 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22309 Z= 0.188 Angle : 0.510 6.556 30398 Z= 0.266 Chirality : 0.039 0.170 3536 Planarity : 0.004 0.070 3723 Dihedral : 14.347 148.571 3463 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.64 % Allowed : 17.49 % Favored : 78.87 % 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: 0.50 (0.16), residues: 2623 helix: 1.13 (0.15), residues: 1276 sheet: -0.50 (0.21), residues: 545 loop : -0.13 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 28 HIS 0.014 0.001 HIS F 153 PHE 0.015 0.001 PHE A 632 TYR 0.013 0.001 TYR D 229 ARG 0.009 0.000 ARG F 149 *********************** 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 407 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 323 time to evaluate : 2.609 Fit side-chains revert: symmetry clash REVERT: A 507 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8515 (tt) REVERT: A 630 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8026 (mm-40) REVERT: A 772 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7826 (tttt) REVERT: A 830 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7580 (mm) REVERT: B 66 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 99 LYS cc_start: 0.8445 (mttt) cc_final: 0.8164 (mmtt) REVERT: B 307 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7373 (tm-30) REVERT: C 51 ASP cc_start: 0.7123 (t0) cc_final: 0.6807 (t0) REVERT: C 133 ASP cc_start: 0.7570 (m-30) cc_final: 0.7332 (m-30) REVERT: C 196 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7275 (p0) REVERT: C 320 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8440 (mm) REVERT: D 56 GLU cc_start: 0.7934 (mp0) cc_final: 0.7616 (mp0) REVERT: D 107 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: D 121 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: D 209 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: D 275 ASP cc_start: 0.7705 (m-30) cc_final: 0.7448 (m-30) REVERT: D 294 LYS cc_start: 0.8085 (mttt) cc_final: 0.7864 (tttp) REVERT: D 356 MET cc_start: 0.8646 (ttp) cc_final: 0.8446 (ttp) REVERT: E 9 ARG cc_start: 0.8597 (ttp-170) cc_final: 0.8219 (ttt180) REVERT: E 31 GLN cc_start: 0.7300 (mt0) cc_final: 0.7014 (pt0) REVERT: E 205 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8165 (mt) REVERT: E 304 ASP cc_start: 0.7557 (m-30) cc_final: 0.7117 (t70) REVERT: F 58 ASP cc_start: 0.7604 (t0) cc_final: 0.7216 (t0) REVERT: F 68 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7686 (mpp) REVERT: F 199 MET cc_start: 0.7392 (ppp) cc_final: 0.7135 (ppp) REVERT: F 211 TYR cc_start: 0.8399 (m-80) cc_final: 0.8056 (m-80) REVERT: F 214 PHE cc_start: 0.7299 (m-10) cc_final: 0.7071 (m-80) REVERT: F 248 LYS cc_start: 0.8001 (mttt) cc_final: 0.7449 (mptt) REVERT: G 23 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8130 (mm) REVERT: G 214 PHE cc_start: 0.8393 (m-10) cc_final: 0.8171 (m-10) REVERT: H 88 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6726 (mm) outliers start: 84 outliers final: 43 residues processed: 377 average time/residue: 1.3675 time to fit residues: 583.2844 Evaluate side-chains 370 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 314 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 81 CYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 246 HIS Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 197 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN C 37 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS F 38 GLN F 44 HIS F 65 ASN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22309 Z= 0.301 Angle : 0.568 7.671 30398 Z= 0.291 Chirality : 0.042 0.246 3536 Planarity : 0.004 0.070 3723 Dihedral : 14.410 152.598 3459 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.46 % Allowed : 17.36 % Favored : 78.18 % 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: 0.56 (0.16), residues: 2623 helix: 1.15 (0.15), residues: 1270 sheet: -0.41 (0.21), residues: 523 loop : -0.10 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 251 HIS 0.007 0.001 HIS F 153 PHE 0.015 0.002 PHE A 409 TYR 0.014 0.002 TYR D 229 ARG 0.006 0.001 ARG F 53 *********************** 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 416 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 313 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 595 GLN cc_start: 0.8721 (tt0) cc_final: 0.8454 (tt0) REVERT: A 630 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: A 772 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7844 (tttt) REVERT: A 830 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7618 (mm) REVERT: B 72 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8575 (tp) REVERT: B 307 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7377 (tm-30) REVERT: C 51 ASP cc_start: 0.7150 (t0) cc_final: 0.6824 (t0) REVERT: C 75 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7949 (mtmt) REVERT: C 133 ASP cc_start: 0.7653 (m-30) cc_final: 0.7430 (m-30) REVERT: C 196 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7184 (p0) REVERT: D 56 GLU cc_start: 0.7960 (mp0) cc_final: 0.7639 (mp0) REVERT: D 107 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: D 121 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: D 209 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: D 275 ASP cc_start: 0.7788 (m-30) cc_final: 0.7524 (m-30) REVERT: D 294 LYS cc_start: 0.8109 (mttt) cc_final: 0.7888 (tttp) REVERT: D 299 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: E 9 ARG cc_start: 0.8636 (ttp-170) cc_final: 0.8220 (ttt180) REVERT: E 31 GLN cc_start: 0.7354 (mt0) cc_final: 0.6998 (pt0) REVERT: E 205 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8257 (mt) REVERT: E 304 ASP cc_start: 0.7528 (m-30) cc_final: 0.7070 (t70) REVERT: F 68 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7731 (mpp) REVERT: F 199 MET cc_start: 0.7461 (ppp) cc_final: 0.6921 (ppp) REVERT: F 211 TYR cc_start: 0.8383 (m-80) cc_final: 0.8077 (m-80) REVERT: F 215 PHE cc_start: 0.8441 (m-10) cc_final: 0.8181 (m-80) REVERT: F 248 LYS cc_start: 0.8032 (mttt) cc_final: 0.7493 (mptt) REVERT: G 23 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8096 (mm) REVERT: H 88 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6795 (mm) outliers start: 103 outliers final: 49 residues processed: 382 average time/residue: 1.3794 time to fit residues: 599.4902 Evaluate side-chains 364 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 300 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 796 MET 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 87 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 CYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 246 HIS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 177 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5224 > 50: distance: 81 - 88: 20.540 distance: 88 - 89: 6.287 distance: 89 - 90: 9.983 distance: 89 - 92: 13.442 distance: 90 - 91: 24.818 distance: 90 - 96: 33.112 distance: 92 - 93: 8.307 distance: 93 - 94: 26.823 distance: 93 - 95: 6.319 distance: 96 - 97: 24.216 distance: 97 - 98: 11.633 distance: 97 - 100: 18.781 distance: 98 - 99: 6.023 distance: 100 - 101: 6.948 distance: 101 - 102: 3.988 distance: 102 - 103: 7.094 distance: 102 - 104: 8.208 distance: 105 - 106: 6.043 distance: 105 - 111: 21.489 distance: 106 - 107: 15.684 distance: 106 - 109: 13.279 distance: 107 - 108: 20.344 distance: 107 - 112: 4.989 distance: 109 - 110: 7.788 distance: 110 - 111: 5.538 distance: 112 - 113: 5.648 distance: 113 - 114: 5.621 distance: 113 - 116: 9.402 distance: 116 - 117: 4.970 distance: 117 - 118: 10.764 distance: 117 - 119: 12.011 distance: 120 - 121: 9.131 distance: 121 - 122: 6.740 distance: 121 - 124: 3.545 distance: 122 - 127: 8.731 distance: 123 - 153: 4.841 distance: 124 - 125: 7.758 distance: 124 - 126: 13.706 distance: 127 - 128: 4.795 distance: 128 - 129: 5.440 distance: 128 - 131: 5.724 distance: 129 - 130: 4.336 distance: 129 - 136: 5.338 distance: 130 - 159: 13.260 distance: 131 - 132: 4.116 distance: 132 - 133: 16.399 distance: 133 - 134: 7.043 distance: 133 - 135: 10.118 distance: 136 - 137: 5.979 distance: 137 - 138: 10.305 distance: 137 - 140: 3.167 distance: 138 - 139: 26.130 distance: 138 - 145: 3.538 distance: 140 - 141: 3.653 distance: 141 - 142: 5.833 distance: 142 - 143: 9.467 distance: 142 - 144: 14.017 distance: 145 - 146: 10.336 distance: 146 - 147: 6.370 distance: 146 - 149: 4.746 distance: 147 - 148: 11.169 distance: 147 - 153: 16.415 distance: 149 - 150: 18.091 distance: 150 - 151: 11.198 distance: 150 - 152: 8.231 distance: 153 - 154: 8.303 distance: 154 - 155: 4.025 distance: 154 - 157: 14.047 distance: 155 - 156: 10.498 distance: 155 - 159: 3.568 distance: 157 - 158: 29.557 distance: 159 - 160: 3.076 distance: 160 - 161: 5.179 distance: 160 - 163: 6.349 distance: 161 - 162: 3.529 distance: 163 - 164: 5.326 distance: 164 - 165: 4.271 distance: 165 - 166: 8.799 distance: 166 - 167: 7.297 distance: 167 - 168: 6.404 distance: 167 - 169: 7.441