Starting phenix.real_space_refine on Thu Aug 8 03:01:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umy_42388/08_2024/8umy_42388_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umy_42388/08_2024/8umy_42388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umy_42388/08_2024/8umy_42388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umy_42388/08_2024/8umy_42388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umy_42388/08_2024/8umy_42388_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umy_42388/08_2024/8umy_42388_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.083 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 "E GLU 231": "OE1" <-> "OE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.75, per 1000 atoms: 0.54 Number of scatterers: 21860 At special positions: 0 Unit cell: (117.576, 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: 8.16 Conformation dependent library (CDL) restraints added in 3.4 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: 123 helices and 14 sheets defined 51.3% alpha, 14.4% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.552A pdb=" N GLU A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.964A 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: 3.908A pdb=" N SER A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.771A 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: 4.122A 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 687 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.835A pdb=" N LEU A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 695 " --> pdb=" O PHE A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 695' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.469A 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: 3.554A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 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: 3.785A 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: 3.614A 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 removed outlier: 3.542A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.679A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.674A 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: 3.649A 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: 3.982A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 removed outlier: 3.622A pdb=" N VAL B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.912A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.732A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.681A 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 30 through 34 removed outlier: 3.678A pdb=" N LEU C 34 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 65 through 78 removed outlier: 3.520A pdb=" N ILE C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) 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 138 Processing helix chain 'C' and resid 138 through 145 removed outlier: 3.607A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.559A 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: 3.791A 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: 4.025A 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 239 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.645A 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: 3.788A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.873A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.177A 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 96 removed outlier: 3.581A 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: 3.840A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 removed outlier: 3.529A pdb=" N ALA D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) 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: 4.016A 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: 3.876A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.644A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.592A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 362 removed outlier: 4.265A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.201A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.862A 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: 4.019A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 6.848A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 117 removed outlier: 3.553A pdb=" N VAL E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 149 removed outlier: 3.682A pdb=" N ARG E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.761A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.618A 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: 3.775A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.676A 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: 4.150A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 72 through 80 removed outlier: 3.699A pdb=" N LYS F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.721A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.601A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 removed outlier: 3.532A pdb=" N LYS G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 151 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 9 through 14 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 76 removed outlier: 3.595A pdb=" N SER H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 76' Processing helix chain 'H' and resid 141 through 151 removed outlier: 3.666A pdb=" N ARG H 146 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS H 148 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) 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: 3.562A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.749A 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: 5.959A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA A 370 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N CYS A 490 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU A 372 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 369 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 371 " --> pdb=" O LEU A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.046A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.448A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.278A 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: 6.188A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 5.950A 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: 6.620A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS E 37 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL E 182 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.871A 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: 6.600A pdb=" N ARG F 5 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR F 60 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU F 3 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 182 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 167 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 205 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.095A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 168 through 170 Processing sheet with id=AB2, first strand: chain 'G' and resid 60 through 62 removed outlier: 3.810A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL H 203 " --> pdb=" O CYS H 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.732A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.310A 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: 3.888A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR H 114 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 67 through 71 removed outlier: 3.536A pdb=" N VAL H 70 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR H 196 " --> pdb=" O LYS H 138 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 7.79 Time building geometry restraints manager: 8.93 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: 7228 1.36 - 1.50: 5630 1.50 - 1.65: 9243 1.65 - 1.80: 78 1.80 - 1.95: 130 Bond restraints: 22309 Sorted by residual: bond pdb=" CA SER F 10 " pdb=" CB SER F 10 " ideal model delta sigma weight residual 1.528 1.476 0.053 1.59e-02 3.96e+03 1.10e+01 bond pdb=" N VAL B 331 " pdb=" CA VAL B 331 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.62e+00 bond pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.28e-02 6.10e+03 7.01e+00 bond pdb=" N MET F 244 " pdb=" CA MET F 244 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.26e-02 6.30e+03 6.81e+00 bond pdb=" N MET A 483 " pdb=" CA MET A 483 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.40e-02 5.10e+03 6.67e+00 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.72: 912 106.72 - 114.03: 12938 114.03 - 121.34: 10795 121.34 - 128.65: 5617 128.65 - 135.96: 136 Bond angle restraints: 30398 Sorted by residual: angle pdb=" N VAL E 235 " pdb=" CA VAL E 235 " pdb=" C VAL E 235 " ideal model delta sigma weight residual 112.35 104.45 7.90 1.41e+00 5.03e-01 3.14e+01 angle pdb=" N ARG E 234 " pdb=" CA ARG E 234 " pdb=" C ARG E 234 " ideal model delta sigma weight residual 113.50 107.43 6.07 1.23e+00 6.61e-01 2.44e+01 angle pdb=" N ILE F 11 " pdb=" CA ILE F 11 " pdb=" CB ILE F 11 " ideal model delta sigma weight residual 110.51 105.16 5.35 1.11e+00 8.12e-01 2.32e+01 angle pdb=" CA ASN B 332 " pdb=" CB ASN B 332 " pdb=" CG ASN B 332 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" C ILE F 11 " pdb=" CA ILE F 11 " pdb=" CB ILE F 11 " ideal model delta sigma weight residual 111.88 106.24 5.64 1.28e+00 6.10e-01 1.94e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.58: 12954 28.58 - 57.16: 636 57.16 - 85.74: 42 85.74 - 114.32: 1 114.32 - 142.90: 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 300.00 157.10 142.90 1 2.00e+01 2.50e-03 4.31e+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 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA LEU E 148 " pdb=" C LEU E 148 " pdb=" N ARG E 149 " pdb=" CA ARG E 149 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3298 0.086 - 0.173: 230 0.173 - 0.259: 5 0.259 - 0.345: 2 0.345 - 0.432: 1 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CA ILE F 11 " pdb=" N ILE F 11 " pdb=" C ILE F 11 " pdb=" CB ILE F 11 " both_signs ideal model delta sigma weight residual False 2.43 2.86 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA GLU A 592 " pdb=" N GLU A 592 " pdb=" C GLU A 592 " pdb=" CB GLU A 592 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB ILE F 11 " pdb=" CA ILE F 11 " pdb=" CG1 ILE F 11 " pdb=" CG2 ILE F 11 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3533 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 699 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 234 " -0.284 9.50e-02 1.11e+02 1.27e-01 9.95e+00 pdb=" NE ARG E 234 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG E 234 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 234 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 234 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 198 " 0.254 9.50e-02 1.11e+02 1.14e-01 7.98e+00 pdb=" NE ARG D 198 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 198 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D 198 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 198 " 0.010 2.00e-02 2.50e+03 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 265 2.64 - 3.21: 18030 3.21 - 3.77: 34623 3.77 - 4.34: 47607 4.34 - 4.90: 78709 Nonbonded interactions: 179234 Sorted by model distance: nonbonded pdb=" OG1 THR C 67 " pdb="MG MG C 401 " model vdw 2.080 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.087 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.094 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.098 2.170 ... (remaining 179229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 59.960 Find NCS groups from input model: 0.500 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:10.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 0.063 22309 Z= 0.202 Angle : 0.633 7.896 30398 Z= 0.366 Chirality : 0.044 0.432 3536 Planarity : 0.007 0.127 3723 Dihedral : 15.227 142.900 8597 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.34 % Allowed : 8.83 % Favored : 88.83 % 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: -1.84 (0.14), residues: 2623 helix: -1.59 (0.12), residues: 1230 sheet: -0.32 (0.22), residues: 532 loop : -0.84 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 590 HIS 0.002 0.001 HIS E 331 PHE 0.016 0.001 PHE A 632 TYR 0.024 0.001 TYR E 238 ARG 0.004 0.000 ARG D 198 *********************** 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 518 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 464 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 HIS cc_start: 0.6660 (m170) cc_final: 0.6173 (m90) REVERT: A 313 LEU cc_start: 0.8558 (mm) cc_final: 0.8169 (tm) REVERT: A 353 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 592 GLU cc_start: 0.7777 (tp30) cc_final: 0.7540 (tt0) REVERT: A 767 ASP cc_start: 0.7793 (t70) cc_final: 0.7509 (t70) REVERT: B 100 ASP cc_start: 0.8106 (m-30) cc_final: 0.7868 (m-30) REVERT: B 148 ASP cc_start: 0.7971 (t70) cc_final: 0.7756 (t0) REVERT: B 159 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7052 (mm-30) REVERT: B 229 MET cc_start: 0.8843 (tpt) cc_final: 0.8595 (tpp) REVERT: B 301 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7102 (mtm110) REVERT: C 307 ASP cc_start: 0.7709 (m-30) cc_final: 0.7488 (m-30) REVERT: D 47 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8232 (mmtt) REVERT: D 102 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7686 (mpp-170) REVERT: D 157 SER cc_start: 0.9184 (m) cc_final: 0.8953 (p) REVERT: D 185 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8200 (mtt-85) REVERT: D 265 ILE cc_start: 0.8350 (tt) cc_final: 0.7808 (tt) REVERT: E 298 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7563 (tm-30) REVERT: E 304 ASP cc_start: 0.7389 (t0) cc_final: 0.7110 (t70) REVERT: F 20 LYS cc_start: 0.8307 (tptm) cc_final: 0.8091 (tptp) REVERT: F 146 ARG cc_start: 0.7942 (tpm170) cc_final: 0.7374 (tpm170) REVERT: F 150 ASP cc_start: 0.7564 (m-30) cc_final: 0.7144 (m-30) REVERT: F 197 ILE cc_start: 0.6305 (mm) cc_final: 0.5903 (tp) REVERT: F 241 ILE cc_start: 0.7503 (mm) cc_final: 0.6805 (mt) REVERT: F 248 LYS cc_start: 0.8793 (ptpt) cc_final: 0.8367 (pttm) REVERT: G 1 MET cc_start: 0.5900 (tpt) cc_final: 0.5527 (tpt) REVERT: G 8 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7672 (tm-30) REVERT: G 91 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7909 (mtm-85) REVERT: G 243 ASP cc_start: 0.7039 (t0) cc_final: 0.6698 (t0) REVERT: G 246 HIS cc_start: 0.7254 (p90) cc_final: 0.6968 (p90) REVERT: G 248 LYS cc_start: 0.8597 (mttt) cc_final: 0.7919 (mttt) REVERT: H 40 MET cc_start: 0.6980 (ttp) cc_final: 0.6687 (mtp) REVERT: H 116 MET cc_start: 0.5727 (mmt) cc_final: 0.5351 (mtm) REVERT: H 140 PRO cc_start: 0.8779 (Cg_exo) cc_final: 0.8406 (Cg_endo) outliers start: 54 outliers final: 17 residues processed: 499 average time/residue: 1.3067 time to fit residues: 743.4262 Evaluate side-chains 364 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 346 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 206 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN A 727 GLN B 48 ASN B 125 GLN B 126 GLN B 182 GLN B 268 GLN B 332 ASN B 346 GLN C 29 GLN C 285 HIS C 330 GLN E 120 GLN F 49 GLN H 125 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1613 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: