Starting phenix.real_space_refine on Thu Aug 8 18:35:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/08_2024/8fuk_29459.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/08_2024/8fuk_29459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/08_2024/8fuk_29459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/08_2024/8fuk_29459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/08_2024/8fuk_29459.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/08_2024/8fuk_29459.cif" } resolution = 3.36 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= 0.026 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 108 5.16 5 C 14806 2.51 5 N 4091 2.21 5 O 4544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "G TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "J GLU 15": "OE1" <-> "OE2" Residue "J PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 23608 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1280 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna2p': 26, 'rna3p': 33} Chain: "A" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2635 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 16, 'TRANS': 312} Chain breaks: 2 Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2696 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2630 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 311} Chain breaks: 2 Chain: "D" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 1 Chain: "E" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain breaks: 2 Chain: "F" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2377 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 280} Chain breaks: 3 Chain: "G" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2653 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 17, 'TRANS': 321} Chain breaks: 4 Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "I" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1507 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 2 Chain: "J" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 870 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain breaks: 3 Time building chain proxies: 17.36, per 1000 atoms: 0.74 Number of scatterers: 23608 At special positions: 0 Unit cell: (118.44, 168.26, 174.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 59 15.00 O 4544 8.00 N 4091 7.00 C 14806 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: 9.30 Conformation dependent library (CDL) restraints added in 3.9 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5300 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 43 sheets defined 37.9% alpha, 18.4% beta 6 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 7.78 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.583A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 6.857A pdb=" N LYS A 144 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.665A pdb=" N THR A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.714A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.528A pdb=" N LYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.826A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 105 through 123 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.922A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 6.627A pdb=" N LYS B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 146 " --> pdb=" O TRP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.894A pdb=" N ASN B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 344 Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.655A pdb=" N GLN C 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.532A pdb=" N LYS C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 139 through 147 removed outlier: 6.710A pdb=" N LYS C 144 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 146 " --> pdb=" O TRP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.783A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 328 through 344 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.581A pdb=" N LYS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.603A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 6.576A pdb=" N LYS D 144 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 146 " --> pdb=" O TRP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.632A pdb=" N ILE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 321 Processing helix chain 'D' and resid 327 through 344 Processing helix chain 'E' and resid 45 through 51 removed outlier: 3.715A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 105 through 123 removed outlier: 3.577A pdb=" N LYS E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.611A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 removed outlier: 6.630A pdb=" N LYS E 144 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 146 " --> pdb=" O TRP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 175 removed outlier: 3.677A pdb=" N TYR E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 186 through 200 removed outlier: 3.874A pdb=" N ILE E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 194 " --> pdb=" O ILE E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 327 through 343 Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.686A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.825A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 removed outlier: 6.520A pdb=" N LYS F 144 " --> pdb=" O TRP F 141 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR F 146 " --> pdb=" O TRP F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 186 through 200 removed outlier: 3.649A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 305 through 311 Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.812A pdb=" N ASN F 323 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 344 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 218 through 230 removed outlier: 3.771A pdb=" N ARG G 228 " --> pdb=" O HIS G 224 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN G 230 " --> pdb=" O HIS G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 411 through 428 removed outlier: 3.753A pdb=" N ARG G 428 " --> pdb=" O ARG G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 499 Processing helix chain 'G' and resid 513 through 519 removed outlier: 4.337A pdb=" N LYS G 517 " --> pdb=" O ASP G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 530 removed outlier: 3.874A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 561 removed outlier: 3.835A pdb=" N GLU G 559 " --> pdb=" O ALA G 555 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP G 560 " --> pdb=" O ALA G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 612 Processing helix chain 'H' and resid 16 through 35 Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.748A pdb=" N GLN H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 111 removed outlier: 3.800A pdb=" N LYS H 109 " --> pdb=" O GLN H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'I' and resid 198 through 206 removed outlier: 3.968A pdb=" N ASN I 202 " --> pdb=" O CYS I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 230 removed outlier: 4.269A pdb=" N GLY I 229 " --> pdb=" O HIS I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 245 removed outlier: 4.408A pdb=" N GLN I 242 " --> pdb=" O PHE I 238 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE I 243 " --> pdb=" O SER I 239 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE I 244 " --> pdb=" O PHE I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 279 through 288 removed outlier: 4.282A pdb=" N ARG I 288 " --> pdb=" O PHE I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 Processing helix chain 'I' and resid 317 through 320 removed outlier: 3.710A pdb=" N ASN I 320 " --> pdb=" O LEU I 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 317 through 320' Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'I' and resid 335 through 345 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 386 through 390 Processing helix chain 'J' and resid 13 through 26 removed outlier: 3.947A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 45 Processing helix chain 'J' and resid 60 through 64 removed outlier: 3.735A pdb=" N ALA J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 81 removed outlier: 3.775A pdb=" N ARG J 71 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 139 removed outlier: 3.887A pdb=" N ALA J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER J 139 " --> pdb=" O ASN J 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 134 through 139' Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 15 removed outlier: 3.613A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 13 through 15 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 42 removed outlier: 7.942A pdb=" N SER A 243 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLN A 72 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 288 through 290 removed outlier: 3.631A pdb=" N HIS A 290 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 295 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 9 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.516A pdb=" N SER B 88 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AB2, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 23 current: chain 'C' and resid 151 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 94 current: chain 'C' and resid 248 through 251 Processing sheet with id=AB6, first strand: chain 'C' and resid 35 through 42 removed outlier: 8.624A pdb=" N SER C 243 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLN C 72 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AB8, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.519A pdb=" N THR C 295 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 103 Processing sheet with id=AC1, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.510A pdb=" N SER D 88 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AC3, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AC4, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AC5, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC6, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AC7, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.551A pdb=" N SER E 92 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 88 " --> pdb=" O CYS E 19 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 152 through 159 Processing sheet with id=AC9, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.524A pdb=" N SER E 88 " --> pdb=" O CYS E 19 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 94 current: chain 'E' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AD2, first strand: chain 'F' and resid 102 through 103 Processing sheet with id=AD3, first strand: chain 'F' and resid 29 through 31 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.260A pdb=" N PHE F 20 " --> pdb=" O PRO F 257 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N VAL F 22 " --> pdb=" O ARG F 255 " (cutoff:3.500A) removed outlier: 14.001A pdb=" N ARG F 255 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 72 through 75 removed outlier: 6.415A pdb=" N SER F 36 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 288 through 289 Processing sheet with id=AD7, first strand: chain 'G' and resid 201 through 203 removed outlier: 3.909A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL G 568 " --> pdb=" O VAL G 625 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 236 through 240 Processing sheet with id=AD9, first strand: chain 'G' and resid 508 through 511 Processing sheet with id=AE1, first strand: chain 'G' and resid 508 through 511 removed outlier: 5.787A pdb=" N PHE G 387 " --> pdb=" O THR G 485 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR G 485 " --> pdb=" O PHE G 387 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G 437 " --> pdb=" O ASN G 484 " (cutoff:3.500A) removed outlier: 15.508A pdb=" N PHE G 438 " --> pdb=" O LEU G 542 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N LEU G 542 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE G 440 " --> pdb=" O LEU G 540 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 398 through 399 removed outlier: 4.037A pdb=" N ASP G 472 " --> pdb=" O ARG G 450 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG G 450 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 41 through 43 Processing sheet with id=AE4, first strand: chain 'H' and resid 41 through 43 removed outlier: 3.600A pdb=" N TYR H 5 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 167 through 171 Processing sheet with id=AE6, first strand: chain 'I' and resid 322 through 323 Processing sheet with id=AE7, first strand: chain 'J' and resid 95 through 96 921 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 9.31 Time building geometry restraints manager: 10.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7250 1.34 - 1.46: 4634 1.46 - 1.58: 12162 1.58 - 1.70: 119 1.70 - 1.82: 160 Bond restraints: 24325 Sorted by residual: bond pdb=" CB PRO J 87 " pdb=" CG PRO J 87 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.01e+01 bond pdb=" CG PRO J 86 " pdb=" CD PRO J 86 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.81e+00 bond pdb=" C4' U 1 30 " pdb=" O4' U 1 30 " ideal model delta sigma weight residual 1.451 1.433 0.018 1.50e-02 4.44e+03 1.52e+00 bond pdb=" C4' C 1 21 " pdb=" C3' C 1 21 " ideal model delta sigma weight residual 1.527 1.509 0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" C4' A 1 12 " pdb=" O4' A 1 12 " ideal model delta sigma weight residual 1.451 1.433 0.018 1.50e-02 4.44e+03 1.43e+00 ... (remaining 24320 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.40: 734 105.40 - 112.57: 12744 112.57 - 119.74: 7872 119.74 - 126.90: 11402 126.90 - 134.07: 543 Bond angle restraints: 33295 Sorted by residual: angle pdb=" CA PRO J 87 " pdb=" N PRO J 87 " pdb=" CD PRO J 87 " ideal model delta sigma weight residual 112.00 101.53 10.47 1.40e+00 5.10e-01 5.60e+01 angle pdb=" N HIS J 31 " pdb=" CA HIS J 31 " pdb=" C HIS J 31 " ideal model delta sigma weight residual 113.29 105.80 7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N MET I 228 " pdb=" CA MET I 228 " pdb=" CB MET I 228 " ideal model delta sigma weight residual 110.01 115.10 -5.09 1.45e+00 4.76e-01 1.23e+01 angle pdb=" CA LYS G 577 " pdb=" CB LYS G 577 " pdb=" CG LYS G 577 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N PRO J 87 " pdb=" CD PRO J 87 " pdb=" CG PRO J 87 " ideal model delta sigma weight residual 103.20 98.24 4.96 1.50e+00 4.44e-01 1.10e+01 ... (remaining 33290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.29: 13056 22.29 - 44.58: 1149 44.58 - 66.87: 230 66.87 - 89.16: 47 89.16 - 111.45: 4 Dihedral angle restraints: 14486 sinusoidal: 6336 harmonic: 8150 Sorted by residual: dihedral pdb=" O4' C 1 21 " pdb=" C1' C 1 21 " pdb=" N1 C 1 21 " pdb=" C2 C 1 21 " ideal model delta sinusoidal sigma weight residual 232.00 148.33 83.67 1 1.70e+01 3.46e-03 2.96e+01 dihedral pdb=" O4' U 1 33 " pdb=" C1' U 1 33 " pdb=" N1 U 1 33 " pdb=" C2 U 1 33 " ideal model delta sinusoidal sigma weight residual -128.00 -44.67 -83.33 1 1.70e+01 3.46e-03 2.94e+01 dihedral pdb=" O4' U 1 22 " pdb=" C1' U 1 22 " pdb=" N1 U 1 22 " pdb=" C2 U 1 22 " ideal model delta sinusoidal sigma weight residual -160.00 -94.98 -65.02 1 1.50e+01 4.44e-03 2.46e+01 ... (remaining 14483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2573 0.037 - 0.074: 827 0.074 - 0.111: 232 0.111 - 0.148: 66 0.148 - 0.184: 7 Chirality restraints: 3705 Sorted by residual: chirality pdb=" CB THR A 270 " pdb=" CA THR A 270 " pdb=" OG1 THR A 270 " pdb=" CG2 THR A 270 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA MET I 228 " pdb=" N MET I 228 " pdb=" C MET I 228 " pdb=" CB MET I 228 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" C1' A 1 12 " pdb=" O4' A 1 12 " pdb=" C2' A 1 12 " pdb=" N9 A 1 12 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 3702 not shown) Planarity restraints: 4033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 281 " 0.411 9.50e-02 1.11e+02 1.85e-01 2.67e+01 pdb=" NE ARG I 281 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG I 281 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG I 281 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG I 281 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO J 86 " -0.061 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO J 87 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO J 87 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO J 87 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 274 " -0.258 9.50e-02 1.11e+02 1.17e-01 1.07e+01 pdb=" NE ARG I 274 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG I 274 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG I 274 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG I 274 " -0.000 2.00e-02 2.50e+03 ... (remaining 4030 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 286 2.63 - 3.20: 21234 3.20 - 3.77: 36377 3.77 - 4.33: 49444 4.33 - 4.90: 83092 Nonbonded interactions: 190433 Sorted by model distance: nonbonded pdb=" OG SER A 94 " pdb=" OE1 GLU A 96 " model vdw 2.068 3.040 nonbonded pdb=" O HIS F 299 " pdb=" OG1 THR F 302 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLU I 256 " pdb=" OH TYR I 306 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 95 " pdb=" O ALA A 197 " model vdw 2.227 3.040 nonbonded pdb=" OE2 GLU D 44 " pdb=" NZ LYS E 343 " model vdw 2.240 3.120 ... (remaining 190428 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'B' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'C' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 348)) selection = (chain 'D' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'E' and (resid 2 through 40 or resid 71 through 228 or resid 243 through \ 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'F' and (resid 2 through 25 or resid 28 through 317 or resid 327 through \ 348)) } 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: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 72.560 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 0.159 24325 Z= 0.193 Angle : 0.564 10.475 33295 Z= 0.304 Chirality : 0.041 0.184 3705 Planarity : 0.006 0.185 4033 Dihedral : 17.109 111.451 9186 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.24 % Allowed : 20.04 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.29 (0.16), residues: 2724 helix: 0.59 (0.18), residues: 883 sheet: 0.76 (0.24), residues: 497 loop : -0.20 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 539 HIS 0.014 0.001 HIS J 31 PHE 0.028 0.001 PHE A 306 TYR 0.020 0.001 TYR E 275 ARG 0.042 0.001 ARG I 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 234 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 132 GLN cc_start: 0.7603 (pm20) cc_final: 0.7053 (mm-40) REVERT: H 173 GLN cc_start: 0.7109 (tm-30) cc_final: 0.5909 (pm20) REVERT: I 388 SER cc_start: 0.7526 (t) cc_final: 0.7315 (p) outliers start: 6 outliers final: 2 residues processed: 236 average time/residue: 0.3512 time to fit residues: 130.5472 Evaluate side-chains 233 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain G residue 263 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN E 218 ASN F 179 GLN G 626 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24325 Z= 0.319 Angle : 0.576 9.453 33295 Z= 0.305 Chirality : 0.042 0.205 3705 Planarity : 0.004 0.044 4033 Dihedral : 13.161 109.566 3904 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.79 % Allowed : 17.60 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.14 (0.16), residues: 2724 helix: 0.52 (0.17), residues: 908 sheet: 0.52 (0.24), residues: 515 loop : -0.29 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.008 0.001 HIS H 29 PHE 0.025 0.002 PHE A 306 TYR 0.018 0.002 TYR B 275 ARG 0.004 0.000 ARG F 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 240 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8297 (mmt) cc_final: 0.8072 (mmt) REVERT: A 306 PHE cc_start: 0.7733 (t80) cc_final: 0.7477 (t80) REVERT: B 97 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8936 (pt) REVERT: G 577 LYS cc_start: 0.8456 (mmtp) cc_final: 0.8202 (mmtp) REVERT: H 173 GLN cc_start: 0.7134 (tm-30) cc_final: 0.5746 (pm20) REVERT: H 190 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: H 194 GLN cc_start: 0.7483 (tt0) cc_final: 0.6966 (tt0) outliers start: 93 outliers final: 52 residues processed: 302 average time/residue: 0.3256 time to fit residues: 158.4571 Evaluate side-chains 268 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 214 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 482 ILE Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 626 GLN Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 210 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 252 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 299 HIS ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24325 Z= 0.227 Angle : 0.523 9.524 33295 Z= 0.276 Chirality : 0.040 0.192 3705 Planarity : 0.004 0.041 4033 Dihedral : 13.028 108.623 3901 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.83 % Allowed : 18.49 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2724 helix: 0.58 (0.17), residues: 912 sheet: 0.44 (0.24), residues: 509 loop : -0.32 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.007 0.001 HIS H 29 PHE 0.012 0.001 PHE A 306 TYR 0.015 0.001 TYR B 275 ARG 0.003 0.000 ARG F 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 226 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8357 (mmp) cc_final: 0.8112 (mmt) REVERT: B 97 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8857 (pt) REVERT: E 57 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8494 (tp) REVERT: E 324 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8376 (ptmm) REVERT: G 577 LYS cc_start: 0.8520 (mmtp) cc_final: 0.8256 (mmtp) REVERT: H 173 GLN cc_start: 0.7005 (tm-30) cc_final: 0.5707 (pm20) REVERT: J 88 GLU cc_start: 0.8441 (tp30) cc_final: 0.8178 (tp30) outliers start: 94 outliers final: 54 residues processed: 294 average time/residue: 0.3451 time to fit residues: 163.6108 Evaluate side-chains 267 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 240 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 ASN ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 105 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24325 Z= 0.198 Angle : 0.501 9.562 33295 Z= 0.264 Chirality : 0.040 0.176 3705 Planarity : 0.004 0.043 4033 Dihedral : 12.946 108.603 3901 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.87 % Allowed : 19.27 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2724 helix: 0.67 (0.17), residues: 913 sheet: 0.39 (0.23), residues: 512 loop : -0.28 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS H 29 PHE 0.014 0.001 PHE J 17 TYR 0.015 0.001 TYR E 275 ARG 0.003 0.000 ARG F 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 222 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8822 (pt) REVERT: B 348 GLN cc_start: 0.8424 (pp30) cc_final: 0.8142 (pp30) REVERT: E 57 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8496 (tp) REVERT: E 324 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8358 (ptmm) REVERT: F 156 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8167 (pp) REVERT: G 577 LYS cc_start: 0.8581 (mmtp) cc_final: 0.8316 (mmtp) REVERT: H 190 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7309 (pm20) outliers start: 95 outliers final: 66 residues processed: 293 average time/residue: 0.3364 time to fit residues: 157.9353 Evaluate side-chains 277 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 207 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 241 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN I 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24325 Z= 0.163 Angle : 0.485 9.514 33295 Z= 0.254 Chirality : 0.039 0.172 3705 Planarity : 0.004 0.045 4033 Dihedral : 12.884 109.013 3901 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.95 % Allowed : 19.59 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2724 helix: 0.82 (0.18), residues: 907 sheet: 0.42 (0.23), residues: 514 loop : -0.24 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.005 0.001 HIS H 29 PHE 0.016 0.001 PHE J 17 TYR 0.016 0.001 TYR E 275 ARG 0.003 0.000 ARG F 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 234 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7857 (mpp) REVERT: B 97 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8793 (pt) REVERT: B 348 GLN cc_start: 0.8404 (pp30) cc_final: 0.8127 (pp30) REVERT: C 183 ASN cc_start: 0.8280 (m-40) cc_final: 0.8029 (m-40) REVERT: E 57 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8507 (tp) REVERT: G 577 LYS cc_start: 0.8559 (mmtp) cc_final: 0.8200 (mmtp) REVERT: I 372 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7995 (mt) REVERT: J 88 GLU cc_start: 0.8372 (tp30) cc_final: 0.8141 (tp30) outliers start: 97 outliers final: 67 residues processed: 304 average time/residue: 0.3444 time to fit residues: 165.7930 Evaluate side-chains 284 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 213 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN E 153 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24325 Z= 0.216 Angle : 0.507 9.572 33295 Z= 0.266 Chirality : 0.040 0.173 3705 Planarity : 0.004 0.045 4033 Dihedral : 12.851 108.050 3901 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.24 % Allowed : 19.67 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 2724 helix: 0.75 (0.17), residues: 909 sheet: 0.42 (0.23), residues: 511 loop : -0.29 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS H 29 PHE 0.018 0.001 PHE J 17 TYR 0.017 0.001 TYR E 275 ARG 0.006 0.000 ARG J 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 219 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8830 (pt) REVERT: B 348 GLN cc_start: 0.8356 (pp30) cc_final: 0.8063 (pp30) REVERT: E 57 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8509 (tp) REVERT: F 156 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (pp) REVERT: G 577 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8339 (mmtp) REVERT: H 190 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: I 333 ASN cc_start: 0.8078 (t0) cc_final: 0.7804 (t0) REVERT: I 372 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8025 (mt) outliers start: 104 outliers final: 84 residues processed: 294 average time/residue: 0.3284 time to fit residues: 154.3345 Evaluate side-chains 298 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 209 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 334 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 196 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 226 optimal weight: 0.4980 chunk 150 optimal weight: 0.6980 chunk 267 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS J 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24325 Z= 0.163 Angle : 0.492 9.520 33295 Z= 0.257 Chirality : 0.039 0.172 3705 Planarity : 0.004 0.046 4033 Dihedral : 12.768 109.059 3901 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.40 % Allowed : 19.84 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.32 (0.16), residues: 2724 helix: 0.83 (0.18), residues: 916 sheet: 0.44 (0.23), residues: 517 loop : -0.24 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 152 HIS 0.007 0.001 HIS J 31 PHE 0.019 0.001 PHE J 17 TYR 0.015 0.001 TYR E 275 ARG 0.003 0.000 ARG F 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 220 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8027 (t80) REVERT: A 96 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: A 220 MET cc_start: 0.8396 (mmp) cc_final: 0.8172 (mmt) REVERT: B 97 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8758 (pt) REVERT: B 348 GLN cc_start: 0.8309 (pp30) cc_final: 0.7968 (pp30) REVERT: E 57 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8518 (tp) REVERT: F 156 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8114 (pp) REVERT: G 577 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8138 (mmtp) REVERT: H 102 ARG cc_start: 0.6164 (mtt180) cc_final: 0.5332 (mtt-85) REVERT: H 190 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: I 333 ASN cc_start: 0.8081 (t0) cc_final: 0.7815 (t0) REVERT: I 372 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7946 (mt) outliers start: 108 outliers final: 78 residues processed: 297 average time/residue: 0.3211 time to fit residues: 152.6442 Evaluate side-chains 297 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 212 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24325 Z= 0.227 Angle : 0.526 9.570 33295 Z= 0.273 Chirality : 0.040 0.196 3705 Planarity : 0.004 0.045 4033 Dihedral : 12.782 108.382 3901 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.11 % Allowed : 20.12 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 2724 helix: 0.69 (0.17), residues: 923 sheet: 0.41 (0.23), residues: 513 loop : -0.29 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 247 HIS 0.005 0.001 HIS B 84 PHE 0.018 0.001 PHE J 17 TYR 0.018 0.001 TYR E 275 ARG 0.003 0.000 ARG F 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 219 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8088 (t80) REVERT: A 96 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: B 348 GLN cc_start: 0.8255 (pp30) cc_final: 0.8025 (pp30) REVERT: E 57 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8514 (tp) REVERT: F 156 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8159 (pp) REVERT: G 577 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8243 (mmtp) REVERT: H 190 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: I 333 ASN cc_start: 0.8164 (t0) cc_final: 0.7909 (t0) REVERT: I 372 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8019 (mt) outliers start: 101 outliers final: 85 residues processed: 292 average time/residue: 0.3526 time to fit residues: 165.5541 Evaluate side-chains 297 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 206 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1592 > 50: distance: 10 - 16: 7.703 distance: 16 - 17: 6.436 distance: 17 - 18: 10.977 distance: 17 - 20: 8.569 distance: 18 - 19: 7.329 distance: 18 - 24: 8.410 distance: 19 - 37: 32.478 distance: 20 - 21: 9.340 distance: 21 - 22: 17.088 distance: 21 - 23: 7.322 distance: 24 - 25: 12.502 distance: 25 - 26: 28.915 distance: 25 - 28: 8.173 distance: 26 - 27: 19.224 distance: 26 - 31: 13.190 distance: 28 - 29: 9.614 distance: 28 - 30: 24.730 distance: 31 - 32: 9.546 distance: 32 - 33: 11.115 distance: 32 - 35: 11.323 distance: 33 - 34: 8.202 distance: 33 - 37: 14.207 distance: 35 - 36: 11.482 distance: 37 - 38: 25.656 distance: 38 - 39: 24.964 distance: 39 - 40: 20.950 distance: 39 - 41: 34.135 distance: 41 - 42: 17.155 distance: 42 - 43: 14.795 distance: 42 - 45: 6.972 distance: 43 - 44: 12.344 distance: 43 - 50: 14.167 distance: 45 - 46: 15.623 distance: 46 - 47: 17.364 distance: 47 - 48: 24.052 distance: 47 - 49: 16.250 distance: 50 - 51: 20.538 distance: 50 - 56: 23.297 distance: 51 - 52: 23.590 distance: 51 - 54: 25.742 distance: 52 - 53: 5.089 distance: 52 - 57: 9.339 distance: 54 - 55: 13.511 distance: 55 - 56: 38.013 distance: 57 - 58: 15.552 distance: 58 - 59: 27.604 distance: 58 - 61: 20.900 distance: 59 - 60: 20.693 distance: 59 - 65: 43.598 distance: 61 - 62: 3.836 distance: 61 - 63: 23.880 distance: 62 - 64: 28.669 distance: 65 - 66: 21.893 distance: 66 - 67: 7.666 distance: 66 - 69: 15.123 distance: 67 - 68: 7.280 distance: 67 - 74: 11.093 distance: 69 - 70: 15.609 distance: 70 - 71: 9.729 distance: 71 - 72: 4.131 distance: 72 - 73: 25.038 distance: 74 - 75: 5.337 distance: 75 - 76: 9.546 distance: 75 - 78: 10.033 distance: 76 - 77: 27.274 distance: 76 - 80: 16.237 distance: 78 - 79: 9.346 distance: 81 - 82: 6.831 distance: 81 - 84: 5.846 distance: 82 - 83: 8.176 distance: 82 - 85: 24.700