Starting phenix.real_space_refine on Tue Mar 19 07:41:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/03_2024/8fuk_29459.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/03_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_29459/03_2024/8fuk_29459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/03_2024/8fuk_29459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/03_2024/8fuk_29459.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fuk_29459/03_2024/8fuk_29459.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.14, per 1000 atoms: 0.51 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: 9.42 Conformation dependent library (CDL) restraints added in 3.7 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: 6.95 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: 7.74 Time building geometry restraints manager: 10.21 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 2.440 nonbonded pdb=" O HIS F 299 " pdb=" OG1 THR F 302 " model vdw 2.217 2.440 nonbonded pdb=" OE1 GLU I 256 " pdb=" OH TYR I 306 " model vdw 2.217 2.440 nonbonded pdb=" OG SER A 95 " pdb=" O ALA A 197 " model vdw 2.227 2.440 nonbonded pdb=" OE2 GLU D 44 " pdb=" NZ LYS E 343 " model vdw 2.240 2.520 ... (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 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.920 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 63.550 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.600 ------------------------------------------------------------------------------- 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 : 2.569 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: 0.3528 time to fit residues: 131.1897 Evaluate side-chains 233 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 2.391 ------------------------------------------------------------------------------- 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: 9.9990 chunk 210 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN F 179 GLN G 626 GLN I 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24325 Z= 0.362 Angle : 0.585 9.381 33295 Z= 0.310 Chirality : 0.043 0.203 3705 Planarity : 0.004 0.043 4033 Dihedral : 13.180 108.534 3904 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.60 % Allowed : 17.76 % Favored : 77.64 % 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: 0.09 (0.16), residues: 2724 helix: 0.52 (0.17), residues: 897 sheet: 0.50 (0.24), residues: 501 loop : -0.34 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 152 HIS 0.008 0.001 HIS H 29 PHE 0.028 0.002 PHE A 306 TYR 0.021 0.002 TYR B 275 ARG 0.004 0.000 ARG B 286 *********************** 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 341 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 228 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7622 (p0) REVERT: B 97 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8937 (pt) REVERT: C 275 TYR cc_start: 0.8149 (p90) cc_final: 0.7898 (p90) REVERT: G 577 LYS cc_start: 0.8402 (mmtp) cc_final: 0.8183 (mmtp) REVERT: H 173 GLN cc_start: 0.7127 (tm-30) cc_final: 0.5694 (pm20) outliers start: 113 outliers final: 68 residues processed: 308 average time/residue: 0.3212 time to fit residues: 160.3563 Evaluate side-chains 284 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 214 time to evaluate : 2.811 ------------------------------------------------------------------------------- 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 174 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 255 ARG 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 B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 162 ASN 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 95 SER 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 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 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 155 VAL 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 293 ASP Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 482 ILE Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 626 GLN Chi-restraints excluded: chain H residue 7 THR 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 I residue 200 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 314 ASP 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 45 ASP Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 55 ASP 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: 0.7980 chunk 78 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 250 optimal weight: 0.0270 chunk 86 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24325 Z= 0.190 Angle : 0.497 9.505 33295 Z= 0.262 Chirality : 0.039 0.190 3705 Planarity : 0.004 0.042 4033 Dihedral : 13.040 108.916 3901 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.87 % Allowed : 18.90 % Favored : 77.23 % 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: 0.71 (0.18), residues: 906 sheet: 0.44 (0.23), residues: 514 loop : -0.26 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.007 0.001 HIS H 29 PHE 0.011 0.001 PHE F 306 TYR 0.017 0.001 TYR E 275 ARG 0.004 0.000 ARG J 20 *********************** 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 321 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 226 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8866 (pt) REVERT: C 275 TYR cc_start: 0.8026 (p90) cc_final: 0.7672 (p90) REVERT: E 57 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8488 (tp) REVERT: E 324 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8365 (ptmm) REVERT: F 156 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8216 (pp) REVERT: G 577 LYS cc_start: 0.8412 (mmtp) cc_final: 0.8111 (mmtp) REVERT: I 278 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8206 (tt) outliers start: 95 outliers final: 53 residues processed: 291 average time/residue: 0.3288 time to fit residues: 152.6771 Evaluate side-chains 269 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 212 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 165 LYS 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 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 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 162 ASN Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 157 THR 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 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 245 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 631 ASN 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 278 LEU Chi-restraints excluded: chain I residue 329 THR 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 55 ASP 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: 8.9990 chunk 190 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 27 optimal weight: 0.0070 chunk 120 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 268 optimal weight: 20.0000 chunk 132 optimal weight: 0.0870 chunk 240 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1437 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= 0.165 Angle : 0.476 9.486 33295 Z= 0.249 Chirality : 0.039 0.169 3705 Planarity : 0.004 0.051 4033 Dihedral : 12.941 108.400 3901 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.15 % Allowed : 19.35 % Favored : 76.50 % 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: 0.33 (0.16), residues: 2724 helix: 0.83 (0.18), residues: 906 sheet: 0.47 (0.23), residues: 515 loop : -0.22 (0.18), residues: 1303 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 0.011 0.001 PHE F 306 TYR 0.017 0.001 TYR E 275 ARG 0.004 0.000 ARG J 20 *********************** 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 329 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 227 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7441 (p0) REVERT: B 97 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8840 (pt) REVERT: C 275 TYR cc_start: 0.8076 (p90) cc_final: 0.7832 (p90) REVERT: H 173 GLN cc_start: 0.6931 (tm-30) cc_final: 0.5534 (pm20) REVERT: I 372 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7984 (mt) outliers start: 102 outliers final: 70 residues processed: 300 average time/residue: 0.3314 time to fit residues: 158.9729 Evaluate side-chains 288 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 215 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 174 ASN 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 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 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 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 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 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 252 ASP 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 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 631 ASN 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 263 LEU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 329 THR 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 55 ASP 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: 8.9990 chunk 152 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN G 520 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** 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: 0.8303 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24325 Z= 0.238 Angle : 0.507 9.534 33295 Z= 0.264 Chirality : 0.040 0.170 3705 Planarity : 0.004 0.042 4033 Dihedral : 12.926 107.793 3901 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.56 % Allowed : 19.47 % Favored : 75.97 % 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: 0.77 (0.18), residues: 907 sheet: 0.41 (0.23), residues: 509 loop : -0.29 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS B 84 PHE 0.013 0.001 PHE F 306 TYR 0.018 0.001 TYR E 275 ARG 0.005 0.000 ARG J 20 *********************** 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 329 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 217 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7538 (p0) REVERT: B 97 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8913 (pt) REVERT: B 348 GLN cc_start: 0.8432 (pp30) cc_final: 0.8120 (pp30) REVERT: C 275 TYR cc_start: 0.8184 (p90) cc_final: 0.7938 (p90) REVERT: E 57 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8492 (tp) REVERT: F 156 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (pp) REVERT: I 256 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7391 (mm-30) REVERT: I 372 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8007 (mt) outliers start: 112 outliers final: 81 residues processed: 300 average time/residue: 0.3273 time to fit residues: 157.4874 Evaluate side-chains 298 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 212 time to evaluate : 2.631 ------------------------------------------------------------------------------- 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 162 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 174 ASN 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 157 THR 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 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 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 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 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 157 THR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 252 ASP 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 153 ASN 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 293 ASP Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 631 ASN 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 148 HIS Chi-restraints excluded: chain H residue 182 SER 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 289 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 55 ASP 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: 0.9980 chunk 241 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 157 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 268 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 124 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN G 230 GLN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN I 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24325 Z= 0.144 Angle : 0.466 9.482 33295 Z= 0.242 Chirality : 0.038 0.169 3705 Planarity : 0.004 0.048 4033 Dihedral : 12.862 108.712 3901 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.91 % Allowed : 20.41 % Favored : 75.68 % 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: 0.43 (0.16), residues: 2724 helix: 0.91 (0.18), residues: 918 sheet: 0.47 (0.23), residues: 519 loop : -0.14 (0.18), residues: 1287 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 0.015 0.001 PHE H 31 TYR 0.017 0.001 TYR E 275 ARG 0.004 0.000 ARG J 20 *********************** 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 326 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 230 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7408 (p0) REVERT: B 97 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8831 (pt) REVERT: B 348 GLN cc_start: 0.8319 (pp30) cc_final: 0.8014 (pp30) REVERT: C 275 TYR cc_start: 0.8114 (p90) cc_final: 0.7813 (p90) REVERT: E 57 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8485 (tp) REVERT: H 173 GLN cc_start: 0.6859 (tm-30) cc_final: 0.5547 (pm20) REVERT: I 333 ASN cc_start: 0.8204 (t0) cc_final: 0.7947 (t0) REVERT: I 372 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7935 (mt) outliers start: 96 outliers final: 74 residues processed: 298 average time/residue: 0.3337 time to fit residues: 156.9534 Evaluate side-chains 293 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 215 time to evaluate : 2.579 ------------------------------------------------------------------------------- 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 162 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 174 ASN 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 3 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 193 MET 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 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL 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 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 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 252 ASP 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 293 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 631 ASN 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 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 289 LEU Chi-restraints excluded: chain I residue 329 THR 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 47 ASN Chi-restraints excluded: chain J residue 55 ASP 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: 10.0000 chunk 30 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 196 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN G 230 GLN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS J 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24325 Z= 0.174 Angle : 0.478 9.459 33295 Z= 0.247 Chirality : 0.039 0.196 3705 Planarity : 0.004 0.050 4033 Dihedral : 12.839 108.077 3901 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.40 % Allowed : 20.49 % Favored : 75.11 % 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: 0.41 (0.16), residues: 2724 helix: 0.91 (0.18), residues: 920 sheet: 0.47 (0.23), residues: 519 loop : -0.19 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.005 0.001 HIS H 29 PHE 0.011 0.001 PHE F 306 TYR 0.018 0.001 TYR E 275 ARG 0.004 0.000 ARG J 20 *********************** 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 324 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 216 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7993 (t80) REVERT: A 174 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7455 (p0) REVERT: B 97 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8820 (pt) REVERT: B 348 GLN cc_start: 0.8314 (pp30) cc_final: 0.8006 (pp30) REVERT: C 275 TYR cc_start: 0.8140 (p90) cc_final: 0.7829 (p90) REVERT: D 208 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: E 57 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8492 (tp) REVERT: E 270 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8309 (p) REVERT: I 256 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7243 (mm-30) REVERT: I 333 ASN cc_start: 0.8229 (t0) cc_final: 0.7988 (t0) REVERT: I 372 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7967 (mt) outliers start: 108 outliers final: 89 residues processed: 297 average time/residue: 0.3425 time to fit residues: 160.8917 Evaluate side-chains 309 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 213 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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 162 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 209 VAL 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 3 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 201 THR 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 52 VAL 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 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 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 208 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 319 VAL 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 157 THR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 270 THR 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 153 ASN 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 293 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 631 ASN 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 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 289 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 55 ASP 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: 0.6980 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN I 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24325 Z= 0.192 Angle : 0.488 9.492 33295 Z= 0.253 Chirality : 0.039 0.175 3705 Planarity : 0.004 0.051 4033 Dihedral : 12.841 107.817 3901 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.40 % Allowed : 20.37 % Favored : 75.23 % 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: 0.38 (0.16), residues: 2724 helix: 0.90 (0.18), residues: 921 sheet: 0.48 (0.23), residues: 519 loop : -0.22 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 247 HIS 0.005 0.001 HIS B 84 PHE 0.011 0.001 PHE F 306 TYR 0.015 0.001 TYR E 275 ARG 0.004 0.000 ARG J 20 *********************** 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 325 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 217 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7975 (t80) REVERT: A 174 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7485 (p0) REVERT: B 97 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8850 (pt) REVERT: B 348 GLN cc_start: 0.8331 (pp30) cc_final: 0.8025 (pp30) REVERT: C 275 TYR cc_start: 0.8156 (p90) cc_final: 0.7847 (p90) REVERT: D 208 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: E 57 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8513 (tp) REVERT: E 270 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8344 (p) REVERT: I 333 ASN cc_start: 0.8242 (t0) cc_final: 0.7918 (t0) REVERT: I 372 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7989 (mt) REVERT: J 39 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7774 (mtp-110) outliers start: 108 outliers final: 89 residues processed: 295 average time/residue: 0.3482 time to fit residues: 164.2042 Evaluate side-chains 311 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 215 time to evaluate : 2.632 ------------------------------------------------------------------------------- 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 162 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 209 VAL 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 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 52 VAL 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 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 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 208 GLU 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 340 ASN Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 270 THR 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 153 ASN 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 293 ASP 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 453 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 631 ASN 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 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 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain I residue 389 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 55 ASP 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 ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 0.0870 chunk 256 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 chunk 249 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN I 265 HIS J 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24325 Z= 0.217 Angle : 0.506 9.822 33295 Z= 0.261 Chirality : 0.039 0.170 3705 Planarity : 0.004 0.052 4033 Dihedral : 12.879 107.521 3901 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.52 % Allowed : 20.57 % Favored : 74.91 % 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: 0.34 (0.16), residues: 2724 helix: 0.91 (0.18), residues: 909 sheet: 0.45 (0.23), residues: 519 loop : -0.28 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 247 HIS 0.005 0.001 HIS B 84 PHE 0.011 0.001 PHE B 89 TYR 0.019 0.001 TYR E 275 ARG 0.004 0.000 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 9 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 330 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 219 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8017 (t80) REVERT: A 174 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7492 (p0) REVERT: B 97 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8862 (pt) REVERT: B 348 GLN cc_start: 0.8358 (pp30) cc_final: 0.8043 (pp30) REVERT: C 275 TYR cc_start: 0.8178 (p90) cc_final: 0.7933 (p90) REVERT: D 208 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: E 57 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8512 (tp) REVERT: G 590 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5627 (mp) REVERT: I 228 MET cc_start: 0.8022 (ppp) cc_final: 0.7270 (mtt) REVERT: I 333 ASN cc_start: 0.8317 (t0) cc_final: 0.8016 (t0) REVERT: I 372 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8020 (mt) REVERT: J 39 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7780 (mtp-110) outliers start: 111 outliers final: 90 residues processed: 301 average time/residue: 0.3285 time to fit residues: 157.5165 Evaluate side-chains 311 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 214 time to evaluate : 2.698 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 209 VAL 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 22 VAL Chi-restraints excluded: chain B residue 97 LEU 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 52 VAL 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 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 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 208 GLU 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 340 ASN Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 252 ASP 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 153 ASN 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 293 ASP 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 453 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 631 ASN 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 I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 1.9990 chunk 264 optimal weight: 0.4980 chunk 161 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 276 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 170 optimal weight: 0.2980 chunk 135 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN I 265 HIS J 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24325 Z= 0.134 Angle : 0.476 10.606 33295 Z= 0.245 Chirality : 0.038 0.169 3705 Planarity : 0.004 0.055 4033 Dihedral : 12.830 108.340 3901 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.71 % Allowed : 21.59 % Favored : 74.70 % 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: 0.49 (0.16), residues: 2724 helix: 1.04 (0.18), residues: 918 sheet: 0.55 (0.23), residues: 517 loop : -0.19 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 247 HIS 0.005 0.001 HIS H 29 PHE 0.022 0.001 PHE J 17 TYR 0.013 0.001 TYR E 275 ARG 0.006 0.000 ARG J 20 ********************** REFINEMENT MACRO_CYCLE 10 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 316 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 225 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7990 (t80) REVERT: A 174 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7418 (p0) REVERT: B 97 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8797 (pt) REVERT: B 348 GLN cc_start: 0.8314 (pp30) cc_final: 0.8086 (pp30) REVERT: C 275 TYR cc_start: 0.8096 (p90) cc_final: 0.7853 (p90) REVERT: D 208 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: E 57 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8490 (tp) REVERT: I 228 MET cc_start: 0.7848 (ppp) cc_final: 0.7184 (mtt) REVERT: I 333 ASN cc_start: 0.8308 (t0) cc_final: 0.8018 (t0) REVERT: I 372 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7912 (mt) REVERT: J 39 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7795 (mtp-110) outliers start: 91 outliers final: 73 residues processed: 291 average time/residue: 0.3406 time to fit residues: 156.9385 Evaluate side-chains 295 residues out of total 2455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 216 time to evaluate : 2.574 ------------------------------------------------------------------------------- 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 162 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 209 VAL 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 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 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL 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 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 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 208 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 252 ASP 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 157 THR Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 293 ASP 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 453 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 631 ASN 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 I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 92 optimal weight: 0.0770 chunk 226 optimal weight: 0.0870 chunk 27 optimal weight: 0.0040 chunk 40 optimal weight: 0.6980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS J 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.144061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102323 restraints weight = 35616.137| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.19 r_work: 0.3201 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2020 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= 0.125 Angle : 0.473 10.600 33295 Z= 0.243 Chirality : 0.038 0.169 3705 Planarity : 0.004 0.053 4033 Dihedral : 12.818 108.058 3901 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.10 % Allowed : 22.16 % Favored : 74.75 % 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: 0.60 (0.16), residues: 2724 helix: 1.11 (0.18), residues: 931 sheet: 0.59 (0.23), residues: 519 loop : -0.13 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 247 HIS 0.010 0.001 HIS J 31 PHE 0.021 0.001 PHE J 17 TYR 0.020 0.001 TYR E 275 ARG 0.005 0.000 ARG J 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5155.05 seconds wall clock time: 94 minutes 21.55 seconds (5661.55 seconds total)