Starting phenix.real_space_refine on Tue Apr 9 21:27:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/04_2024/8fod_29346_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/04_2024/8fod_29346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/04_2024/8fod_29346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/04_2024/8fod_29346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/04_2024/8fod_29346_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/04_2024/8fod_29346_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 Fe 4 7.16 5 S 79 5.16 5 C 11110 2.51 5 N 2971 2.21 5 O 3325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 361": "OE1" <-> "OE2" Residue "1 PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 ASP 416": "OD1" <-> "OD2" Residue "1 ASP 633": "OD1" <-> "OD2" Residue "1 PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 718": "OE1" <-> "OE2" Residue "1 TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 727": "OE1" <-> "OE2" Residue "1 GLU 753": "OE1" <-> "OE2" Residue "1 TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1072": "OD1" <-> "OD2" Residue "1 TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1111": "OE1" <-> "OE2" Residue "1 TYR 1309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 1363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1405": "OE1" <-> "OE2" Residue "1 TYR 1448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "C PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 490": "OD1" <-> "OD2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 541": "OD1" <-> "OD2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17489 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 7607 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7552 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 50, 'TRANS': 932} Chain breaks: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 983, 7552 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 50, 'TRANS': 932} Chain breaks: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 7626 Chain: "A" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3052 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 359} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3507 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3484 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 419} Chain breaks: 5 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 433, 3484 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 419} Chain breaks: 5 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 3532 Chain: "C" Number of atoms: 3315 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 428, 3291 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 428, 3291 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 3339 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12831 SG CYS B 336 35.046 94.020 79.568 1.00 12.48 S ATOM 13601 SG CYS B 434 35.839 88.518 76.597 1.00 8.05 S ATOM 13475 SG CYS B 417 40.736 91.345 79.050 1.00 4.95 S ATOM 13912 SG CYS B 474 38.847 93.635 73.896 1.00 3.46 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AASN 1 745 " occ=0.31 ... (14 atoms not shown) pdb=" ND2BASN 1 745 " occ=0.69 residue: pdb=" N AGLN 1 941 " occ=0.41 ... (16 atoms not shown) pdb=" NE2BGLN 1 941 " occ=0.59 residue: pdb=" N AHIS 11044 " occ=0.39 ... (18 atoms not shown) pdb=" NE2BHIS 11044 " occ=0.61 residue: pdb=" N AASP 11414 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.55 residue: pdb=" N AASP C 263 " occ=0.93 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.07 residue: pdb=" N ACYS C 399 " occ=0.28 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.72 Time building chain proxies: 15.46, per 1000 atoms: 0.88 Number of scatterers: 17489 At special positions: 0 Unit cell: (114.264, 130.824, 148.212, 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) Fe 4 26.01 S 79 16.00 O 3325 8.00 N 2971 7.00 C 11110 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: 6.37 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " Number of angles added : 12 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 17 sheets defined 43.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain '1' and resid 403 through 418 removed outlier: 3.590A pdb=" N ILE 1 411 " --> pdb=" O HIS 1 407 " (cutoff:3.500A) Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 481 through 489 Processing helix chain '1' and resid 522 through 524 No H-bonds generated for 'chain '1' and resid 522 through 524' Processing helix chain '1' and resid 598 through 605 Processing helix chain '1' and resid 616 through 630 Processing helix chain '1' and resid 644 through 655 Processing helix chain '1' and resid 660 through 663 Processing helix chain '1' and resid 682 through 690 Processing helix chain '1' and resid 702 through 706 Processing helix chain '1' and resid 716 through 724 Processing helix chain '1' and resid 738 through 741 Processing helix chain '1' and resid 744 through 767 Processing helix chain '1' and resid 770 through 781 Processing helix chain '1' and resid 785 through 789 Processing helix chain '1' and resid 793 through 808 removed outlier: 3.759A pdb=" N LEU 1 801 " --> pdb=" O ASN 1 797 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN 1 808 " --> pdb=" O GLU 1 804 " (cutoff:3.500A) Processing helix chain '1' and resid 869 through 876 Processing helix chain '1' and resid 906 through 926 removed outlier: 3.642A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 930 through 953 removed outlier: 4.666A pdb=" N TYR 1 951 " --> pdb=" O ALA 1 947 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY 1 952 " --> pdb=" O ASN 1 948 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N CYS 1 953 " --> pdb=" O SER 1 949 " (cutoff:3.500A) Processing helix chain '1' and resid 964 through 987 Processing helix chain '1' and resid 1009 through 1026 Processing helix chain '1' and resid 1080 through 1093 Processing helix chain '1' and resid 1101 through 1119 Processing helix chain '1' and resid 1124 through 1127 Processing helix chain '1' and resid 1137 through 1139 No H-bonds generated for 'chain '1' and resid 1137 through 1139' Processing helix chain '1' and resid 1147 through 1155 Processing helix chain '1' and resid 1196 through 1200 Processing helix chain '1' and resid 1202 through 1204 No H-bonds generated for 'chain '1' and resid 1202 through 1204' Processing helix chain '1' and resid 1210 through 1215 Processing helix chain '1' and resid 1219 through 1225 removed outlier: 3.525A pdb=" N ARG 11224 " --> pdb=" O ALA 11220 " (cutoff:3.500A) Processing helix chain '1' and resid 1276 through 1279 removed outlier: 4.522A pdb=" N ASP 11279 " --> pdb=" O ARG 11276 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1276 through 1279' Processing helix chain '1' and resid 1323 through 1343 removed outlier: 4.064A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1382 through 1396 removed outlier: 3.835A pdb=" N PHE 11396 " --> pdb=" O PHE 11392 " (cutoff:3.500A) Processing helix chain '1' and resid 1398 through 1402 Processing helix chain '1' and resid 1424 through 1433 Processing helix chain '1' and resid 1435 through 1449 removed outlier: 4.109A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 40 through 43 No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 90 through 95 removed outlier: 4.974A pdb=" N ASP A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.777A pdb=" N ASP A 118 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 removed outlier: 3.595A pdb=" N GLU A 150 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP A 151 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 211 through 228 Proline residue: A 222 - end of helix removed outlier: 4.169A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 270 through 284 removed outlier: 3.711A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 removed outlier: 4.319A pdb=" N ASP A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.654A pdb=" N LYS A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 72 through 95 Processing helix chain 'B' and resid 99 through 112 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 121 through 139 Processing helix chain 'B' and resid 142 through 162 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 192 through 207 removed outlier: 4.920A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 255 through 280 Proline residue: B 279 - end of helix Processing helix chain 'B' and resid 285 through 298 Proline residue: B 289 - end of helix removed outlier: 4.346A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.961A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.697A pdb=" N TYR B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 435 through 438 No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 500 through 514 Processing helix chain 'C' and resid 255 through 276 removed outlier: 4.011A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 325 No H-bonds generated for 'chain 'C' and resid 322 through 325' Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 461 through 468 Processing helix chain 'C' and resid 470 through 475 removed outlier: 4.279A pdb=" N THR C 475 " --> pdb=" O PRO C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 541 No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 556 through 566 Processing helix chain 'C' and resid 614 through 616 No H-bonds generated for 'chain 'C' and resid 614 through 616' Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 694 through 697 No H-bonds generated for 'chain 'C' and resid 694 through 697' Processing sheet with id= A, first strand: chain '1' and resid 525 through 527 removed outlier: 6.956A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL 1 515 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL 1 517 " --> pdb=" O GLN 1 385 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 425 through 431 removed outlier: 7.688A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE 1 395 " --> pdb=" O LEU 1 446 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 695 through 698 removed outlier: 3.545A pdb=" N SER 1 542 " --> pdb=" O THR 1 560 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 1 544 " --> pdb=" O SER 1 558 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER 1 558 " --> pdb=" O GLN 1 544 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL 1 557 " --> pdb=" O ARG 1 587 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG 1 609 " --> pdb=" O THR 1 584 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL 1 586 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG 1 611 " --> pdb=" O VAL 1 586 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 854 through 856 removed outlier: 4.752A pdb=" N VAL 11037 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU 11052 " --> pdb=" O LYS 11039 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU 11041 " --> pdb=" O ALA 11050 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA 11050 " --> pdb=" O LEU 11041 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 1034 through 1038 removed outlier: 6.327A pdb=" N VAL 1 862 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL 11037 " --> pdb=" O VAL 1 860 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL 1 860 " --> pdb=" O VAL 11037 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 1129 through 1132 Processing sheet with id= G, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.559A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 1305 through 1307 Processing sheet with id= I, first strand: chain '1' and resid 1346 through 1348 Processing sheet with id= J, first strand: chain 'A' and resid 47 through 50 Processing sheet with id= K, first strand: chain 'A' and resid 108 through 112 Processing sheet with id= L, first strand: chain 'B' and resid 225 through 228 removed outlier: 3.547A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.856A pdb=" N VAL C 330 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 301 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 340 through 342 Processing sheet with id= O, first strand: chain 'C' and resid 375 through 377 removed outlier: 4.240A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 681 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 515 through 518 removed outlier: 6.468A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N MET C 518 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU C 484 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.458A pdb=" N ILE C 630 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 648 " --> pdb=" O MET C 631 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.40 Time building geometry restraints manager: 6.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 7227 1.39 - 1.61: 10531 1.61 - 1.84: 103 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 17873 Sorted by residual: bond pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 1.473 1.579 -0.106 1.40e-02 5.10e+03 5.73e+01 bond pdb=" CD GLN 1 544 " pdb=" NE2 GLN 1 544 " ideal model delta sigma weight residual 1.328 1.192 0.136 2.10e-02 2.27e+03 4.19e+01 bond pdb=" CA ALA 1 649 " pdb=" CB ALA 1 649 " ideal model delta sigma weight residual 1.528 1.463 0.065 1.56e-02 4.11e+03 1.74e+01 bond pdb=" C HIS A 210 " pdb=" O HIS A 210 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.36e-02 5.41e+03 1.39e+01 bond pdb=" CA PRO A 247 " pdb=" C PRO A 247 " ideal model delta sigma weight residual 1.520 1.571 -0.052 1.42e-02 4.96e+03 1.34e+01 ... (remaining 17868 not shown) Histogram of bond angle deviations from ideal: 73.57 - 87.92: 13 87.92 - 102.28: 50 102.28 - 116.63: 12230 116.63 - 130.98: 11927 130.98 - 145.34: 64 Bond angle restraints: 24284 Sorted by residual: angle pdb=" CA PRO A 247 " pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 112.00 83.12 28.88 1.40e+00 5.10e-01 4.26e+02 angle pdb=" CA HIS A 210 " pdb=" C HIS A 210 " pdb=" O HIS A 210 " ideal model delta sigma weight residual 119.80 114.12 5.68 1.00e+00 1.00e+00 3.22e+01 angle pdb=" CA HIS A 210 " pdb=" C HIS A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 118.85 123.89 -5.04 9.50e-01 1.11e+00 2.81e+01 angle pdb=" C LEU A 246 " pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 125.00 145.34 -20.34 4.10e+00 5.95e-02 2.46e+01 angle pdb=" C ILE 11409 " pdb=" CA ILE 11409 " pdb=" CB ILE 11409 " ideal model delta sigma weight residual 112.02 105.87 6.15 1.31e+00 5.83e-01 2.21e+01 ... (remaining 24279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 9817 17.67 - 35.34: 833 35.34 - 53.02: 176 53.02 - 70.69: 33 70.69 - 88.36: 20 Dihedral angle restraints: 10879 sinusoidal: 4251 harmonic: 6628 Sorted by residual: dihedral pdb=" CA LEU A 246 " pdb=" C LEU A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LYS B 393 " pdb=" C LYS B 393 " pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta harmonic sigma weight residual 180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR B 71 " pdb=" C THR B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 10876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2513 0.087 - 0.173: 214 0.173 - 0.260: 5 0.260 - 0.346: 1 0.346 - 0.433: 2 Chirality restraints: 2735 Sorted by residual: chirality pdb=" CA PRO A 211 " pdb=" N PRO A 211 " pdb=" C PRO A 211 " pdb=" CB PRO A 211 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CB VAL C 326 " pdb=" CA VAL C 326 " pdb=" CG1 VAL C 326 " pdb=" CG2 VAL C 326 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB ILE C 632 " pdb=" CA ILE C 632 " pdb=" CG1 ILE C 632 " pdb=" CG2 ILE C 632 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 2732 not shown) Planarity restraints: 3165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 246 " 0.089 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A 247 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 1 462 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO 1 463 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO 1 463 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO 1 463 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 35 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 36 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " -0.048 5.00e-02 4.00e+02 ... (remaining 3162 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 672 2.71 - 3.26: 17881 3.26 - 3.81: 27938 3.81 - 4.35: 34806 4.35 - 4.90: 58936 Nonbonded interactions: 140233 Sorted by model distance: nonbonded pdb=" OH TYR A 209 " pdb=" OD1 ASP A 303 " model vdw 2.167 2.440 nonbonded pdb=" OH TYR A 23 " pdb=" O PRO A 328 " model vdw 2.185 2.440 nonbonded pdb=" O ARG 1 537 " pdb=" N ASP 1 633 " model vdw 2.208 2.520 nonbonded pdb=" OD2 ASP C 541 " pdb=" OH TYR C 571 " model vdw 2.248 2.440 nonbonded pdb=" O THR B 166 " pdb=" OG1 THR B 169 " model vdw 2.257 2.440 ... (remaining 140228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 4.460 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 62.520 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 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 : 0.006 0.154 17873 Z= 0.356 Angle : 0.831 28.882 24284 Z= 0.470 Chirality : 0.048 0.433 2735 Planarity : 0.006 0.111 3165 Dihedral : 14.421 88.359 6575 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 0.27 % Allowed : 11.69 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.31 (0.18), residues: 2221 helix: 0.67 (0.16), residues: 1022 sheet: -0.20 (0.32), residues: 244 loop : -0.02 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 695 HIS 0.012 0.002 HIS B 131 PHE 0.029 0.003 PHE C 268 TYR 0.025 0.002 TYR A 59 ARG 0.031 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 308 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 449 LEU cc_start: 0.7627 (mp) cc_final: 0.7416 (mp) REVERT: 1 567 ILE cc_start: 0.8432 (mm) cc_final: 0.8135 (mm) REVERT: 1 703 MET cc_start: 0.7040 (tpt) cc_final: 0.6415 (tpt) REVERT: 1 855 LEU cc_start: 0.6916 (tt) cc_final: 0.6689 (tp) REVERT: 1 980 ASN cc_start: 0.5490 (t0) cc_final: 0.5245 (t0) REVERT: 1 1015 ILE cc_start: 0.5503 (mm) cc_final: 0.5087 (tt) REVERT: 1 1436 GLU cc_start: 0.6239 (tt0) cc_final: 0.6004 (tt0) REVERT: 1 1438 MET cc_start: 0.5856 (mmt) cc_final: 0.5210 (mmp) REVERT: A 49 MET cc_start: 0.4492 (mtt) cc_final: 0.4257 (mtm) REVERT: B 96 ASN cc_start: 0.6739 (m-40) cc_final: 0.6181 (m-40) REVERT: B 119 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6895 (tm-30) REVERT: B 224 PHE cc_start: 0.6363 (m-80) cc_final: 0.5975 (m-10) REVERT: B 277 TYR cc_start: 0.5576 (m-80) cc_final: 0.5170 (m-80) REVERT: B 388 MET cc_start: 0.7428 (mmm) cc_final: 0.7044 (mmt) REVERT: B 443 ARG cc_start: 0.6224 (mtp180) cc_final: 0.6011 (mtp180) outliers start: 5 outliers final: 1 residues processed: 311 average time/residue: 0.3167 time to fit residues: 147.5883 Evaluate side-chains 208 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 294 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 67 optimal weight: 0.0970 chunk 105 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 935 GLN 1 941 GLN A 11024 ASN 11088 HIS 11194 HIS A 210 HIS ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 339 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17873 Z= 0.306 Angle : 0.675 13.577 24284 Z= 0.349 Chirality : 0.046 0.340 2735 Planarity : 0.006 0.070 3165 Dihedral : 5.008 30.950 2421 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.39 % Allowed : 12.27 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.28 (0.18), residues: 2221 helix: 0.77 (0.16), residues: 1019 sheet: -0.42 (0.30), residues: 263 loop : -0.13 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 695 HIS 0.009 0.002 HIS B 131 PHE 0.029 0.003 PHE B 375 TYR 0.020 0.002 TYR B 352 ARG 0.007 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: 1 449 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7559 (mp) REVERT: 1 629 VAL cc_start: 0.7168 (p) cc_final: 0.6953 (t) REVERT: 1 1015 ILE cc_start: 0.5415 (mm) cc_final: 0.5095 (tt) REVERT: 1 1053 THR cc_start: 0.6260 (p) cc_final: 0.6055 (p) REVERT: 1 1100 GLU cc_start: 0.5415 (pm20) cc_final: 0.5149 (pt0) REVERT: 1 1438 MET cc_start: 0.6015 (mmt) cc_final: 0.5145 (mmp) REVERT: A 51 PHE cc_start: 0.4650 (OUTLIER) cc_final: 0.3746 (t80) REVERT: B 119 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7163 (tm-30) REVERT: B 128 TYR cc_start: 0.5783 (OUTLIER) cc_final: 0.3931 (m-80) REVERT: B 234 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6328 (tt0) REVERT: B 277 TYR cc_start: 0.5796 (m-80) cc_final: 0.5350 (m-80) REVERT: C 392 SER cc_start: 0.4952 (m) cc_final: 0.4525 (p) REVERT: C 402 TYR cc_start: 0.6705 (m-80) cc_final: 0.5942 (m-80) outliers start: 45 outliers final: 20 residues processed: 257 average time/residue: 0.2892 time to fit residues: 114.0964 Evaluate side-chains 231 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 643 VAL Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 217 optimal weight: 0.0870 chunk 179 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 983 GLN A 60 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B 418 HIS ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17873 Z= 0.186 Angle : 0.572 12.559 24284 Z= 0.291 Chirality : 0.042 0.308 2735 Planarity : 0.005 0.063 3165 Dihedral : 4.563 27.661 2421 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.59 % Allowed : 13.71 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2221 helix: 1.09 (0.16), residues: 1018 sheet: -0.54 (0.30), residues: 249 loop : -0.01 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 695 HIS 0.008 0.001 HIS B 418 PHE 0.019 0.002 PHE B 75 TYR 0.023 0.002 TYR B 397 ARG 0.009 0.001 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 449 LEU cc_start: 0.7744 (mp) cc_final: 0.7473 (mp) REVERT: 1 1015 ILE cc_start: 0.5341 (mm) cc_final: 0.4926 (tt) REVERT: 1 1040 LYS cc_start: 0.7252 (mtpp) cc_final: 0.6691 (mtpt) REVERT: 1 1053 THR cc_start: 0.6276 (p) cc_final: 0.5996 (p) REVERT: 1 1168 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6802 (pt) REVERT: 1 1438 MET cc_start: 0.5723 (mmt) cc_final: 0.4512 (mmp) REVERT: B 119 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7035 (tm-30) REVERT: B 234 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6217 (tt0) REVERT: B 277 TYR cc_start: 0.5919 (m-80) cc_final: 0.5488 (m-80) REVERT: C 392 SER cc_start: 0.5141 (m) cc_final: 0.4720 (p) outliers start: 29 outliers final: 20 residues processed: 227 average time/residue: 0.2832 time to fit residues: 100.6153 Evaluate side-chains 218 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 470 THR Chi-restraints excluded: chain 1 residue 555 GLU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 643 VAL Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 213 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 523 GLN 11388 GLN 11450 ASN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17873 Z= 0.347 Angle : 0.703 13.038 24284 Z= 0.361 Chirality : 0.046 0.376 2735 Planarity : 0.006 0.058 3165 Dihedral : 5.090 22.786 2419 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 3.03 % Allowed : 13.02 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.06 (0.18), residues: 2221 helix: 0.73 (0.16), residues: 1002 sheet: -0.74 (0.32), residues: 241 loop : -0.35 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 376 HIS 0.040 0.002 HIS B 418 PHE 0.046 0.003 PHE B 375 TYR 0.024 0.002 TYR 11391 ARG 0.016 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 208 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 416 ASP cc_start: 0.6405 (m-30) cc_final: 0.6159 (m-30) REVERT: 1 798 GLU cc_start: 0.6504 (tt0) cc_final: 0.6303 (mt-10) REVERT: 1 1015 ILE cc_start: 0.5422 (mm) cc_final: 0.4928 (tt) REVERT: 1 1053 THR cc_start: 0.6384 (p) cc_final: 0.6141 (p) REVERT: 1 1168 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6823 (pt) REVERT: 1 1303 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7272 (m-40) REVERT: 1 1351 SER cc_start: 0.7673 (m) cc_final: 0.7166 (p) REVERT: 1 1438 MET cc_start: 0.5705 (mmt) cc_final: 0.4780 (mmp) REVERT: A 51 PHE cc_start: 0.4868 (OUTLIER) cc_final: 0.3228 (m-80) REVERT: B 121 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7602 (tt) REVERT: B 128 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.4419 (m-80) REVERT: B 234 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6112 (tt0) REVERT: B 415 TRP cc_start: 0.6759 (OUTLIER) cc_final: 0.6339 (m-10) REVERT: C 272 ILE cc_start: 0.6151 (OUTLIER) cc_final: 0.5876 (mm) REVERT: C 392 SER cc_start: 0.5429 (m) cc_final: 0.4834 (p) REVERT: C 425 LYS cc_start: 0.7424 (mttt) cc_final: 0.6356 (tptt) REVERT: C 480 ILE cc_start: 0.7675 (mt) cc_final: 0.7422 (mp) outliers start: 54 outliers final: 32 residues processed: 248 average time/residue: 0.2850 time to fit residues: 111.0709 Evaluate side-chains 234 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 469 ASP Chi-restraints excluded: chain 1 residue 470 THR Chi-restraints excluded: chain 1 residue 555 GLU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 647 VAL Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1303 ASN Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 182 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17873 Z= 0.225 Angle : 0.589 11.921 24284 Z= 0.300 Chirality : 0.044 0.493 2735 Planarity : 0.005 0.056 3165 Dihedral : 4.772 18.924 2419 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.39 % Allowed : 14.72 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.25 (0.18), residues: 2221 helix: 0.93 (0.16), residues: 1006 sheet: -0.75 (0.31), residues: 257 loop : -0.27 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 376 HIS 0.012 0.001 HIS B 418 PHE 0.034 0.002 PHE B 375 TYR 0.020 0.002 TYR A 154 ARG 0.005 0.001 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 733 ILE cc_start: 0.8427 (mt) cc_final: 0.8224 (mm) REVERT: 1 1015 ILE cc_start: 0.5408 (mm) cc_final: 0.4900 (tt) REVERT: 1 1053 THR cc_start: 0.6389 (p) cc_final: 0.6158 (p) REVERT: 1 1168 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6786 (pt) REVERT: 1 1351 SER cc_start: 0.7770 (m) cc_final: 0.7295 (p) REVERT: 1 1438 MET cc_start: 0.5723 (mmt) cc_final: 0.4441 (mmp) REVERT: B 87 LEU cc_start: 0.6897 (mp) cc_final: 0.6553 (mp) REVERT: B 128 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.4275 (m-80) REVERT: B 234 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6066 (tt0) REVERT: B 415 TRP cc_start: 0.6686 (OUTLIER) cc_final: 0.6177 (m-10) REVERT: C 272 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5834 (mm) REVERT: C 392 SER cc_start: 0.5423 (m) cc_final: 0.4820 (p) REVERT: C 425 LYS cc_start: 0.7431 (mttt) cc_final: 0.6364 (tptt) REVERT: C 480 ILE cc_start: 0.7609 (mt) cc_final: 0.7347 (mp) outliers start: 42 outliers final: 30 residues processed: 235 average time/residue: 0.2929 time to fit residues: 108.4204 Evaluate side-chains 228 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 470 THR Chi-restraints excluded: chain 1 residue 555 GLU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 643 VAL Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1188 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11404 GLN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17873 Z= 0.186 Angle : 0.561 11.651 24284 Z= 0.284 Chirality : 0.042 0.365 2735 Planarity : 0.005 0.058 3165 Dihedral : 4.550 18.393 2419 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.02 % Allowed : 15.14 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.40 (0.18), residues: 2221 helix: 1.07 (0.16), residues: 1012 sheet: -0.60 (0.31), residues: 270 loop : -0.23 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 376 HIS 0.017 0.001 HIS B 418 PHE 0.036 0.002 PHE B 375 TYR 0.014 0.001 TYR B 352 ARG 0.007 0.000 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 733 ILE cc_start: 0.8372 (mt) cc_final: 0.8014 (mm) REVERT: 1 1015 ILE cc_start: 0.5364 (mm) cc_final: 0.4928 (tt) REVERT: 1 1040 LYS cc_start: 0.7244 (mtpp) cc_final: 0.6729 (mtpt) REVERT: 1 1053 THR cc_start: 0.6376 (p) cc_final: 0.6111 (p) REVERT: 1 1168 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6890 (mt) REVERT: 1 1351 SER cc_start: 0.7848 (m) cc_final: 0.7427 (p) REVERT: 1 1438 MET cc_start: 0.5702 (mmt) cc_final: 0.4410 (mmp) REVERT: B 87 LEU cc_start: 0.6952 (mp) cc_final: 0.6628 (mp) REVERT: B 128 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.4150 (m-80) REVERT: B 234 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6077 (tt0) REVERT: B 415 TRP cc_start: 0.6594 (OUTLIER) cc_final: 0.6059 (m-10) REVERT: C 392 SER cc_start: 0.5388 (m) cc_final: 0.4746 (p) REVERT: C 425 LYS cc_start: 0.7449 (mttt) cc_final: 0.6412 (tptt) REVERT: C 480 ILE cc_start: 0.7564 (mt) cc_final: 0.7353 (mp) outliers start: 35 outliers final: 28 residues processed: 226 average time/residue: 0.2919 time to fit residues: 104.0647 Evaluate side-chains 231 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 470 THR Chi-restraints excluded: chain 1 residue 555 GLU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 643 VAL Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1188 SER Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11404 GLN A 168 HIS ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17873 Z= 0.250 Angle : 0.603 11.996 24284 Z= 0.307 Chirality : 0.044 0.374 2735 Planarity : 0.005 0.060 3165 Dihedral : 4.741 22.984 2419 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.60 % Allowed : 15.14 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.22 (0.18), residues: 2221 helix: 0.90 (0.16), residues: 1017 sheet: -0.68 (0.31), residues: 266 loop : -0.32 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 376 HIS 0.012 0.001 HIS B 418 PHE 0.043 0.002 PHE B 375 TYR 0.021 0.002 TYR A 154 ARG 0.008 0.001 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 208 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 715 ASP cc_start: 0.7368 (m-30) cc_final: 0.7061 (t0) REVERT: 1 733 ILE cc_start: 0.8395 (mt) cc_final: 0.8042 (mm) REVERT: 1 1015 ILE cc_start: 0.5450 (mm) cc_final: 0.4931 (tt) REVERT: 1 1040 LYS cc_start: 0.7253 (mtpp) cc_final: 0.6727 (mtpt) REVERT: 1 1053 THR cc_start: 0.6489 (p) cc_final: 0.6202 (p) REVERT: 1 1168 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6790 (pt) REVERT: 1 1303 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7192 (m-40) REVERT: 1 1351 SER cc_start: 0.8009 (m) cc_final: 0.7642 (p) REVERT: 1 1438 MET cc_start: 0.5660 (mmt) cc_final: 0.4356 (mmp) REVERT: A 148 LEU cc_start: 0.5090 (mt) cc_final: 0.4807 (mt) REVERT: B 87 LEU cc_start: 0.7126 (mp) cc_final: 0.6799 (mp) REVERT: B 121 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7612 (tt) REVERT: B 128 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.4239 (m-80) REVERT: B 196 TYR cc_start: 0.8075 (t80) cc_final: 0.7857 (t80) REVERT: B 234 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6055 (tt0) REVERT: B 415 TRP cc_start: 0.6633 (OUTLIER) cc_final: 0.6252 (m-10) REVERT: C 272 ILE cc_start: 0.6144 (OUTLIER) cc_final: 0.5873 (mm) REVERT: C 392 SER cc_start: 0.5385 (m) cc_final: 0.4803 (p) REVERT: C 425 LYS cc_start: 0.7717 (mttt) cc_final: 0.6573 (tptt) REVERT: C 480 ILE cc_start: 0.7681 (mt) cc_final: 0.7391 (mp) REVERT: C 672 CYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7861 (p) outliers start: 46 outliers final: 34 residues processed: 241 average time/residue: 0.2803 time to fit residues: 105.0720 Evaluate side-chains 241 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 555 GLU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 643 VAL Chi-restraints excluded: chain 1 residue 647 VAL Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1188 SER Chi-restraints excluded: chain 1 residue 1197 ASN Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1303 ASN Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 728 HIS A 34 HIS A 183 GLN A 198 ASN A 323 HIS B 185 ASN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 17873 Z= 0.400 Angle : 0.759 12.752 24284 Z= 0.389 Chirality : 0.049 0.574 2735 Planarity : 0.006 0.058 3165 Dihedral : 5.527 23.592 2419 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.19 % Allowed : 15.30 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.51 (0.17), residues: 2221 helix: 0.32 (0.16), residues: 1008 sheet: -0.95 (0.31), residues: 259 loop : -0.75 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 376 HIS 0.008 0.002 HIS B 293 PHE 0.050 0.003 PHE B 375 TYR 0.026 0.003 TYR 11391 ARG 0.010 0.001 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 206 time to evaluate : 2.228 Fit side-chains REVERT: 1 551 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6510 (pm20) REVERT: 1 661 SER cc_start: 0.6940 (OUTLIER) cc_final: 0.6739 (t) REVERT: 1 715 ASP cc_start: 0.7594 (m-30) cc_final: 0.7284 (t0) REVERT: 1 1053 THR cc_start: 0.6480 (p) cc_final: 0.6215 (p) REVERT: 1 1168 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6875 (pt) REVERT: 1 1276 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.4970 (tpt170) REVERT: 1 1296 PHE cc_start: 0.7979 (t80) cc_final: 0.7777 (t80) REVERT: 1 1303 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7418 (m-40) REVERT: 1 1351 SER cc_start: 0.8062 (m) cc_final: 0.7726 (p) REVERT: 1 1438 MET cc_start: 0.5600 (mmt) cc_final: 0.4195 (mmm) REVERT: A 148 LEU cc_start: 0.5304 (mt) cc_final: 0.5063 (mt) REVERT: B 121 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7780 (tt) REVERT: B 128 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.4480 (m-80) REVERT: B 234 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6205 (tt0) REVERT: B 298 TYR cc_start: 0.5011 (OUTLIER) cc_final: 0.3572 (t80) REVERT: B 415 TRP cc_start: 0.6679 (OUTLIER) cc_final: 0.6429 (m-10) REVERT: C 425 LYS cc_start: 0.7839 (mttt) cc_final: 0.6683 (tptt) REVERT: C 480 ILE cc_start: 0.7737 (mt) cc_final: 0.7422 (mp) outliers start: 57 outliers final: 37 residues processed: 247 average time/residue: 0.2928 time to fit residues: 113.4229 Evaluate side-chains 238 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 469 ASP Chi-restraints excluded: chain 1 residue 470 THR Chi-restraints excluded: chain 1 residue 551 GLU Chi-restraints excluded: chain 1 residue 555 GLU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 643 VAL Chi-restraints excluded: chain 1 residue 647 VAL Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1188 SER Chi-restraints excluded: chain 1 residue 1197 ASN Chi-restraints excluded: chain 1 residue 1276 ARG Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1303 ASN Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 0.0970 chunk 186 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 130 optimal weight: 40.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 198 ASN B 185 ASN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17873 Z= 0.202 Angle : 0.589 11.185 24284 Z= 0.300 Chirality : 0.043 0.193 2735 Planarity : 0.005 0.058 3165 Dihedral : 4.923 22.663 2419 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.34 % Allowed : 16.63 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 (0.18), residues: 2221 helix: 0.70 (0.16), residues: 1022 sheet: -0.92 (0.31), residues: 275 loop : -0.51 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 376 HIS 0.013 0.001 HIS A 34 PHE 0.033 0.002 PHE B 375 TYR 0.025 0.002 TYR A 154 ARG 0.010 0.001 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 1.993 Fit side-chains REVERT: 1 551 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6396 (pm20) REVERT: 1 685 PHE cc_start: 0.7279 (t80) cc_final: 0.7068 (t80) REVERT: 1 715 ASP cc_start: 0.7280 (m-30) cc_final: 0.6964 (t0) REVERT: 1 1040 LYS cc_start: 0.7251 (mtpp) cc_final: 0.6725 (mtpt) REVERT: 1 1053 THR cc_start: 0.6453 (p) cc_final: 0.6163 (p) REVERT: 1 1168 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6911 (pt) REVERT: 1 1276 ARG cc_start: 0.5482 (OUTLIER) cc_final: 0.4746 (tpt170) REVERT: 1 1351 SER cc_start: 0.8044 (m) cc_final: 0.7750 (p) REVERT: 1 1438 MET cc_start: 0.5481 (mmt) cc_final: 0.4058 (mmm) REVERT: A 148 LEU cc_start: 0.5117 (mt) cc_final: 0.4867 (mt) REVERT: B 121 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7733 (tt) REVERT: B 128 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.4251 (m-80) REVERT: B 234 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6189 (tt0) REVERT: B 298 TYR cc_start: 0.4805 (OUTLIER) cc_final: 0.3294 (t80) REVERT: B 415 TRP cc_start: 0.6481 (OUTLIER) cc_final: 0.6051 (m-10) REVERT: C 425 LYS cc_start: 0.7778 (mttt) cc_final: 0.6637 (tptt) REVERT: C 480 ILE cc_start: 0.7719 (mt) cc_final: 0.7440 (mp) outliers start: 41 outliers final: 29 residues processed: 233 average time/residue: 0.2923 time to fit residues: 105.6674 Evaluate side-chains 232 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 551 GLU Chi-restraints excluded: chain 1 residue 555 GLU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 643 VAL Chi-restraints excluded: chain 1 residue 647 VAL Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1098 ASP Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1197 ASN Chi-restraints excluded: chain 1 residue 1276 ARG Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 135 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 139 optimal weight: 0.0020 overall best weight: 2.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 185 ASN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17873 Z= 0.229 Angle : 0.609 11.356 24284 Z= 0.309 Chirality : 0.043 0.189 2735 Planarity : 0.005 0.060 3165 Dihedral : 4.879 24.512 2419 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.13 % Allowed : 16.95 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.04 (0.18), residues: 2221 helix: 0.77 (0.16), residues: 1018 sheet: -0.88 (0.31), residues: 274 loop : -0.53 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 376 HIS 0.008 0.001 HIS B 131 PHE 0.032 0.002 PHE B 375 TYR 0.023 0.002 TYR A 154 ARG 0.013 0.001 ARG C 654 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 193 time to evaluate : 2.278 Fit side-chains REVERT: 1 551 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6396 (pm20) REVERT: 1 685 PHE cc_start: 0.7304 (t80) cc_final: 0.7096 (t80) REVERT: 1 715 ASP cc_start: 0.7257 (m-30) cc_final: 0.6959 (t0) REVERT: 1 1053 THR cc_start: 0.6482 (p) cc_final: 0.6214 (p) REVERT: 1 1168 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.6930 (pt) REVERT: 1 1276 ARG cc_start: 0.5424 (OUTLIER) cc_final: 0.4660 (tpt170) REVERT: 1 1351 SER cc_start: 0.8009 (m) cc_final: 0.7674 (p) REVERT: 1 1438 MET cc_start: 0.5390 (mmt) cc_final: 0.4035 (mmm) REVERT: A 148 LEU cc_start: 0.5173 (mt) cc_final: 0.4910 (mt) REVERT: B 121 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7705 (tt) REVERT: B 128 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.4255 (m-80) REVERT: B 234 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6125 (tt0) REVERT: B 298 TYR cc_start: 0.4857 (OUTLIER) cc_final: 0.3370 (t80) REVERT: B 415 TRP cc_start: 0.6540 (OUTLIER) cc_final: 0.6113 (m-10) REVERT: C 425 LYS cc_start: 0.7804 (mttt) cc_final: 0.6656 (tptt) REVERT: C 480 ILE cc_start: 0.7701 (mt) cc_final: 0.7410 (mp) outliers start: 37 outliers final: 28 residues processed: 216 average time/residue: 0.3106 time to fit residues: 104.8434 Evaluate side-chains 226 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 520 ASP Chi-restraints excluded: chain 1 residue 551 GLU Chi-restraints excluded: chain 1 residue 555 GLU Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 647 VAL Chi-restraints excluded: chain 1 residue 744 VAL Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1098 ASP Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1197 ASN Chi-restraints excluded: chain 1 residue 1276 ARG Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 154 optimal weight: 0.4980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 198 ASN B 96 ASN B 185 ASN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.173671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.160893 restraints weight = 103040.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.162886 restraints weight = 99010.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.163703 restraints weight = 37681.599| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4100 r_free = 0.4100 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4100 r_free = 0.4100 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.4100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17873 Z= 0.224 Angle : 0.599 11.436 24284 Z= 0.303 Chirality : 0.043 0.175 2735 Planarity : 0.005 0.060 3165 Dihedral : 4.860 26.140 2419 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.23 % Allowed : 16.68 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.00 (0.18), residues: 2221 helix: 0.82 (0.16), residues: 1018 sheet: -0.89 (0.31), residues: 271 loop : -0.51 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 376 HIS 0.015 0.001 HIS A 34 PHE 0.032 0.002 PHE B 375 TYR 0.022 0.002 TYR A 154 ARG 0.009 0.001 ARG C 654 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.94 seconds wall clock time: 64 minutes 30.75 seconds (3870.75 seconds total)