Starting phenix.real_space_refine on Sat Feb 17 13:45:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/02_2024/8fok_29352_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/02_2024/8fok_29352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/02_2024/8fok_29352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/02_2024/8fok_29352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/02_2024/8fok_29352_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/02_2024/8fok_29352_updated.pdb" } resolution = 3.56 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 34 5.49 5 S 94 5.16 5 C 11854 2.51 5 N 3234 2.21 5 O 3607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ASP 358": "OD1" <-> "OD2" Residue "1 PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 392": "OE1" <-> "OE2" Residue "1 PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 483": "OE1" <-> "OE2" Residue "1 PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 631": "OD1" <-> "OD2" Residue "1 ASP 646": "OD1" <-> "OD2" Residue "1 PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 689": "OD1" <-> "OD2" Residue "1 ASP 698": "OD1" <-> "OD2" Residue "1 GLU 725": "OE1" <-> "OE2" Residue "1 GLU 852": "OE1" <-> "OE2" Residue "1 ASP 864": "OD1" <-> "OD2" Residue "1 ASP 889": "OD1" <-> "OD2" Residue "1 ASP 891": "OD1" <-> "OD2" Residue "1 GLU 900": "OE1" <-> "OE2" Residue "1 TYR 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1007": "OD1" <-> "OD2" Residue "1 PHE 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1067": "OE1" <-> "OE2" Residue "1 ASP 1072": "OD1" <-> "OD2" Residue "1 GLU 1100": "OE1" <-> "OE2" Residue "1 GLU 1105": "OE1" <-> "OE2" Residue "1 TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1215": "OE1" <-> "OE2" Residue "1 ASP 1244": "OD1" <-> "OD2" Residue "1 ASP 1260": "OD1" <-> "OD2" Residue "1 GLU 1399": "OE1" <-> "OE2" Residue "1 ASP 1413": "OD1" <-> "OD2" Residue "1 GLU 1432": "OE1" <-> "OE2" Residue "1 GLU 1436": "OE1" <-> "OE2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 430": "OD1" <-> "OD2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 611": "OD1" <-> "OD2" Residue "C TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18827 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 8250 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1046, 8242 Classifications: {'peptide': 1046} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 50, 'TRANS': 995} Chain breaks: 5 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 1046, 8242 Classifications: {'peptide': 1046} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 50, 'TRANS': 995} Chain breaks: 5 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 8385 Chain: "A" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2866 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 333} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3555 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3532 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 416} Chain breaks: 5 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 430, 3532 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 416} Chain breaks: 5 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 3581 Chain: "C" Number of atoms: 3428 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3414 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 433, 3414 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3476 Chain: "T" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 415 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "P" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 305 Classifications: {'DNA': 4, 'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 13} 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 13324 SG CYS B 336 56.588 105.469 67.146 1.00 50.15 S ATOM 14113 SG CYS B 434 61.539 104.824 63.164 1.00 54.17 S ATOM 13981 SG CYS B 417 62.615 105.241 69.680 1.00 45.11 S ATOM 14430 SG CYS B 474 60.780 110.248 66.747 1.00 62.10 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASP 11414 " occ=0.25 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.75 residue: pdb=" N AASP C 263 " occ=0.30 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.70 residue: pdb=" N ACYS C 399 " occ=0.95 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.05 Time building chain proxies: 16.76, per 1000 atoms: 0.89 Number of scatterers: 18827 At special positions: 0 Unit cell: (95.22, 160.632, 163.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 94 16.00 P 34 15.00 O 3607 8.00 N 3234 7.00 C 11854 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: 7.87 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " Number of angles added : 12 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 18 sheets defined 43.3% alpha, 11.2% beta 5 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 8.21 Creating SS restraints... Processing helix chain '1' and resid 403 through 418 Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 481 through 488 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 683 through 690 Processing helix chain '1' and resid 702 through 707 Processing helix chain '1' and resid 716 through 723 Processing helix chain '1' and resid 738 through 742 removed outlier: 4.170A pdb=" N ASN 1 742 " --> pdb=" O GLN 1 739 " (cutoff:3.500A) Processing helix chain '1' and resid 745 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 794 through 808 removed outlier: 3.546A pdb=" N ASN 1 808 " --> pdb=" O GLU 1 804 " (cutoff:3.500A) Processing helix chain '1' and resid 868 through 876 Processing helix chain '1' and resid 905 through 924 Processing helix chain '1' and resid 933 through 954 removed outlier: 3.516A pdb=" N TYR 1 951 " --> pdb=" O ALA 1 947 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU 1 954 " --> pdb=" O MET 1 950 " (cutoff:3.500A) Processing helix chain '1' and resid 964 through 988 Processing helix chain '1' and resid 1009 through 1026 removed outlier: 3.713A pdb=" N ILE 11015 " --> pdb=" O ASP 11011 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU 11025 " --> pdb=" O ARG 11021 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG 11026 " --> pdb=" O LEU 11022 " (cutoff:3.500A) Processing helix chain '1' and resid 1080 through 1094 Processing helix chain '1' and resid 1099 through 1118 Processing helix chain '1' and resid 1124 through 1127 Processing helix chain '1' and resid 1147 through 1158 Processing helix chain '1' and resid 1190 through 1192 No H-bonds generated for 'chain '1' and resid 1190 through 1192' Processing helix chain '1' and resid 1196 through 1199 No H-bonds generated for 'chain '1' and resid 1196 through 1199' Processing helix chain '1' and resid 1210 through 1216 Processing helix chain '1' and resid 1219 through 1225 Processing helix chain '1' and resid 1234 through 1241 Processing helix chain '1' and resid 1245 through 1253 removed outlier: 3.760A pdb=" N ARG 11250 " --> pdb=" O LYS 11246 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG 11251 " --> pdb=" O LYS 11247 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU 11252 " --> pdb=" O TYR 11248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY 11253 " --> pdb=" O PHE 11249 " (cutoff:3.500A) Processing helix chain '1' and resid 1267 through 1270 No H-bonds generated for 'chain '1' and resid 1267 through 1270' Processing helix chain '1' and resid 1273 through 1278 Processing helix chain '1' and resid 1323 through 1342 removed outlier: 4.305A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1382 through 1396 removed outlier: 3.710A 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 1451 removed outlier: 3.663A pdb=" N VAL 11445 " --> pdb=" O GLY 11441 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP 11451 " --> pdb=" O LYS 11447 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 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: 4.958A pdb=" N ASP A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 4.800A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.873A pdb=" N GLU A 150 " --> pdb=" O ALA A 147 " (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: 4.128A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.330A 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 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 270 through 284 removed outlier: 3.631A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 removed outlier: 4.184A pdb=" N ASP A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.592A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 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 376 through 393 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 137 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 206 removed outlier: 4.728A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.713A 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 238 removed outlier: 3.673A pdb=" N ASN B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 283 Proline residue: B 279 - end of helix removed outlier: 4.489A pdb=" N GLU B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 298 Proline residue: B 289 - end of helix removed outlier: 3.583A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.484A 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 364 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 401 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 451 Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'C' and resid 254 through 276 removed outlier: 3.660A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' 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 445 Processing helix chain 'C' and resid 461 through 468 Processing helix chain 'C' and resid 470 through 475 removed outlier: 3.580A 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 567 Processing helix chain 'C' and resid 614 through 620 removed outlier: 3.790A pdb=" N LEU C 617 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) 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 496 through 498 removed outlier: 6.561A pdb=" N GLN 1 353 " --> pdb=" O LYS 1 373 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS 1 373 " --> pdb=" O GLN 1 353 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL 1 515 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 6.528A 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: 7.583A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 609 through 612 removed outlier: 3.607A pdb=" N VAL 1 586 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS 1 553 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN 1 544 " --> pdb=" O VAL 1 557 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE 1 559 " --> pdb=" O SER 1 542 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER 1 542 " --> pdb=" O ILE 1 559 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU 1 561 " --> pdb=" O SER 1 540 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER 1 540 " --> pdb=" O LEU 1 561 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA 1 563 " --> pdb=" O CYS 1 538 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS 1 538 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 634 through 637 removed outlier: 6.122A pdb=" N LEU 1 695 " --> pdb=" O ILE 1 635 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY 1 637 " --> pdb=" O LEU 1 695 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N CYS 1 697 " --> pdb=" O GLY 1 637 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '1' and resid 854 through 856 removed outlier: 7.007A pdb=" N LYS 11048 " --> pdb=" O HIS 11044 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 1032 through 1034 removed outlier: 4.426A pdb=" N CYS 11006 " --> pdb=" O TYR 1 859 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N LEU 1 861 " --> pdb=" O THR 11004 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR 11004 " --> pdb=" O LEU 1 861 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N MET 1 863 " --> pdb=" O ILE 11002 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE 11002 " --> pdb=" O MET 1 863 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE 1 865 " --> pdb=" O VAL 11000 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N VAL 11000 " --> pdb=" O PHE 1 865 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR 1 994 " --> pdb=" O MET 11001 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 1129 through 1132 Processing sheet with id= H, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.436A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '1' and resid 1305 through 1307 Processing sheet with id= J, first strand: chain '1' and resid 1346 through 1348 Processing sheet with id= K, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.601A pdb=" N ARG A 79 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 108 through 112 Processing sheet with id= M, first strand: chain 'B' and resid 226 through 228 removed outlier: 3.547A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 329 through 331 removed outlier: 4.131A pdb=" N ALA C 349 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 340 through 342 Processing sheet with id= P, first strand: chain 'C' and resid 375 through 377 removed outlier: 4.291A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 681 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 515 through 518 removed outlier: 5.937A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET C 518 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU C 484 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 522 through 524 removed outlier: 3.643A pdb=" N PHE C 524 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 630 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 648 " --> pdb=" O MET C 631 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 1973 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 8.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 3616 1.33 - 1.57: 15474 1.57 - 1.80: 164 1.80 - 2.04: 35 2.04 - 2.28: 13 Bond restraints: 19302 Sorted by residual: bond pdb=" CB PRO 1 894 " pdb=" CG PRO 1 894 " ideal model delta sigma weight residual 1.492 2.278 -0.786 5.00e-02 4.00e+02 2.47e+02 bond pdb=" C LEU 1 954 " pdb=" N GLY 1 955 " ideal model delta sigma weight residual 1.331 1.518 -0.187 1.46e-02 4.69e+03 1.64e+02 bond pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 1.503 1.114 0.389 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CG PRO 11266 " pdb=" CD PRO 11266 " ideal model delta sigma weight residual 1.503 1.181 0.322 3.40e-02 8.65e+02 8.98e+01 bond pdb=" CB PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 1.492 1.089 0.403 5.00e-02 4.00e+02 6.50e+01 ... (remaining 19297 not shown) Histogram of bond angle deviations from ideal: 23.80 - 49.02: 1 49.02 - 74.24: 13 74.24 - 99.46: 8 99.46 - 124.68: 25896 124.68 - 149.90: 366 Bond angle restraints: 26284 Sorted by residual: angle pdb=" CB PRO 1 894 " pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 106.10 23.80 82.30 3.20e+00 9.77e-02 6.62e+02 angle pdb=" CA PRO 1 894 " pdb=" N PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 112.00 78.26 33.74 1.40e+00 5.10e-01 5.81e+02 angle pdb=" N PRO 11266 " pdb=" CD PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 103.20 75.01 28.19 1.50e+00 4.44e-01 3.53e+02 angle pdb=" CA PRO 11266 " pdb=" CB PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 104.50 73.13 31.37 1.90e+00 2.77e-01 2.73e+02 angle pdb=" N PRO 1 894 " pdb=" CD PRO 1 894 " pdb=" CG PRO 1 894 " ideal model delta sigma weight residual 103.20 122.16 -18.96 1.50e+00 4.44e-01 1.60e+02 ... (remaining 26279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.27: 11026 28.27 - 56.54: 593 56.54 - 84.81: 71 84.81 - 113.07: 9 113.07 - 141.34: 1 Dihedral angle restraints: 11700 sinusoidal: 5005 harmonic: 6695 Sorted by residual: dihedral pdb=" N PRO 1 894 " pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " pdb=" CB PRO 1 894 " ideal model delta sinusoidal sigma weight residual 30.00 171.34 -141.34 1 1.50e+01 4.44e-03 7.60e+01 dihedral pdb=" N PRO 11266 " pdb=" CG PRO 11266 " pdb=" CD PRO 11266 " pdb=" CB PRO 11266 " ideal model delta sinusoidal sigma weight residual 30.00 97.28 -67.28 1 1.50e+01 4.44e-03 2.62e+01 dihedral pdb=" CA ALA C 349 " pdb=" C ALA C 349 " pdb=" N PHE C 350 " pdb=" CA PHE C 350 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2267 0.046 - 0.092: 495 0.092 - 0.138: 156 0.138 - 0.184: 5 0.184 - 0.230: 4 Chirality restraints: 2927 Sorted by residual: chirality pdb=" CG LEU C 510 " pdb=" CB LEU C 510 " pdb=" CD1 LEU C 510 " pdb=" CD2 LEU C 510 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU 1 449 " pdb=" CB LEU 1 449 " pdb=" CD1 LEU 1 449 " pdb=" CD2 LEU 1 449 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE 1 462 " pdb=" N ILE 1 462 " pdb=" C ILE 1 462 " pdb=" CB ILE 1 462 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 2924 not shown) Planarity restraints: 3278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU 1 954 " -0.034 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C LEU 1 954 " 0.110 2.00e-02 2.50e+03 pdb=" O LEU 1 954 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY 1 955 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 1 902 " 0.023 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ASP 1 902 " -0.095 2.00e-02 2.50e+03 pdb=" O ASP 1 902 " 0.040 2.00e-02 2.50e+03 pdb=" N GLN 1 903 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 633 " -0.085 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO C 634 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO C 634 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 634 " -0.064 5.00e-02 4.00e+02 ... (remaining 3275 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 449 2.69 - 3.24: 18682 3.24 - 3.80: 30551 3.80 - 4.35: 40386 4.35 - 4.90: 65526 Nonbonded interactions: 155594 Sorted by model distance: nonbonded pdb=" O THR 1 774 " pdb=" OG1 THR 1 778 " model vdw 2.141 2.440 nonbonded pdb=" OH TYR A 18 " pdb=" O PHE A 329 " model vdw 2.152 2.440 nonbonded pdb=" OH TYR B 51 " pdb=" OH TYR B 129 " model vdw 2.184 2.440 nonbonded pdb=" O TYR 1 859 " pdb=" OG1 THR 11004 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR A 209 " pdb=" OD1 ASP A 303 " model vdw 2.243 2.440 ... (remaining 155589 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=1.00 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: 1.470 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: 4.540 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 68.970 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.110 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 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 : 0.008 0.786 19302 Z= 0.637 Angle : 0.924 82.304 26284 Z= 0.471 Chirality : 0.042 0.230 2927 Planarity : 0.006 0.120 3278 Dihedral : 16.601 141.343 7356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.15 % Allowed : 17.14 % Favored : 82.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.45 % 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: 0.89 (0.18), residues: 2239 helix: 1.26 (0.16), residues: 1032 sheet: -0.23 (0.30), residues: 265 loop : 0.23 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 376 HIS 0.009 0.001 HIS A 27 PHE 0.021 0.002 PHE C 350 TYR 0.017 0.001 TYR 1 766 ARG 0.009 0.001 ARG 1 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.7815 (mt) cc_final: 0.7553 (mt) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.3370 time to fit residues: 55.0580 Evaluate side-chains 69 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 1244 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 178 optimal weight: 0.0060 chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 overall best weight: 7.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 385 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11433 GLN A 60 ASN B 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.789 19302 Z= 0.638 Angle : 0.854 81.279 26284 Z= 0.399 Chirality : 0.043 0.286 2927 Planarity : 0.005 0.091 3278 Dihedral : 10.081 84.447 2885 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.26 % Allowed : 16.39 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.92 (0.18), residues: 2239 helix: 1.28 (0.16), residues: 1026 sheet: -0.25 (0.30), residues: 270 loop : 0.29 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 376 HIS 0.007 0.001 HIS 1 684 PHE 0.019 0.002 PHE B 399 TYR 0.020 0.002 TYR B 503 ARG 0.004 0.001 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 74 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8057 (mt) cc_final: 0.7798 (mt) REVERT: 1 855 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7100 (tp) REVERT: 1 883 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8384 (m) REVERT: 1 1001 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7217 (mmt) outliers start: 45 outliers final: 24 residues processed: 117 average time/residue: 0.3052 time to fit residues: 56.7318 Evaluate side-chains 94 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1382 ASP Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 224 optimal weight: 0.0000 chunk 184 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 844 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.741 19302 Z= 0.587 Angle : 0.794 76.881 26284 Z= 0.371 Chirality : 0.042 0.174 2927 Planarity : 0.005 0.077 3278 Dihedral : 10.031 83.027 2883 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.21 % Allowed : 16.49 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.88 (0.18), residues: 2239 helix: 1.24 (0.16), residues: 1028 sheet: -0.25 (0.31), residues: 256 loop : 0.26 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 376 HIS 0.006 0.001 HIS 1 684 PHE 0.018 0.002 PHE B 399 TYR 0.019 0.001 TYR B 503 ARG 0.005 0.000 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 69 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8151 (mt) cc_final: 0.7868 (mt) REVERT: 1 883 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8350 (m) REVERT: 1 1330 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8295 (tp) outliers start: 44 outliers final: 30 residues processed: 112 average time/residue: 0.3052 time to fit residues: 54.2231 Evaluate side-chains 100 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 68 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 788 THR Chi-restraints excluded: chain 1 residue 844 GLN Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1382 ASP Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11421 GLN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 19302 Z= 0.369 Angle : 0.604 15.828 26284 Z= 0.318 Chirality : 0.042 0.163 2927 Planarity : 0.005 0.114 3278 Dihedral : 10.066 81.509 2883 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.56 % Allowed : 16.79 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.75 (0.18), residues: 2239 helix: 1.12 (0.16), residues: 1027 sheet: -0.35 (0.31), residues: 258 loop : 0.22 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 376 HIS 0.005 0.001 HIS C 606 PHE 0.019 0.002 PHE B 399 TYR 0.020 0.002 TYR B 503 ARG 0.006 0.001 ARG 1 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 66 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 584 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8702 (t) REVERT: 1 1001 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7215 (mmt) REVERT: 1 1073 MET cc_start: 0.6986 (mpp) cc_final: 0.6743 (mpp) REVERT: 1 1330 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8351 (tp) outliers start: 51 outliers final: 40 residues processed: 115 average time/residue: 0.2888 time to fit residues: 54.4285 Evaluate side-chains 108 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 65 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 584 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 788 THR Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1000 VAL Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1382 ASP Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 188 optimal weight: 0.1980 chunk 152 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19302 Z= 0.168 Angle : 0.510 10.192 26284 Z= 0.263 Chirality : 0.040 0.155 2927 Planarity : 0.004 0.075 3278 Dihedral : 9.851 79.263 2883 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.01 % Allowed : 17.69 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2239 helix: 1.40 (0.16), residues: 1024 sheet: -0.16 (0.31), residues: 262 loop : 0.35 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 PHE 0.013 0.001 PHE B 399 TYR 0.014 0.001 TYR B 503 ARG 0.003 0.000 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 71 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8170 (mt) cc_final: 0.7899 (mt) REVERT: B 74 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: B 388 MET cc_start: 0.5067 (mmp) cc_final: 0.4768 (tpt) outliers start: 40 outliers final: 23 residues processed: 111 average time/residue: 0.3210 time to fit residues: 57.2654 Evaluate side-chains 93 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 788 THR Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1382 ASP Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 54 optimal weight: 0.2980 chunk 220 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 844 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19302 Z= 0.242 Angle : 0.520 9.702 26284 Z= 0.266 Chirality : 0.040 0.154 2927 Planarity : 0.004 0.058 3278 Dihedral : 9.818 77.466 2883 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.36 % Allowed : 17.69 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2239 helix: 1.40 (0.16), residues: 1026 sheet: -0.23 (0.31), residues: 259 loop : 0.37 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 PHE 0.015 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.003 0.000 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 67 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8243 (mt) cc_final: 0.7978 (mt) REVERT: B 61 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6628 (t80) REVERT: B 74 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: B 388 MET cc_start: 0.5064 (mmp) cc_final: 0.4778 (tpt) outliers start: 47 outliers final: 34 residues processed: 112 average time/residue: 0.2846 time to fit residues: 52.0458 Evaluate side-chains 100 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 64 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 788 THR Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 125 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 0.0370 chunk 123 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19302 Z= 0.224 Angle : 0.512 8.081 26284 Z= 0.263 Chirality : 0.040 0.153 2927 Planarity : 0.004 0.057 3278 Dihedral : 9.795 75.860 2883 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 18.15 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2239 helix: 1.47 (0.16), residues: 1019 sheet: -0.35 (0.30), residues: 265 loop : 0.43 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 PHE 0.015 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.003 0.000 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 67 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8205 (mt) cc_final: 0.7928 (mt) REVERT: B 61 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6680 (t80) REVERT: B 388 MET cc_start: 0.5047 (mmp) cc_final: 0.4759 (tpt) outliers start: 43 outliers final: 36 residues processed: 108 average time/residue: 0.3043 time to fit residues: 53.8497 Evaluate side-chains 102 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 65 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 778 THR Chi-restraints excluded: chain 1 residue 788 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 30.0000 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 66 optimal weight: 0.0270 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS 1 736 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19302 Z= 0.262 Angle : 0.521 8.777 26284 Z= 0.267 Chirality : 0.040 0.152 2927 Planarity : 0.004 0.057 3278 Dihedral : 9.812 75.759 2883 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.21 % Allowed : 18.15 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2239 helix: 1.45 (0.17), residues: 1019 sheet: -0.41 (0.30), residues: 265 loop : 0.42 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 1 671 HIS 0.006 0.001 HIS 1 407 PHE 0.016 0.001 PHE B 399 TYR 0.017 0.001 TYR B 503 ARG 0.004 0.000 ARG 1 975 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 66 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8220 (mt) cc_final: 0.7941 (mt) REVERT: B 61 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.6758 (t80) REVERT: B 388 MET cc_start: 0.5043 (mmp) cc_final: 0.4752 (tpt) outliers start: 44 outliers final: 40 residues processed: 108 average time/residue: 0.3133 time to fit residues: 55.2018 Evaluate side-chains 104 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 63 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 778 THR Chi-restraints excluded: chain 1 residue 788 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1257 ASN Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1382 ASP Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.2980 chunk 210 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19302 Z= 0.227 Angle : 0.511 8.685 26284 Z= 0.262 Chirality : 0.040 0.153 2927 Planarity : 0.004 0.056 3278 Dihedral : 9.808 76.088 2883 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 18.20 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2239 helix: 1.48 (0.17), residues: 1019 sheet: -0.43 (0.30), residues: 254 loop : 0.43 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.010 0.001 HIS 1 407 PHE 0.015 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.004 0.000 ARG 1 975 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 64 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8231 (mt) cc_final: 0.7944 (mt) REVERT: B 61 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6744 (t80) REVERT: B 388 MET cc_start: 0.4995 (mmp) cc_final: 0.4706 (tpt) outliers start: 43 outliers final: 40 residues processed: 105 average time/residue: 0.2818 time to fit residues: 48.9328 Evaluate side-chains 105 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 64 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 778 THR Chi-restraints excluded: chain 1 residue 788 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1257 ASN Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1382 ASP Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 chunk 18 optimal weight: 0.0020 chunk 139 optimal weight: 0.0670 chunk 110 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.8730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 754 ASN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 980 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19302 Z= 0.141 Angle : 0.484 8.461 26284 Z= 0.247 Chirality : 0.039 0.154 2927 Planarity : 0.004 0.057 3278 Dihedral : 9.697 76.148 2883 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.35 % Allowed : 18.75 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2239 helix: 1.60 (0.17), residues: 1020 sheet: -0.24 (0.29), residues: 268 loop : 0.50 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 671 HIS 0.006 0.001 HIS 1 684 PHE 0.012 0.001 PHE B 399 TYR 0.017 0.001 TYR B 55 ARG 0.005 0.000 ARG 1 975 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 492 MET cc_start: 0.8335 (mmm) cc_final: 0.8097 (mmm) REVERT: 1 771 LEU cc_start: 0.8185 (mt) cc_final: 0.7913 (mt) REVERT: B 388 MET cc_start: 0.5041 (mmp) cc_final: 0.4768 (tpt) outliers start: 27 outliers final: 23 residues processed: 92 average time/residue: 0.3078 time to fit residues: 45.7039 Evaluate side-chains 88 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 65 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 778 THR Chi-restraints excluded: chain 1 residue 788 THR Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1382 ASP Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.039256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.029718 restraints weight = 393761.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.031379 restraints weight = 147860.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.031978 restraints weight = 67781.413| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19302 Z= 0.235 Angle : 0.507 8.896 26284 Z= 0.258 Chirality : 0.039 0.151 2927 Planarity : 0.004 0.058 3278 Dihedral : 9.734 77.745 2883 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.35 % Allowed : 18.80 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2239 helix: 1.61 (0.17), residues: 1019 sheet: -0.26 (0.30), residues: 263 loop : 0.49 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 PHE 0.015 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.005 0.000 ARG 1 975 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.96 seconds wall clock time: 54 minutes 11.05 seconds (3251.05 seconds total)