Starting phenix.real_space_refine on Thu Aug 6 14:21:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v54_42979/08_2026/8v54_42979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v54_42979/08_2026/8v54_42979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v54_42979/08_2026/8v54_42979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v54_42979/08_2026/8v54_42979.map" model { file = "/net/cci-nas-00/data/ceres_data/8v54_42979/08_2026/8v54_42979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v54_42979/08_2026/8v54_42979.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 79 5.16 5 C 9877 2.51 5 N 2759 2.21 5 O 2967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15728 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7599 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 894} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3624 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 417, 3358 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 417, 3358 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3167 Chain: "C" Number of atoms: 3562 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 392} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 392} Chain breaks: 1 bond proxies already assigned to first conformer: 3128 Chain: "P" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 465 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 478 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Residues with excluded nonbonded symmetry interactions: 65 residue: pdb=" N APHE B 145 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 145 " occ=0.50 residue: pdb=" N ALEU B 147 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 147 " occ=0.50 residue: pdb=" N AVAL B 148 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL B 148 " occ=0.50 residue: pdb=" N ASER B 149 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 149 " occ=0.50 residue: pdb=" N AALA B 150 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 150 " occ=0.50 residue: pdb=" N AGLU B 151 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 151 " occ=0.50 residue: pdb=" N ATHR B 152 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 152 " occ=0.50 residue: pdb=" N ALEU B 153 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 153 " occ=0.50 residue: pdb=" N AARG B 154 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 154 " occ=0.50 residue: pdb=" N AGLU B 155 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 155 " occ=0.50 residue: pdb=" N AILE B 156 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE B 156 " occ=0.50 residue: pdb=" N ALEU B 157 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 157 " occ=0.50 ... (remaining 53 not shown) Time building chain proxies: 4.30, per 1000 atoms: 0.27 Number of scatterers: 15728 At special positions: 0 Unit cell: (103.592, 109.044, 149.027, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 46 15.00 O 2967 8.00 N 2759 7.00 C 9877 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 - 3.00 Amino acid : True - 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: 1.33 Conformation dependent library (CDL) restraints added in 891.1 milliseconds 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 13 sheets defined 48.3% alpha, 13.8% beta 20 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.562A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 278 No H-bonds generated for 'chain 'A' and resid 277 through 278' Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 344 through 350 removed outlier: 4.194A pdb=" N TRP A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.857A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 4.534A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 5.904A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 554 removed outlier: 3.542A pdb=" N LEU A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.977A pdb=" N LYS A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 776 removed outlier: 4.100A pdb=" N GLU A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 810 removed outlier: 5.038A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 858 through 862 Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.633A pdb=" N VAL A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 940 removed outlier: 3.692A pdb=" N THR A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 936 " --> pdb=" O HIS A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 956 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 990 removed outlier: 4.377A pdb=" N GLU A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 removed outlier: 3.544A pdb=" N SER A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.789A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1169 removed outlier: 3.690A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 removed outlier: 3.672A pdb=" N VAL A1177 " --> pdb=" O PRO A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 64 through 76 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.637A pdb=" N GLY B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.586A pdb=" N ALEU B 153 " --> pdb=" O ASER B 149 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N BASP B 159 " --> pdb=" O BGLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 177 Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.740A pdb=" N GLU B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.164A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.623A pdb=" N TYR B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.628A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.522A pdb=" N BASP C 159 " --> pdb=" O BGLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 177 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.941A pdb=" N GLU C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.782A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.030A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.608A pdb=" N TYR C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.640A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.704A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.918A pdb=" N LEU C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 419 " --> pdb=" O GLY C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.517A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.622A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA A 212 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 266 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 292 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA3, first strand: chain 'A' and resid 747 through 749 removed outlier: 3.710A pdb=" N GLN A 780 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 6.990A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A1137 " --> pdb=" O ALA A 889 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1218 " --> pdb=" O VAL A1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 992 through 994 removed outlier: 3.730A pdb=" N LEU A 992 " --> pdb=" O LYS A1050 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A1050 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP A 994 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A1048 " --> pdb=" O TRP A 994 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.567A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 230 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 237 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 291 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 289 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR B 302 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 287 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRP B 304 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS B 285 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 148 removed outlier: 3.816A pdb=" N GLY C 179 " --> pdb=" O ALEU C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.620A pdb=" N LYS B 329 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.334A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.538A pdb=" N ALA C 209 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 210 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 238 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB4, first strand: chain 'C' and resid 413 through 414 removed outlier: 7.199A pdb=" N TRP C 414 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS C 382 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 441 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4741 1.33 - 1.45: 2935 1.45 - 1.57: 8319 1.57 - 1.70: 90 1.70 - 1.82: 124 Bond restraints: 16209 Sorted by residual: bond pdb=" C3' DG P 30 " pdb=" C2' DG P 30 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DC T 21 " pdb=" C2' DC T 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG T 13 " pdb=" C2' DG T 13 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.75e+00 bond pdb=" C3' DT T 5 " pdb=" C2' DT T 5 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.20e+00 bond pdb=" C3' DG P 25 " pdb=" C2' DG P 25 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.18e+00 ... (remaining 16204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 21624 1.39 - 2.77: 457 2.77 - 4.16: 71 4.16 - 5.54: 12 5.54 - 6.93: 2 Bond angle restraints: 22166 Sorted by residual: angle pdb=" N PRO A 783 " pdb=" CA PRO A 783 " pdb=" CB PRO A 783 " ideal model delta sigma weight residual 102.81 109.74 -6.93 6.70e-01 2.23e+00 1.07e+02 angle pdb=" O4' DT T 8 " pdb=" C4' DT T 8 " pdb=" C3' DT T 8 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT P 26 " pdb=" C4 DT P 26 " pdb=" O4 DT P 26 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT P 18 " pdb=" C4 DT P 18 " pdb=" O4 DT P 18 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 22161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8798 17.80 - 35.60: 529 35.60 - 53.40: 189 53.40 - 71.20: 43 71.20 - 89.00: 3 Dihedral angle restraints: 9562 sinusoidal: 4219 harmonic: 5343 Sorted by residual: dihedral pdb=" CA ILE A 744 " pdb=" C ILE A 744 " pdb=" N PRO A 745 " pdb=" CA PRO A 745 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP A 743 " pdb=" C ASP A 743 " pdb=" N ILE A 744 " pdb=" CA ILE A 744 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" N PRO A 783 " pdb=" C PRO A 783 " pdb=" CA PRO A 783 " pdb=" CB PRO A 783 " ideal model delta harmonic sigma weight residual 115.10 122.92 -7.82 0 2.50e+00 1.60e-01 9.78e+00 ... (remaining 9559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1930 0.049 - 0.099: 387 0.099 - 0.148: 87 0.148 - 0.197: 1 0.197 - 0.246: 1 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA PRO A 783 " pdb=" N PRO A 783 " pdb=" C PRO A 783 " pdb=" CB PRO A 783 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' DA P 24 " pdb=" C4' DA P 24 " pdb=" O3' DA P 24 " pdb=" C2' DA P 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA ILE A 744 " pdb=" N ILE A 744 " pdb=" C ILE A 744 " pdb=" CB ILE A 744 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2403 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 73 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 21 " -0.006 2.00e-02 2.50e+03 1.15e-02 2.95e+00 pdb=" N1 DC T 21 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DC T 21 " -0.023 2.00e-02 2.50e+03 pdb=" O2 DC T 21 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DC T 21 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DC T 21 " -0.015 2.00e-02 2.50e+03 pdb=" N4 DC T 21 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC T 21 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC T 21 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 240 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 241 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.021 5.00e-02 4.00e+02 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 777 2.72 - 3.27: 15860 3.27 - 3.81: 26512 3.81 - 4.36: 30920 4.36 - 4.90: 51649 Nonbonded interactions: 125718 Sorted by model distance: nonbonded pdb=" O VAL A1101 " pdb=" OG SER A1104 " model vdw 2.178 3.040 nonbonded pdb=" O AVAL B 174 " pdb=" OG ASER B 178 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP C 280 " pdb=" N ARG C 284 " model vdw 2.188 3.120 nonbonded pdb=" O BVAL C 174 " pdb=" OG BSER C 178 " model vdw 2.205 3.040 nonbonded pdb=" O ASP A 293 " pdb=" OG SER A 296 " model vdw 2.213 3.040 ... (remaining 125713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 63 through 144 or resid 146 or resid 179 through 356 or re \ sid 369 through 483)) selection = (chain 'C' and (resid 63 through 144 or resid 146 or resid 179 through 483)) } 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=0.50 max=1.00 mean=0.97 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: 1.920 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.004 0.038 16209 Z= 0.254 Angle : 0.503 6.926 22166 Z= 0.328 Chirality : 0.041 0.246 2406 Planarity : 0.004 0.046 2692 Dihedral : 13.242 88.997 6116 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.81 % Allowed : 6.51 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1837 helix: 1.75 (0.19), residues: 779 sheet: 0.18 (0.32), residues: 239 loop : -0.21 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 264 TYR 0.010 0.001 TYR B 478 PHE 0.014 0.001 PHE C 403 TRP 0.014 0.001 TRP A 859 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.25 (16209) covalent geometry : angle 0.50297 / 0.33 (22166) hydrogen bonds : bond 0.18405 / 12.86 ( 767) hydrogen bonds : angle 6.77645 / 4.78 ( 2137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 614 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.7750 (p0) cc_final: 0.7539 (p0) REVERT: A 76 ILE cc_start: 0.8480 (mm) cc_final: 0.8039 (mm) REVERT: A 79 LEU cc_start: 0.8146 (mt) cc_final: 0.7862 (mp) REVERT: A 145 LYS cc_start: 0.8111 (tptp) cc_final: 0.7762 (tptp) REVERT: A 159 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6827 (pp30) REVERT: A 193 ARG cc_start: 0.7769 (ttt180) cc_final: 0.7417 (tpp80) REVERT: A 234 SER cc_start: 0.7462 (p) cc_final: 0.7092 (m) REVERT: A 264 GLN cc_start: 0.8109 (pt0) cc_final: 0.7445 (pt0) REVERT: A 275 ARG cc_start: 0.8010 (tmt90) cc_final: 0.7740 (tpt-90) REVERT: A 304 LEU cc_start: 0.8329 (mt) cc_final: 0.8062 (mt) REVERT: A 405 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7362 (tm-30) REVERT: A 439 GLN cc_start: 0.7969 (pt0) cc_final: 0.7759 (pt0) REVERT: A 443 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6641 (ttt-90) REVERT: A 447 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7071 (mm-30) REVERT: A 457 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7576 (ttp-170) REVERT: A 459 MET cc_start: 0.7138 (tpp) cc_final: 0.6842 (tpp) REVERT: A 484 TRP cc_start: 0.8307 (m-90) cc_final: 0.7465 (m-90) REVERT: A 490 TRP cc_start: 0.7806 (m100) cc_final: 0.7588 (m100) REVERT: A 566 LEU cc_start: 0.8885 (mt) cc_final: 0.8668 (mm) REVERT: A 579 ARG cc_start: 0.6395 (mtt180) cc_final: 0.5891 (mtt180) REVERT: A 607 TRP cc_start: 0.8168 (t-100) cc_final: 0.7852 (t-100) REVERT: A 755 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8265 (mmtt) REVERT: A 758 ASN cc_start: 0.8006 (m-40) cc_final: 0.7556 (t0) REVERT: A 769 ASP cc_start: 0.7989 (p0) cc_final: 0.7536 (p0) REVERT: A 772 PRO cc_start: 0.8905 (Cg_exo) cc_final: 0.8225 (Cg_endo) REVERT: A 816 LEU cc_start: 0.8509 (tp) cc_final: 0.8297 (tp) REVERT: A 821 LEU cc_start: 0.8455 (mt) cc_final: 0.8249 (mt) REVERT: A 832 ASP cc_start: 0.8194 (t0) cc_final: 0.7834 (t70) REVERT: A 841 LEU cc_start: 0.8484 (mp) cc_final: 0.8224 (mt) REVERT: A 873 GLU cc_start: 0.8036 (pm20) cc_final: 0.7243 (pm20) REVERT: A 877 MET cc_start: 0.7538 (mmm) cc_final: 0.7278 (mmm) REVERT: A 882 PRO cc_start: 0.8897 (Cg_exo) cc_final: 0.8631 (Cg_endo) REVERT: A 890 ASP cc_start: 0.7707 (t0) cc_final: 0.7388 (t0) REVERT: A 893 SER cc_start: 0.7045 (t) cc_final: 0.6483 (p) REVERT: A 916 PHE cc_start: 0.7696 (t80) cc_final: 0.7086 (t80) REVERT: A 920 THR cc_start: 0.7677 (m) cc_final: 0.7468 (p) REVERT: A 922 GLN cc_start: 0.7466 (tt0) cc_final: 0.7082 (tp40) REVERT: A 934 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8147 (mmpt) REVERT: A 981 LYS cc_start: 0.8262 (tttt) cc_final: 0.7817 (tptt) REVERT: A 985 MET cc_start: 0.7327 (ttp) cc_final: 0.6935 (ttp) REVERT: A 1057 MET cc_start: 0.7831 (ppp) cc_final: 0.7486 (ppp) REVERT: A 1060 LYS cc_start: 0.8049 (tptp) cc_final: 0.7600 (tptp) REVERT: A 1062 GLU cc_start: 0.7997 (pt0) cc_final: 0.7593 (mt-10) REVERT: A 1071 ARG cc_start: 0.7795 (mpp80) cc_final: 0.7324 (mtm-85) REVERT: A 1084 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 1111 LEU cc_start: 0.8509 (mt) cc_final: 0.8284 (mt) REVERT: A 1112 MET cc_start: 0.8278 (mtm) cc_final: 0.7974 (mtp) REVERT: A 1120 PHE cc_start: 0.7803 (m-10) cc_final: 0.7180 (m-80) REVERT: A 1126 ASP cc_start: 0.6546 (m-30) cc_final: 0.6295 (m-30) REVERT: A 1136 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6340 (mt-10) REVERT: A 1145 ASP cc_start: 0.6405 (m-30) cc_final: 0.6194 (m-30) REVERT: A 1154 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7611 (mm-40) REVERT: A 1195 MET cc_start: 0.7314 (ttm) cc_final: 0.7091 (ttm) REVERT: A 1202 ASN cc_start: 0.7687 (m-40) cc_final: 0.6728 (m110) REVERT: A 1207 GLU cc_start: 0.7523 (pm20) cc_final: 0.7019 (pm20) REVERT: A 1219 ASP cc_start: 0.7945 (t0) cc_final: 0.7576 (t0) REVERT: A 1222 GLN cc_start: 0.8552 (mp10) cc_final: 0.8034 (mp10) REVERT: B 71 GLU cc_start: 0.7981 (tt0) cc_final: 0.7780 (tm-30) REVERT: B 72 ILE cc_start: 0.8623 (mm) cc_final: 0.8373 (mm) REVERT: B 88 ARG cc_start: 0.7932 (ptp-170) cc_final: 0.7578 (ptp90) REVERT: B 113 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6964 (mm-30) REVERT: B 132 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7831 (m-70) REVERT: B 134 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8082 (mtmt) REVERT: B 180 LYS cc_start: 0.8312 (ptmt) cc_final: 0.7653 (ptmt) REVERT: B 183 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6787 (mt-10) REVERT: B 191 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7402 (mt-10) REVERT: B 192 HIS cc_start: 0.7908 (m90) cc_final: 0.7516 (m-70) REVERT: B 199 LEU cc_start: 0.8166 (tp) cc_final: 0.7966 (tp) REVERT: B 201 ASN cc_start: 0.8067 (m110) cc_final: 0.7364 (m110) REVERT: B 230 SER cc_start: 0.7788 (t) cc_final: 0.7527 (p) REVERT: B 288 LYS cc_start: 0.7378 (mttt) cc_final: 0.6879 (mtpt) REVERT: B 291 TYR cc_start: 0.7454 (t80) cc_final: 0.7251 (t80) REVERT: B 292 ASN cc_start: 0.7980 (t0) cc_final: 0.7773 (t0) REVERT: B 310 GLU cc_start: 0.7555 (mp0) cc_final: 0.7239 (mp0) REVERT: B 339 ASN cc_start: 0.7138 (t0) cc_final: 0.6896 (t0) REVERT: B 349 TYR cc_start: 0.8404 (m-10) cc_final: 0.8047 (m-10) REVERT: B 396 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7180 (ttm110) REVERT: B 409 ASN cc_start: 0.8317 (m110) cc_final: 0.8113 (m-40) REVERT: B 412 SER cc_start: 0.8462 (t) cc_final: 0.8139 (p) REVERT: B 426 GLU cc_start: 0.7950 (pp20) cc_final: 0.7426 (tm-30) REVERT: B 431 LYS cc_start: 0.8554 (tttt) cc_final: 0.8163 (tppt) REVERT: B 457 SER cc_start: 0.8164 (t) cc_final: 0.7843 (p) REVERT: B 465 MET cc_start: 0.7857 (mtm) cc_final: 0.7622 (mtm) REVERT: B 466 MET cc_start: 0.7873 (mtp) cc_final: 0.7654 (ttm) REVERT: B 470 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7646 (mtpp) REVERT: B 483 LYS cc_start: 0.6370 (tttt) cc_final: 0.5965 (tttp) REVERT: C 75 ARG cc_start: 0.7920 (mtp85) cc_final: 0.7600 (mtp85) REVERT: C 77 HIS cc_start: 0.6595 (m-70) cc_final: 0.6391 (m-70) REVERT: C 80 SER cc_start: 0.8458 (t) cc_final: 0.8132 (m) REVERT: C 92 LEU cc_start: 0.8435 (mt) cc_final: 0.8150 (mp) REVERT: C 109 ASN cc_start: 0.7925 (m-40) cc_final: 0.7655 (m-40) REVERT: C 110 LEU cc_start: 0.7991 (tm) cc_final: 0.7609 (tt) REVERT: C 183 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6229 (mt-10) REVERT: C 216 HIS cc_start: 0.8076 (m90) cc_final: 0.7402 (m-70) REVERT: C 234 LYS cc_start: 0.7995 (mttt) cc_final: 0.7763 (mttt) REVERT: C 256 LEU cc_start: 0.8493 (tp) cc_final: 0.8204 (tt) REVERT: C 259 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7568 (mtp85) REVERT: C 262 TRP cc_start: 0.7981 (t60) cc_final: 0.7611 (t60) REVERT: C 280 ASP cc_start: 0.6503 (p0) cc_final: 0.6059 (p0) REVERT: C 287 ASN cc_start: 0.7286 (t0) cc_final: 0.6770 (t0) REVERT: C 288 LYS cc_start: 0.8215 (mttt) cc_final: 0.7633 (mttt) REVERT: C 291 TYR cc_start: 0.8269 (t80) cc_final: 0.7720 (t80) REVERT: C 299 LEU cc_start: 0.8507 (tp) cc_final: 0.8237 (tt) REVERT: C 301 GLU cc_start: 0.7266 (tt0) cc_final: 0.6714 (tt0) REVERT: C 305 ASN cc_start: 0.7749 (t0) cc_final: 0.7525 (t0) REVERT: C 306 LEU cc_start: 0.8778 (mt) cc_final: 0.8325 (mm) REVERT: C 328 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7676 (mtt180) REVERT: C 336 LEU cc_start: 0.8469 (mt) cc_final: 0.8028 (mm) REVERT: C 346 MET cc_start: 0.7398 (tmm) cc_final: 0.6884 (tmm) REVERT: C 371 VAL cc_start: 0.8508 (p) cc_final: 0.8272 (m) REVERT: C 372 LEU cc_start: 0.8618 (mt) cc_final: 0.8339 (mp) REVERT: C 378 LEU cc_start: 0.8597 (mt) cc_final: 0.8387 (mt) REVERT: C 421 MET cc_start: 0.6933 (mtt) cc_final: 0.6500 (mtt) REVERT: C 426 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7868 (mt-10) REVERT: C 427 GLN cc_start: 0.8296 (mt0) cc_final: 0.7790 (mt0) REVERT: C 430 SER cc_start: 0.8561 (t) cc_final: 0.8166 (p) REVERT: C 434 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 448 LEU cc_start: 0.7730 (mt) cc_final: 0.7517 (mt) REVERT: C 458 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7846 (ttp-170) REVERT: C 466 MET cc_start: 0.7311 (ttm) cc_final: 0.7045 (ttm) outliers start: 11 outliers final: 5 residues processed: 622 average time/residue: 0.1332 time to fit residues: 119.0867 Evaluate side-chains 564 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 558 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS A 134 ASN A 238 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 354 ASN A 388 ASN ** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN A1102 GLN B 132 HIS B 187 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 409 ASN B 427 GLN C 77 HIS C 279 GLN C 305 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091625 restraints weight = 63771.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096894 restraints weight = 26977.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100364 restraints weight = 14802.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102765 restraints weight = 9453.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104348 restraints weight = 6711.368| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16209 Z= 0.333 Angle : 0.703 11.537 22166 Z= 0.382 Chirality : 0.049 0.308 2406 Planarity : 0.006 0.058 2692 Dihedral : 15.098 89.054 2496 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.13 % Allowed : 1.75 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1837 helix: 1.27 (0.18), residues: 779 sheet: -0.21 (0.32), residues: 234 loop : -0.58 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 232 TYR 0.044 0.003 TYR B 315 PHE 0.041 0.003 PHE A 273 TRP 0.040 0.003 TRP A 486 HIS 0.020 0.002 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.33 (16209) covalent geometry : angle 0.70259 / 0.38 (22166) hydrogen bonds : bond 0.05920 / 4.12 ( 767) hydrogen bonds : angle 5.71638 / 4.09 ( 2137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8471 (mm) cc_final: 0.8153 (mm) REVERT: A 79 LEU cc_start: 0.8123 (mt) cc_final: 0.7847 (mp) REVERT: A 110 HIS cc_start: 0.7408 (m90) cc_final: 0.6692 (m90) REVERT: A 145 LYS cc_start: 0.8222 (tptp) cc_final: 0.7805 (tptp) REVERT: A 159 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6702 (pp30) REVERT: A 205 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7202 (mm-30) REVERT: A 264 GLN cc_start: 0.7892 (pt0) cc_final: 0.7608 (pm20) REVERT: A 280 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 289 MET cc_start: 0.7459 (ttm) cc_final: 0.6487 (ttm) REVERT: A 299 MET cc_start: 0.7488 (tpt) cc_final: 0.7049 (tmm) REVERT: A 354 ASN cc_start: 0.7738 (m-40) cc_final: 0.7299 (m-40) REVERT: A 358 GLU cc_start: 0.7609 (mp0) cc_final: 0.7400 (mp0) REVERT: A 375 GLU cc_start: 0.7431 (pt0) cc_final: 0.7072 (pt0) REVERT: A 393 MET cc_start: 0.7064 (ttm) cc_final: 0.6714 (ttm) REVERT: A 405 GLU cc_start: 0.7606 (tp30) cc_final: 0.7082 (tm-30) REVERT: A 439 GLN cc_start: 0.7809 (pt0) cc_final: 0.7593 (pt0) REVERT: A 443 ARG cc_start: 0.7017 (ttt-90) cc_final: 0.6408 (ttt-90) REVERT: A 449 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7819 (tp-100) REVERT: A 453 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7532 (mm-30) REVERT: A 484 TRP cc_start: 0.8153 (m-90) cc_final: 0.7517 (m-90) REVERT: A 487 ASP cc_start: 0.8349 (m-30) cc_final: 0.8091 (m-30) REVERT: A 565 HIS cc_start: 0.7763 (t70) cc_final: 0.7225 (t-170) REVERT: A 566 LEU cc_start: 0.8900 (mt) cc_final: 0.8543 (mm) REVERT: A 607 TRP cc_start: 0.8240 (t-100) cc_final: 0.7736 (t60) REVERT: A 617 ARG cc_start: 0.7042 (ttt90) cc_final: 0.6834 (mtp85) REVERT: A 755 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8191 (mmtt) REVERT: A 758 ASN cc_start: 0.7976 (m-40) cc_final: 0.7548 (t0) REVERT: A 769 ASP cc_start: 0.7481 (p0) cc_final: 0.6976 (p0) REVERT: A 812 MET cc_start: 0.7557 (mpp) cc_final: 0.7278 (mpp) REVERT: A 816 LEU cc_start: 0.8484 (tp) cc_final: 0.8155 (tp) REVERT: A 821 LEU cc_start: 0.8391 (mt) cc_final: 0.8139 (mt) REVERT: A 826 ILE cc_start: 0.8029 (mt) cc_final: 0.7809 (pt) REVERT: A 832 ASP cc_start: 0.8121 (t0) cc_final: 0.7350 (t0) REVERT: A 877 MET cc_start: 0.7226 (mmm) cc_final: 0.6999 (mmm) REVERT: A 893 SER cc_start: 0.7220 (t) cc_final: 0.6686 (p) REVERT: A 910 MET cc_start: 0.7414 (tpt) cc_final: 0.7146 (tpp) REVERT: A 916 PHE cc_start: 0.7983 (t80) cc_final: 0.7378 (t80) REVERT: A 922 GLN cc_start: 0.7492 (tt0) cc_final: 0.7019 (tp40) REVERT: A 944 GLU cc_start: 0.8350 (pm20) cc_final: 0.7904 (pm20) REVERT: A 981 LYS cc_start: 0.8283 (tttt) cc_final: 0.7756 (tppt) REVERT: A 985 MET cc_start: 0.7083 (ttp) cc_final: 0.6685 (ttp) REVERT: A 1057 MET cc_start: 0.7736 (ppp) cc_final: 0.7487 (ppp) REVERT: A 1060 LYS cc_start: 0.8112 (tptp) cc_final: 0.7619 (tptp) REVERT: A 1062 GLU cc_start: 0.7892 (pt0) cc_final: 0.7644 (mt-10) REVERT: A 1093 MET cc_start: 0.7178 (pmm) cc_final: 0.6716 (pmm) REVERT: A 1109 LEU cc_start: 0.8815 (tp) cc_final: 0.8600 (tt) REVERT: A 1112 MET cc_start: 0.8511 (mtm) cc_final: 0.8162 (mtp) REVERT: A 1116 MET cc_start: 0.7436 (tpt) cc_final: 0.6515 (tpt) REVERT: A 1120 PHE cc_start: 0.8071 (m-10) cc_final: 0.7782 (m-80) REVERT: A 1126 ASP cc_start: 0.6565 (m-30) cc_final: 0.6198 (m-30) REVERT: A 1136 GLU cc_start: 0.5907 (mt-10) cc_final: 0.5703 (mt-10) REVERT: A 1148 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7666 (ttp-170) REVERT: A 1168 LEU cc_start: 0.8750 (mt) cc_final: 0.8473 (mt) REVERT: A 1222 GLN cc_start: 0.8468 (mp10) cc_final: 0.8152 (mp10) REVERT: B 72 ILE cc_start: 0.8398 (mm) cc_final: 0.8155 (mm) REVERT: B 77 HIS cc_start: 0.6930 (m-70) cc_final: 0.6522 (m-70) REVERT: B 88 ARG cc_start: 0.8084 (ptp-170) cc_final: 0.7722 (ptp90) REVERT: B 108 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7982 (ttmm) REVERT: B 113 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6717 (mm-30) REVERT: B 123 GLU cc_start: 0.7581 (pt0) cc_final: 0.7228 (pt0) REVERT: B 134 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8102 (mtmt) REVERT: B 180 LYS cc_start: 0.8352 (ptmt) cc_final: 0.7634 (ptmt) REVERT: B 183 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6925 (mt-10) REVERT: B 191 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 192 HIS cc_start: 0.8208 (m90) cc_final: 0.7834 (m-70) REVERT: B 201 ASN cc_start: 0.7925 (m110) cc_final: 0.7470 (m110) REVERT: B 257 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7391 (mtp85) REVERT: B 262 TRP cc_start: 0.7963 (t60) cc_final: 0.6778 (t60) REVERT: B 288 LYS cc_start: 0.7022 (mttt) cc_final: 0.6456 (mtpt) REVERT: B 310 GLU cc_start: 0.7579 (mp0) cc_final: 0.7241 (mp0) REVERT: B 315 TYR cc_start: 0.7786 (m-80) cc_final: 0.7403 (m-80) REVERT: B 339 ASN cc_start: 0.7031 (t0) cc_final: 0.6696 (t0) REVERT: B 349 TYR cc_start: 0.8334 (m-10) cc_final: 0.7924 (m-10) REVERT: B 352 ASP cc_start: 0.7413 (t0) cc_final: 0.7080 (t0) REVERT: B 353 SER cc_start: 0.8272 (p) cc_final: 0.8022 (p) REVERT: B 378 LEU cc_start: 0.8355 (mp) cc_final: 0.8113 (mt) REVERT: B 396 ARG cc_start: 0.7573 (ttm170) cc_final: 0.7184 (ttm110) REVERT: B 412 SER cc_start: 0.8254 (t) cc_final: 0.7791 (p) REVERT: B 431 LYS cc_start: 0.8418 (tttt) cc_final: 0.8111 (tppt) REVERT: B 435 MET cc_start: 0.7339 (mtp) cc_final: 0.7064 (mtp) REVERT: B 446 THR cc_start: 0.8289 (m) cc_final: 0.7862 (m) REVERT: B 449 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7265 (mt-10) REVERT: B 457 SER cc_start: 0.7867 (t) cc_final: 0.7516 (p) REVERT: B 460 THR cc_start: 0.8619 (p) cc_final: 0.8108 (p) REVERT: B 462 MET cc_start: 0.8044 (mmt) cc_final: 0.7705 (mmt) REVERT: B 465 MET cc_start: 0.7554 (mtm) cc_final: 0.7218 (mtm) REVERT: B 466 MET cc_start: 0.7340 (mtp) cc_final: 0.7076 (ttm) REVERT: B 467 HIS cc_start: 0.8240 (t-90) cc_final: 0.7880 (t70) REVERT: B 472 LYS cc_start: 0.8137 (ttpp) cc_final: 0.7775 (ttpp) REVERT: C 69 LEU cc_start: 0.8621 (tt) cc_final: 0.8356 (tt) REVERT: C 75 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7600 (mtp85) REVERT: C 80 SER cc_start: 0.8539 (t) cc_final: 0.8226 (m) REVERT: C 92 LEU cc_start: 0.8609 (mt) cc_final: 0.8357 (mm) REVERT: C 146 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.6954 (mmt180) REVERT: C 183 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6502 (mt-10) REVERT: C 203 ARG cc_start: 0.7506 (ttt180) cc_final: 0.7134 (ttt180) REVERT: C 234 LYS cc_start: 0.7920 (mttt) cc_final: 0.7714 (mttt) REVERT: C 235 THR cc_start: 0.7041 (p) cc_final: 0.6589 (p) REVERT: C 256 LEU cc_start: 0.8536 (tp) cc_final: 0.8289 (tp) REVERT: C 259 ARG cc_start: 0.7678 (mtp85) cc_final: 0.7392 (mtp85) REVERT: C 262 TRP cc_start: 0.7944 (t60) cc_final: 0.7484 (t60) REVERT: C 287 ASN cc_start: 0.7126 (t0) cc_final: 0.6921 (t0) REVERT: C 288 LYS cc_start: 0.8206 (mttt) cc_final: 0.7720 (mttt) REVERT: C 291 TYR cc_start: 0.8086 (t80) cc_final: 0.7801 (t80) REVERT: C 299 LEU cc_start: 0.8534 (tp) cc_final: 0.8327 (tt) REVERT: C 301 GLU cc_start: 0.7380 (tt0) cc_final: 0.6638 (tt0) REVERT: C 306 LEU cc_start: 0.8450 (mt) cc_final: 0.8007 (mm) REVERT: C 336 LEU cc_start: 0.8297 (mt) cc_final: 0.7873 (mm) REVERT: C 346 MET cc_start: 0.7176 (tmm) cc_final: 0.6501 (tmm) REVERT: C 354 PHE cc_start: 0.7775 (t80) cc_final: 0.7551 (t80) REVERT: C 371 VAL cc_start: 0.8449 (p) cc_final: 0.8155 (m) REVERT: C 421 MET cc_start: 0.6415 (mtt) cc_final: 0.6188 (mtt) REVERT: C 427 GLN cc_start: 0.8265 (mt0) cc_final: 0.7733 (mt0) REVERT: C 430 SER cc_start: 0.8494 (t) cc_final: 0.8069 (p) REVERT: C 431 LYS cc_start: 0.8448 (tttt) cc_final: 0.8149 (tttt) REVERT: C 434 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7767 (mt-10) REVERT: C 456 ARG cc_start: 0.7635 (ttt90) cc_final: 0.7426 (ttt90) REVERT: C 466 MET cc_start: 0.6944 (ttm) cc_final: 0.6569 (ttm) REVERT: C 470 LYS cc_start: 0.8652 (mttt) cc_final: 0.8249 (mttt) outliers start: 0 outliers final: 0 residues processed: 575 average time/residue: 0.1350 time to fit residues: 111.5552 Evaluate side-chains 547 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 124 optimal weight: 0.0010 chunk 42 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS A 410 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 ASN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN C 313 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.093878 restraints weight = 62780.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099241 restraints weight = 26286.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102762 restraints weight = 14386.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105152 restraints weight = 9159.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106761 restraints weight = 6545.213| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16209 Z= 0.169 Angle : 0.583 9.869 22166 Z= 0.313 Chirality : 0.043 0.190 2406 Planarity : 0.005 0.055 2692 Dihedral : 14.946 89.886 2496 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.19 % Allowed : 2.38 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1837 helix: 1.55 (0.19), residues: 784 sheet: -0.05 (0.34), residues: 236 loop : -0.48 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 827 TYR 0.034 0.002 TYR B 315 PHE 0.026 0.002 PHE C 242 TRP 0.020 0.002 TRP A 490 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (16209) covalent geometry : angle 0.58256 / 0.31 (22166) hydrogen bonds : bond 0.04700 / 3.25 ( 767) hydrogen bonds : angle 5.24049 / 3.74 ( 2137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 583 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8397 (mm) cc_final: 0.8153 (mm) REVERT: A 79 LEU cc_start: 0.8123 (mt) cc_final: 0.7817 (mp) REVERT: A 110 HIS cc_start: 0.7405 (m90) cc_final: 0.6607 (m90) REVERT: A 145 LYS cc_start: 0.8192 (tptp) cc_final: 0.7763 (tptp) REVERT: A 159 GLN cc_start: 0.7115 (tm-30) cc_final: 0.6673 (pp30) REVERT: A 193 ARG cc_start: 0.7173 (ttp-110) cc_final: 0.6960 (ptm160) REVERT: A 264 GLN cc_start: 0.7925 (pt0) cc_final: 0.7525 (pm20) REVERT: A 280 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 289 MET cc_start: 0.7074 (ttm) cc_final: 0.6563 (ttm) REVERT: A 299 MET cc_start: 0.7472 (tpt) cc_final: 0.7265 (mmm) REVERT: A 354 ASN cc_start: 0.7626 (m-40) cc_final: 0.7416 (m-40) REVERT: A 355 SER cc_start: 0.7772 (t) cc_final: 0.7544 (t) REVERT: A 375 GLU cc_start: 0.7410 (pt0) cc_final: 0.7013 (pt0) REVERT: A 393 MET cc_start: 0.7153 (ttm) cc_final: 0.6899 (ttm) REVERT: A 405 GLU cc_start: 0.7569 (tp30) cc_final: 0.7249 (tm-30) REVERT: A 427 MET cc_start: 0.7659 (ttm) cc_final: 0.7431 (ttm) REVERT: A 443 ARG cc_start: 0.6942 (ttt-90) cc_final: 0.6427 (ttt-90) REVERT: A 449 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7798 (tp-100) REVERT: A 453 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7527 (mm-30) REVERT: A 484 TRP cc_start: 0.8126 (m-90) cc_final: 0.7445 (m-90) REVERT: A 487 ASP cc_start: 0.8312 (m-30) cc_final: 0.8077 (m-30) REVERT: A 565 HIS cc_start: 0.7564 (t70) cc_final: 0.7247 (t-170) REVERT: A 566 LEU cc_start: 0.8892 (mt) cc_final: 0.8598 (mm) REVERT: A 586 THR cc_start: 0.8202 (t) cc_final: 0.7927 (p) REVERT: A 607 TRP cc_start: 0.8218 (t-100) cc_final: 0.7887 (t60) REVERT: A 617 ARG cc_start: 0.6962 (ttt90) cc_final: 0.6754 (mtp85) REVERT: A 758 ASN cc_start: 0.7918 (m-40) cc_final: 0.7445 (t0) REVERT: A 769 ASP cc_start: 0.7386 (p0) cc_final: 0.6867 (p0) REVERT: A 812 MET cc_start: 0.7516 (mpp) cc_final: 0.7177 (mpp) REVERT: A 816 LEU cc_start: 0.8464 (tp) cc_final: 0.8098 (tp) REVERT: A 821 LEU cc_start: 0.8351 (mt) cc_final: 0.8032 (mt) REVERT: A 832 ASP cc_start: 0.8066 (t0) cc_final: 0.7390 (t0) REVERT: A 853 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7548 (mtp85) REVERT: A 877 MET cc_start: 0.7188 (mmm) cc_final: 0.6954 (mmm) REVERT: A 893 SER cc_start: 0.7232 (t) cc_final: 0.6682 (p) REVERT: A 910 MET cc_start: 0.7248 (tpt) cc_final: 0.7031 (tpp) REVERT: A 916 PHE cc_start: 0.7974 (t80) cc_final: 0.7615 (t80) REVERT: A 919 MET cc_start: 0.7559 (mtt) cc_final: 0.7205 (mpp) REVERT: A 922 GLN cc_start: 0.7469 (tt0) cc_final: 0.7015 (tp40) REVERT: A 981 LYS cc_start: 0.8294 (tttt) cc_final: 0.7795 (tptt) REVERT: A 1057 MET cc_start: 0.7774 (ppp) cc_final: 0.7527 (ppp) REVERT: A 1060 LYS cc_start: 0.8077 (tptp) cc_final: 0.7580 (tptp) REVERT: A 1062 GLU cc_start: 0.7846 (pt0) cc_final: 0.7619 (mt-10) REVERT: A 1093 MET cc_start: 0.7057 (pmm) cc_final: 0.6652 (pmm) REVERT: A 1109 LEU cc_start: 0.8811 (tp) cc_final: 0.8552 (tt) REVERT: A 1111 LEU cc_start: 0.8619 (mt) cc_final: 0.8261 (mt) REVERT: A 1112 MET cc_start: 0.8465 (mtm) cc_final: 0.8068 (mtp) REVERT: A 1113 LEU cc_start: 0.8599 (mp) cc_final: 0.8326 (mm) REVERT: A 1126 ASP cc_start: 0.6489 (m-30) cc_final: 0.6274 (m-30) REVERT: A 1136 GLU cc_start: 0.5847 (mt-10) cc_final: 0.5638 (mt-10) REVERT: A 1137 VAL cc_start: 0.8306 (t) cc_final: 0.7508 (m) REVERT: A 1148 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7544 (ttp-170) REVERT: A 1219 ASP cc_start: 0.7780 (t0) cc_final: 0.7516 (t70) REVERT: A 1222 GLN cc_start: 0.8468 (mp10) cc_final: 0.7841 (mp10) REVERT: B 77 HIS cc_start: 0.6919 (m-70) cc_final: 0.6601 (m-70) REVERT: B 88 ARG cc_start: 0.8003 (ptp-170) cc_final: 0.7695 (ptp90) REVERT: B 108 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7997 (ttmm) REVERT: B 113 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6664 (mm-30) REVERT: B 123 GLU cc_start: 0.7562 (pt0) cc_final: 0.7151 (pt0) REVERT: B 131 LEU cc_start: 0.7726 (mt) cc_final: 0.7454 (mp) REVERT: B 134 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7913 (mtmt) REVERT: B 180 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7691 (ptmt) REVERT: B 183 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6884 (mt-10) REVERT: B 191 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7057 (mt-10) REVERT: B 192 HIS cc_start: 0.8150 (m90) cc_final: 0.7693 (m-70) REVERT: B 201 ASN cc_start: 0.7887 (m110) cc_final: 0.7460 (m110) REVERT: B 235 THR cc_start: 0.8265 (m) cc_final: 0.8047 (m) REVERT: B 288 LYS cc_start: 0.7063 (mttt) cc_final: 0.6468 (mtpt) REVERT: B 304 TRP cc_start: 0.7860 (m100) cc_final: 0.7577 (m100) REVERT: B 310 GLU cc_start: 0.7581 (mp0) cc_final: 0.7244 (mp0) REVERT: B 315 TYR cc_start: 0.7888 (m-80) cc_final: 0.7514 (m-80) REVERT: B 352 ASP cc_start: 0.7278 (t0) cc_final: 0.6913 (t0) REVERT: B 353 SER cc_start: 0.8225 (p) cc_final: 0.7969 (p) REVERT: B 396 ARG cc_start: 0.7529 (ttm170) cc_final: 0.7135 (ttm110) REVERT: B 400 GLN cc_start: 0.7703 (tt0) cc_final: 0.7471 (tp40) REVERT: B 412 SER cc_start: 0.8284 (t) cc_final: 0.7797 (p) REVERT: B 427 GLN cc_start: 0.8299 (pt0) cc_final: 0.7443 (pm20) REVERT: B 431 LYS cc_start: 0.8379 (tttt) cc_final: 0.8004 (tppt) REVERT: B 435 MET cc_start: 0.7289 (mtp) cc_final: 0.6972 (mtp) REVERT: B 446 THR cc_start: 0.8285 (m) cc_final: 0.7881 (m) REVERT: B 449 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7266 (mt-10) REVERT: B 457 SER cc_start: 0.7892 (t) cc_final: 0.7541 (p) REVERT: B 460 THR cc_start: 0.8517 (p) cc_final: 0.8125 (p) REVERT: B 461 THR cc_start: 0.8245 (p) cc_final: 0.7908 (t) REVERT: B 462 MET cc_start: 0.7982 (mmt) cc_final: 0.7721 (mmt) REVERT: B 465 MET cc_start: 0.7593 (mtm) cc_final: 0.7212 (mtm) REVERT: B 466 MET cc_start: 0.7355 (mtp) cc_final: 0.6977 (ttp) REVERT: B 467 HIS cc_start: 0.8153 (t-90) cc_final: 0.7818 (t70) REVERT: C 71 GLU cc_start: 0.8341 (tt0) cc_final: 0.8139 (tt0) REVERT: C 75 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7587 (mtp85) REVERT: C 80 SER cc_start: 0.8537 (t) cc_final: 0.8144 (m) REVERT: C 89 ASP cc_start: 0.7994 (m-30) cc_final: 0.7672 (m-30) REVERT: C 92 LEU cc_start: 0.8625 (mt) cc_final: 0.8386 (mp) REVERT: C 107 ARG cc_start: 0.7465 (ttm170) cc_final: 0.7255 (ttp80) REVERT: C 121 PHE cc_start: 0.8010 (m-10) cc_final: 0.7805 (m-10) REVERT: C 146 ARG cc_start: 0.7415 (mmt-90) cc_final: 0.6905 (mmt180) REVERT: C 183 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6463 (mt-10) REVERT: C 231 ILE cc_start: 0.7975 (mt) cc_final: 0.7751 (mt) REVERT: C 233 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6295 (mp0) REVERT: C 234 LYS cc_start: 0.7957 (mttt) cc_final: 0.7656 (mttt) REVERT: C 235 THR cc_start: 0.7003 (p) cc_final: 0.6517 (p) REVERT: C 242 PHE cc_start: 0.6912 (m-10) cc_final: 0.6704 (m-10) REVERT: C 256 LEU cc_start: 0.8447 (tp) cc_final: 0.8221 (tp) REVERT: C 259 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7343 (mtp85) REVERT: C 262 TRP cc_start: 0.7864 (t60) cc_final: 0.7200 (t60) REVERT: C 287 ASN cc_start: 0.7149 (t0) cc_final: 0.6908 (t0) REVERT: C 288 LYS cc_start: 0.8236 (mttt) cc_final: 0.7735 (mttt) REVERT: C 291 TYR cc_start: 0.8084 (t80) cc_final: 0.7807 (t80) REVERT: C 299 LEU cc_start: 0.8538 (tp) cc_final: 0.8244 (tt) REVERT: C 301 GLU cc_start: 0.7354 (tt0) cc_final: 0.6616 (tt0) REVERT: C 305 ASN cc_start: 0.7549 (t0) cc_final: 0.7307 (t0) REVERT: C 306 LEU cc_start: 0.8302 (mt) cc_final: 0.7973 (mm) REVERT: C 336 LEU cc_start: 0.8330 (mt) cc_final: 0.7949 (mt) REVERT: C 343 ASP cc_start: 0.6998 (m-30) cc_final: 0.6488 (m-30) REVERT: C 347 LEU cc_start: 0.8276 (mm) cc_final: 0.7321 (mm) REVERT: C 371 VAL cc_start: 0.8368 (p) cc_final: 0.8037 (m) REVERT: C 421 MET cc_start: 0.6475 (mtt) cc_final: 0.6268 (mtt) REVERT: C 427 GLN cc_start: 0.8250 (mt0) cc_final: 0.7728 (mt0) REVERT: C 430 SER cc_start: 0.8450 (t) cc_final: 0.7935 (p) REVERT: C 431 LYS cc_start: 0.8391 (tttt) cc_final: 0.8150 (tttt) REVERT: C 434 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7586 (mt-10) REVERT: C 466 MET cc_start: 0.6896 (ttm) cc_final: 0.6556 (ttm) REVERT: C 470 LYS cc_start: 0.8603 (mttt) cc_final: 0.8175 (mttt) outliers start: 1 outliers final: 1 residues processed: 583 average time/residue: 0.1290 time to fit residues: 108.3230 Evaluate side-chains 538 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 537 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 127 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 74 optimal weight: 0.0370 chunk 168 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 HIS ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 277 HIS A 420 HIS A 468 ASN A 565 HIS A 906 HIS A 945 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.093949 restraints weight = 62961.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099293 restraints weight = 26309.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102840 restraints weight = 14318.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105158 restraints weight = 9110.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106861 restraints weight = 6478.602| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16209 Z= 0.157 Angle : 0.570 13.359 22166 Z= 0.303 Chirality : 0.043 0.184 2406 Planarity : 0.005 0.064 2692 Dihedral : 14.896 89.896 2496 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.13 % Allowed : 1.94 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1837 helix: 1.60 (0.19), residues: 787 sheet: 0.13 (0.34), residues: 236 loop : -0.45 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1071 TYR 0.031 0.002 TYR B 315 PHE 0.027 0.002 PHE C 242 TRP 0.022 0.002 TRP A 572 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (16209) covalent geometry : angle 0.56966 / 0.30 (22166) hydrogen bonds : bond 0.04318 / 2.97 ( 767) hydrogen bonds : angle 4.98208 / 3.54 ( 2137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 574 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8312 (mm) cc_final: 0.8087 (mm) REVERT: A 79 LEU cc_start: 0.8094 (mt) cc_final: 0.7842 (mp) REVERT: A 110 HIS cc_start: 0.7305 (m90) cc_final: 0.6508 (m90) REVERT: A 121 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7777 (Cg_endo) REVERT: A 145 LYS cc_start: 0.8162 (tptp) cc_final: 0.7752 (tptp) REVERT: A 159 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6661 (pp30) REVERT: A 189 ILE cc_start: 0.7719 (pt) cc_final: 0.7506 (pt) REVERT: A 191 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7140 (mm-30) REVERT: A 193 ARG cc_start: 0.7205 (ttp-110) cc_final: 0.6944 (ptm160) REVERT: A 264 GLN cc_start: 0.7936 (pt0) cc_final: 0.7577 (pm20) REVERT: A 270 ASN cc_start: 0.7287 (m-40) cc_final: 0.6999 (m-40) REVERT: A 280 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 289 MET cc_start: 0.7168 (ttm) cc_final: 0.6758 (ttm) REVERT: A 295 MET cc_start: 0.7439 (ttt) cc_final: 0.6768 (ttm) REVERT: A 308 GLN cc_start: 0.7905 (mt0) cc_final: 0.7285 (mt0) REVERT: A 354 ASN cc_start: 0.7598 (m-40) cc_final: 0.7292 (m110) REVERT: A 355 SER cc_start: 0.7693 (t) cc_final: 0.7425 (t) REVERT: A 358 GLU cc_start: 0.7543 (mp0) cc_final: 0.7227 (mp0) REVERT: A 375 GLU cc_start: 0.7413 (pt0) cc_final: 0.7002 (pt0) REVERT: A 393 MET cc_start: 0.7248 (ttm) cc_final: 0.6965 (ttm) REVERT: A 405 GLU cc_start: 0.7551 (tp30) cc_final: 0.6803 (tp30) REVERT: A 443 ARG cc_start: 0.6910 (ttt-90) cc_final: 0.6408 (ttt-90) REVERT: A 447 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 487 ASP cc_start: 0.8333 (m-30) cc_final: 0.8074 (m-30) REVERT: A 566 LEU cc_start: 0.8906 (mt) cc_final: 0.8669 (mm) REVERT: A 586 THR cc_start: 0.8085 (t) cc_final: 0.7851 (p) REVERT: A 607 TRP cc_start: 0.8364 (t-100) cc_final: 0.7948 (t60) REVERT: A 750 PHE cc_start: 0.7050 (m-80) cc_final: 0.6516 (m-80) REVERT: A 758 ASN cc_start: 0.7917 (m-40) cc_final: 0.7445 (t0) REVERT: A 769 ASP cc_start: 0.7394 (p0) cc_final: 0.7185 (p0) REVERT: A 812 MET cc_start: 0.7410 (mpp) cc_final: 0.7150 (mpp) REVERT: A 816 LEU cc_start: 0.8426 (tp) cc_final: 0.8081 (tp) REVERT: A 821 LEU cc_start: 0.8317 (mt) cc_final: 0.8101 (mt) REVERT: A 823 ARG cc_start: 0.7633 (tmt170) cc_final: 0.7262 (tmt-80) REVERT: A 832 ASP cc_start: 0.8165 (t0) cc_final: 0.7470 (t0) REVERT: A 853 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7738 (mtp85) REVERT: A 873 GLU cc_start: 0.7662 (pm20) cc_final: 0.7066 (pm20) REVERT: A 877 MET cc_start: 0.7155 (mmm) cc_final: 0.6747 (tpp) REVERT: A 893 SER cc_start: 0.7288 (t) cc_final: 0.6675 (p) REVERT: A 910 MET cc_start: 0.7211 (tpt) cc_final: 0.6985 (tpp) REVERT: A 919 MET cc_start: 0.7590 (mtt) cc_final: 0.7240 (mpp) REVERT: A 922 GLN cc_start: 0.7384 (tt0) cc_final: 0.6555 (tp-100) REVERT: A 934 LYS cc_start: 0.8341 (mmpt) cc_final: 0.8118 (mmtt) REVERT: A 981 LYS cc_start: 0.8276 (tttt) cc_final: 0.7712 (tppt) REVERT: A 1057 MET cc_start: 0.7780 (ppp) cc_final: 0.7554 (ppp) REVERT: A 1060 LYS cc_start: 0.8108 (tptp) cc_final: 0.7653 (tptp) REVERT: A 1062 GLU cc_start: 0.7839 (pt0) cc_final: 0.7538 (mt-10) REVERT: A 1093 MET cc_start: 0.6961 (pmm) cc_final: 0.6604 (pmm) REVERT: A 1111 LEU cc_start: 0.8596 (mt) cc_final: 0.8349 (mt) REVERT: A 1112 MET cc_start: 0.8451 (mtm) cc_final: 0.8083 (mtp) REVERT: A 1126 ASP cc_start: 0.6577 (m-30) cc_final: 0.6347 (m-30) REVERT: A 1137 VAL cc_start: 0.8239 (t) cc_final: 0.7753 (p) REVERT: A 1145 ASP cc_start: 0.6160 (m-30) cc_final: 0.5007 (m-30) REVERT: A 1148 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7565 (ttp-170) REVERT: A 1202 ASN cc_start: 0.7637 (m-40) cc_final: 0.7233 (m110) REVERT: A 1219 ASP cc_start: 0.7689 (t0) cc_final: 0.7462 (t70) REVERT: A 1222 GLN cc_start: 0.8487 (mp10) cc_final: 0.7902 (mp10) REVERT: B 71 GLU cc_start: 0.7953 (pp20) cc_final: 0.7725 (pp20) REVERT: B 77 HIS cc_start: 0.6919 (m-70) cc_final: 0.6666 (m170) REVERT: B 88 ARG cc_start: 0.8011 (ptp-170) cc_final: 0.7724 (ptp90) REVERT: B 108 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7853 (ttmm) REVERT: B 113 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6728 (mm-30) REVERT: B 123 GLU cc_start: 0.7534 (pt0) cc_final: 0.7160 (pt0) REVERT: B 134 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7915 (mtmt) REVERT: B 180 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7670 (ptmt) REVERT: B 183 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6876 (mt-10) REVERT: B 191 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7193 (mt-10) REVERT: B 201 ASN cc_start: 0.7862 (m110) cc_final: 0.7509 (m110) REVERT: B 210 GLN cc_start: 0.7490 (tt0) cc_final: 0.7227 (tt0) REVERT: B 251 TRP cc_start: 0.7256 (m100) cc_final: 0.6751 (m100) REVERT: B 288 LYS cc_start: 0.7100 (mttt) cc_final: 0.6484 (mtpt) REVERT: B 304 TRP cc_start: 0.7840 (m100) cc_final: 0.7464 (m100) REVERT: B 306 LEU cc_start: 0.8030 (mm) cc_final: 0.7826 (mm) REVERT: B 310 GLU cc_start: 0.7617 (mp0) cc_final: 0.7350 (mp0) REVERT: B 315 TYR cc_start: 0.7929 (m-80) cc_final: 0.7566 (m-80) REVERT: B 339 ASN cc_start: 0.6955 (t0) cc_final: 0.6521 (t0) REVERT: B 352 ASP cc_start: 0.7311 (t0) cc_final: 0.6968 (t0) REVERT: B 396 ARG cc_start: 0.7567 (ttm170) cc_final: 0.7173 (ttm110) REVERT: B 400 GLN cc_start: 0.7708 (tt0) cc_final: 0.7485 (tp40) REVERT: B 412 SER cc_start: 0.8295 (t) cc_final: 0.7795 (p) REVERT: B 431 LYS cc_start: 0.8309 (tttt) cc_final: 0.7958 (tppt) REVERT: B 435 MET cc_start: 0.7184 (mtp) cc_final: 0.6953 (mtp) REVERT: B 446 THR cc_start: 0.8276 (m) cc_final: 0.7902 (m) REVERT: B 449 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7256 (mt-10) REVERT: B 457 SER cc_start: 0.8028 (t) cc_final: 0.7673 (p) REVERT: B 461 THR cc_start: 0.8263 (p) cc_final: 0.7952 (t) REVERT: B 462 MET cc_start: 0.7986 (mmt) cc_final: 0.7704 (mmt) REVERT: B 465 MET cc_start: 0.7582 (mtm) cc_final: 0.7157 (mtm) REVERT: B 466 MET cc_start: 0.7367 (mtp) cc_final: 0.7001 (ttp) REVERT: B 467 HIS cc_start: 0.8124 (t-90) cc_final: 0.7875 (t70) REVERT: C 71 GLU cc_start: 0.8308 (tt0) cc_final: 0.8093 (tt0) REVERT: C 75 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7680 (mtp85) REVERT: C 80 SER cc_start: 0.8562 (t) cc_final: 0.8214 (m) REVERT: C 89 ASP cc_start: 0.8013 (m-30) cc_final: 0.7701 (m-30) REVERT: C 92 LEU cc_start: 0.8623 (mt) cc_final: 0.8363 (mm) REVERT: C 107 ARG cc_start: 0.7445 (ttm170) cc_final: 0.7233 (ttp80) REVERT: C 110 LEU cc_start: 0.7861 (tt) cc_final: 0.7594 (tp) REVERT: C 146 ARG cc_start: 0.7360 (mmt-90) cc_final: 0.7010 (mmt180) REVERT: C 183 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6435 (mt-10) REVERT: C 194 VAL cc_start: 0.7920 (m) cc_final: 0.7660 (p) REVERT: C 231 ILE cc_start: 0.7994 (mt) cc_final: 0.7789 (mt) REVERT: C 234 LYS cc_start: 0.7991 (mttt) cc_final: 0.7608 (mttt) REVERT: C 242 PHE cc_start: 0.6842 (m-10) cc_final: 0.6388 (m-10) REVERT: C 243 THR cc_start: 0.7769 (t) cc_final: 0.7462 (p) REVERT: C 256 LEU cc_start: 0.8451 (tp) cc_final: 0.8182 (tp) REVERT: C 259 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7353 (mtp85) REVERT: C 262 TRP cc_start: 0.7862 (t60) cc_final: 0.7191 (t60) REVERT: C 280 ASP cc_start: 0.6287 (p0) cc_final: 0.5840 (p0) REVERT: C 287 ASN cc_start: 0.7120 (t0) cc_final: 0.6904 (t0) REVERT: C 288 LYS cc_start: 0.8265 (mttt) cc_final: 0.7760 (mttt) REVERT: C 291 TYR cc_start: 0.8071 (t80) cc_final: 0.7806 (t80) REVERT: C 301 GLU cc_start: 0.7344 (tt0) cc_final: 0.6596 (tt0) REVERT: C 305 ASN cc_start: 0.7567 (t0) cc_final: 0.7338 (t0) REVERT: C 306 LEU cc_start: 0.8381 (mt) cc_final: 0.8028 (mm) REVERT: C 336 LEU cc_start: 0.8330 (mt) cc_final: 0.8009 (mt) REVERT: C 346 MET cc_start: 0.7058 (tmm) cc_final: 0.6602 (tmm) REVERT: C 371 VAL cc_start: 0.8386 (p) cc_final: 0.8001 (m) REVERT: C 373 LYS cc_start: 0.8229 (mttt) cc_final: 0.7805 (ptpp) REVERT: C 396 ARG cc_start: 0.7790 (ttm170) cc_final: 0.6758 (ttm170) REVERT: C 400 GLN cc_start: 0.7830 (mt0) cc_final: 0.6813 (mt0) REVERT: C 404 ASN cc_start: 0.8067 (m-40) cc_final: 0.7511 (m110) REVERT: C 415 PRO cc_start: 0.8678 (Cg_endo) cc_final: 0.8462 (Cg_exo) REVERT: C 421 MET cc_start: 0.6494 (mtt) cc_final: 0.6279 (mtt) REVERT: C 426 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7615 (mt-10) REVERT: C 427 GLN cc_start: 0.8261 (mt0) cc_final: 0.7777 (mt0) REVERT: C 430 SER cc_start: 0.8452 (t) cc_final: 0.7965 (p) REVERT: C 431 LYS cc_start: 0.8379 (tttt) cc_final: 0.8152 (tttt) REVERT: C 434 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7594 (mt-10) REVERT: C 466 MET cc_start: 0.6919 (ttm) cc_final: 0.6606 (ttm) REVERT: C 470 LYS cc_start: 0.8580 (mttt) cc_final: 0.8204 (mttt) outliers start: 0 outliers final: 0 residues processed: 574 average time/residue: 0.1292 time to fit residues: 106.9706 Evaluate side-chains 532 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 472 GLN A 564 GLN B 192 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 409 ASN B 427 GLN C 279 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094717 restraints weight = 59846.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100001 restraints weight = 25313.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103469 restraints weight = 13774.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105609 restraints weight = 8757.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107276 restraints weight = 6386.513| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16209 Z= 0.149 Angle : 0.561 10.999 22166 Z= 0.300 Chirality : 0.042 0.183 2406 Planarity : 0.005 0.055 2692 Dihedral : 14.838 89.620 2496 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.19 % Allowed : 1.50 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1837 helix: 1.69 (0.19), residues: 789 sheet: 0.13 (0.34), residues: 236 loop : -0.48 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.027 0.002 TYR B 315 PHE 0.024 0.002 PHE C 242 TRP 0.020 0.002 TRP A 169 HIS 0.010 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (16209) covalent geometry : angle 0.56116 / 0.30 (22166) hydrogen bonds : bond 0.04164 / 2.85 ( 767) hydrogen bonds : angle 4.86048 / 3.45 ( 2137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 574 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8437 (mm) cc_final: 0.8219 (mm) REVERT: A 79 LEU cc_start: 0.8084 (mt) cc_final: 0.7815 (mp) REVERT: A 110 HIS cc_start: 0.7303 (m90) cc_final: 0.6515 (m90) REVERT: A 121 PRO cc_start: 0.8042 (Cg_exo) cc_final: 0.7665 (Cg_endo) REVERT: A 145 LYS cc_start: 0.8144 (tptp) cc_final: 0.7715 (tptp) REVERT: A 159 GLN cc_start: 0.7113 (tm-30) cc_final: 0.6660 (pp30) REVERT: A 189 ILE cc_start: 0.7723 (pt) cc_final: 0.7504 (pt) REVERT: A 191 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7221 (mm-30) REVERT: A 264 GLN cc_start: 0.7969 (pt0) cc_final: 0.7695 (pm20) REVERT: A 280 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7042 (mm-30) REVERT: A 289 MET cc_start: 0.7189 (ttm) cc_final: 0.6581 (ttm) REVERT: A 299 MET cc_start: 0.7361 (mmm) cc_final: 0.7109 (tmm) REVERT: A 308 GLN cc_start: 0.7859 (mt0) cc_final: 0.7267 (mt0) REVERT: A 355 SER cc_start: 0.7714 (t) cc_final: 0.7420 (t) REVERT: A 358 GLU cc_start: 0.7595 (mp0) cc_final: 0.7239 (mp0) REVERT: A 393 MET cc_start: 0.7263 (ttm) cc_final: 0.7022 (ttm) REVERT: A 405 GLU cc_start: 0.7512 (tp30) cc_final: 0.6771 (tp30) REVERT: A 443 ARG cc_start: 0.6894 (ttt-90) cc_final: 0.6382 (ttt-90) REVERT: A 487 ASP cc_start: 0.8272 (m-30) cc_final: 0.8033 (m-30) REVERT: A 565 HIS cc_start: 0.7349 (t-90) cc_final: 0.7137 (t-170) REVERT: A 566 LEU cc_start: 0.8833 (mt) cc_final: 0.8627 (mm) REVERT: A 586 THR cc_start: 0.8072 (t) cc_final: 0.7811 (p) REVERT: A 607 TRP cc_start: 0.8364 (t-100) cc_final: 0.7843 (t60) REVERT: A 608 ASP cc_start: 0.7995 (t0) cc_final: 0.7548 (t0) REVERT: A 610 PHE cc_start: 0.7891 (m-80) cc_final: 0.7561 (m-80) REVERT: A 750 PHE cc_start: 0.7129 (m-80) cc_final: 0.6571 (m-80) REVERT: A 758 ASN cc_start: 0.7929 (m-40) cc_final: 0.7463 (t0) REVERT: A 812 MET cc_start: 0.7421 (mpp) cc_final: 0.7145 (mpp) REVERT: A 816 LEU cc_start: 0.8431 (tp) cc_final: 0.8075 (tp) REVERT: A 821 LEU cc_start: 0.8323 (mt) cc_final: 0.8088 (mt) REVERT: A 823 ARG cc_start: 0.7587 (tmt170) cc_final: 0.6930 (tmt-80) REVERT: A 832 ASP cc_start: 0.8072 (t0) cc_final: 0.7369 (t0) REVERT: A 853 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7724 (mtp85) REVERT: A 873 GLU cc_start: 0.7640 (pm20) cc_final: 0.7068 (pm20) REVERT: A 877 MET cc_start: 0.7099 (mmm) cc_final: 0.6700 (tpp) REVERT: A 893 SER cc_start: 0.7268 (t) cc_final: 0.6625 (p) REVERT: A 919 MET cc_start: 0.7587 (mtt) cc_final: 0.7204 (mmp) REVERT: A 922 GLN cc_start: 0.7394 (tt0) cc_final: 0.6918 (tp40) REVERT: A 934 LYS cc_start: 0.8334 (mmpt) cc_final: 0.8042 (mmtt) REVERT: A 981 LYS cc_start: 0.8263 (tttt) cc_final: 0.7714 (tppt) REVERT: A 1057 MET cc_start: 0.7790 (ppp) cc_final: 0.7554 (ppp) REVERT: A 1060 LYS cc_start: 0.8153 (tptp) cc_final: 0.7673 (tptp) REVERT: A 1062 GLU cc_start: 0.7841 (pt0) cc_final: 0.7531 (mt-10) REVERT: A 1093 MET cc_start: 0.6864 (pmm) cc_final: 0.6574 (pmm) REVERT: A 1109 LEU cc_start: 0.8844 (tp) cc_final: 0.8626 (tt) REVERT: A 1111 LEU cc_start: 0.8599 (mt) cc_final: 0.8313 (mt) REVERT: A 1112 MET cc_start: 0.8440 (mtm) cc_final: 0.8089 (mtp) REVERT: A 1116 MET cc_start: 0.7662 (tpt) cc_final: 0.7294 (tpt) REVERT: A 1126 ASP cc_start: 0.6474 (m-30) cc_final: 0.6197 (m-30) REVERT: A 1148 ARG cc_start: 0.7808 (mtp180) cc_final: 0.6897 (ttm-80) REVERT: A 1202 ASN cc_start: 0.7673 (m-40) cc_final: 0.7225 (m110) REVERT: A 1222 GLN cc_start: 0.8492 (mp10) cc_final: 0.7879 (mp10) REVERT: B 77 HIS cc_start: 0.6901 (m-70) cc_final: 0.6636 (m170) REVERT: B 88 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.7710 (ptp90) REVERT: B 108 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7829 (ttmm) REVERT: B 113 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6722 (mm-30) REVERT: B 123 GLU cc_start: 0.7500 (pt0) cc_final: 0.7231 (pt0) REVERT: B 131 LEU cc_start: 0.7856 (mt) cc_final: 0.7579 (mp) REVERT: B 134 LYS cc_start: 0.8387 (mtmt) cc_final: 0.7929 (mtmt) REVERT: B 180 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7667 (ptmt) REVERT: B 183 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6914 (mt-10) REVERT: B 191 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7167 (mt-10) REVERT: B 192 HIS cc_start: 0.8145 (m90) cc_final: 0.7723 (m-70) REVERT: B 201 ASN cc_start: 0.7826 (m110) cc_final: 0.7469 (m110) REVERT: B 210 GLN cc_start: 0.7463 (tt0) cc_final: 0.7223 (tt0) REVERT: B 257 ARG cc_start: 0.7561 (ttm110) cc_final: 0.7346 (mtp85) REVERT: B 288 LYS cc_start: 0.7109 (mttt) cc_final: 0.6455 (mtpt) REVERT: B 304 TRP cc_start: 0.7812 (m100) cc_final: 0.7407 (m100) REVERT: B 310 GLU cc_start: 0.7593 (mp0) cc_final: 0.7341 (mp0) REVERT: B 315 TYR cc_start: 0.7871 (m-80) cc_final: 0.7543 (m-80) REVERT: B 339 ASN cc_start: 0.7031 (t0) cc_final: 0.6503 (t0) REVERT: B 352 ASP cc_start: 0.7224 (t0) cc_final: 0.6908 (t0) REVERT: B 353 SER cc_start: 0.8167 (p) cc_final: 0.7964 (p) REVERT: B 378 LEU cc_start: 0.8386 (mp) cc_final: 0.8055 (mt) REVERT: B 396 ARG cc_start: 0.7560 (ttm170) cc_final: 0.7147 (ttm110) REVERT: B 400 GLN cc_start: 0.7685 (tt0) cc_final: 0.7470 (tp40) REVERT: B 407 LEU cc_start: 0.7949 (mt) cc_final: 0.7742 (mm) REVERT: B 412 SER cc_start: 0.8290 (t) cc_final: 0.7799 (p) REVERT: B 431 LYS cc_start: 0.8321 (tttt) cc_final: 0.7928 (tppt) REVERT: B 435 MET cc_start: 0.7147 (mtp) cc_final: 0.6885 (mtp) REVERT: B 446 THR cc_start: 0.8293 (m) cc_final: 0.7931 (m) REVERT: B 449 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7237 (mt-10) REVERT: B 457 SER cc_start: 0.7923 (t) cc_final: 0.7586 (p) REVERT: B 460 THR cc_start: 0.8492 (p) cc_final: 0.8120 (p) REVERT: B 462 MET cc_start: 0.7940 (mmt) cc_final: 0.7693 (mmt) REVERT: B 465 MET cc_start: 0.7558 (mtm) cc_final: 0.7138 (mtm) REVERT: B 466 MET cc_start: 0.7321 (mtp) cc_final: 0.6968 (ttp) REVERT: C 71 GLU cc_start: 0.8313 (tt0) cc_final: 0.8082 (tt0) REVERT: C 75 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7639 (mtp85) REVERT: C 80 SER cc_start: 0.8569 (t) cc_final: 0.8161 (m) REVERT: C 89 ASP cc_start: 0.7979 (m-30) cc_final: 0.7675 (m-30) REVERT: C 92 LEU cc_start: 0.8622 (mt) cc_final: 0.8368 (mm) REVERT: C 107 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7192 (ttp80) REVERT: C 110 LEU cc_start: 0.7878 (tt) cc_final: 0.7672 (tp) REVERT: C 146 ARG cc_start: 0.7310 (mmt-90) cc_final: 0.6992 (mmt180) REVERT: C 183 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6401 (mt-10) REVERT: C 194 VAL cc_start: 0.7874 (m) cc_final: 0.7665 (p) REVERT: C 231 ILE cc_start: 0.7935 (mt) cc_final: 0.7733 (mm) REVERT: C 233 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6256 (mt-10) REVERT: C 234 LYS cc_start: 0.8091 (mttt) cc_final: 0.7647 (mttt) REVERT: C 242 PHE cc_start: 0.6866 (m-10) cc_final: 0.6516 (m-10) REVERT: C 243 THR cc_start: 0.7854 (t) cc_final: 0.7524 (p) REVERT: C 256 LEU cc_start: 0.8451 (tp) cc_final: 0.8182 (tp) REVERT: C 259 ARG cc_start: 0.7768 (mtp85) cc_final: 0.7345 (mtp85) REVERT: C 262 TRP cc_start: 0.7847 (t60) cc_final: 0.7189 (t60) REVERT: C 287 ASN cc_start: 0.7117 (t0) cc_final: 0.6862 (t0) REVERT: C 288 LYS cc_start: 0.8287 (mttt) cc_final: 0.7715 (mttt) REVERT: C 291 TYR cc_start: 0.8040 (t80) cc_final: 0.7821 (t80) REVERT: C 301 GLU cc_start: 0.7360 (tt0) cc_final: 0.6633 (tt0) REVERT: C 305 ASN cc_start: 0.7505 (t0) cc_final: 0.7279 (t0) REVERT: C 306 LEU cc_start: 0.8372 (mt) cc_final: 0.7960 (mm) REVERT: C 336 LEU cc_start: 0.8349 (mt) cc_final: 0.7982 (mt) REVERT: C 346 MET cc_start: 0.6975 (tmm) cc_final: 0.6275 (tmm) REVERT: C 371 VAL cc_start: 0.8220 (p) cc_final: 0.7992 (m) REVERT: C 373 LYS cc_start: 0.8284 (mttt) cc_final: 0.7610 (ptpp) REVERT: C 396 ARG cc_start: 0.7844 (ttm170) cc_final: 0.6803 (ttm170) REVERT: C 400 GLN cc_start: 0.7891 (mt0) cc_final: 0.7242 (mt0) REVERT: C 415 PRO cc_start: 0.8677 (Cg_endo) cc_final: 0.8450 (Cg_exo) REVERT: C 421 MET cc_start: 0.6459 (mtt) cc_final: 0.6199 (mtt) REVERT: C 426 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7603 (mt-10) REVERT: C 427 GLN cc_start: 0.8254 (mt0) cc_final: 0.7760 (mt0) REVERT: C 430 SER cc_start: 0.8453 (t) cc_final: 0.7949 (p) REVERT: C 431 LYS cc_start: 0.8359 (tttt) cc_final: 0.8145 (tttt) REVERT: C 434 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 466 MET cc_start: 0.6957 (ttm) cc_final: 0.6683 (ttm) REVERT: C 470 LYS cc_start: 0.8538 (mttt) cc_final: 0.8180 (mttt) outliers start: 1 outliers final: 1 residues processed: 574 average time/residue: 0.1248 time to fit residues: 102.9221 Evaluate side-chains 530 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 122 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 277 HIS A 354 ASN A 398 GLN A 468 ASN A 564 GLN A 843 GLN A 906 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.091225 restraints weight = 88960.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097256 restraints weight = 32571.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101211 restraints weight = 16602.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103786 restraints weight = 10102.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105451 restraints weight = 7043.471| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16209 Z= 0.191 Angle : 0.582 13.583 22166 Z= 0.312 Chirality : 0.043 0.183 2406 Planarity : 0.005 0.054 2692 Dihedral : 14.853 89.622 2496 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 0.13 % Allowed : 1.56 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1837 helix: 1.70 (0.19), residues: 785 sheet: 0.04 (0.34), residues: 234 loop : -0.56 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1071 TYR 0.026 0.002 TYR B 315 PHE 0.017 0.002 PHE C 242 TRP 0.023 0.002 TRP A 572 HIS 0.009 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (16209) covalent geometry : angle 0.58199 / 0.31 (22166) hydrogen bonds : bond 0.04296 / 2.96 ( 767) hydrogen bonds : angle 4.87746 / 3.46 ( 2137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8424 (mm) cc_final: 0.8223 (mm) REVERT: A 79 LEU cc_start: 0.8072 (mt) cc_final: 0.7828 (mp) REVERT: A 110 HIS cc_start: 0.7318 (m90) cc_final: 0.6561 (m90) REVERT: A 159 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6648 (pp30) REVERT: A 289 MET cc_start: 0.7081 (ttm) cc_final: 0.6727 (ttm) REVERT: A 295 MET cc_start: 0.7729 (ttm) cc_final: 0.6826 (ttm) REVERT: A 299 MET cc_start: 0.7329 (mmm) cc_final: 0.6976 (tmm) REVERT: A 354 ASN cc_start: 0.7435 (m-40) cc_final: 0.7150 (m-40) REVERT: A 393 MET cc_start: 0.7246 (ttm) cc_final: 0.6942 (ttm) REVERT: A 398 GLN cc_start: 0.7938 (pt0) cc_final: 0.7579 (tt0) REVERT: A 439 GLN cc_start: 0.8183 (pm20) cc_final: 0.7429 (pm20) REVERT: A 443 ARG cc_start: 0.6954 (ttt-90) cc_final: 0.6412 (ttt-90) REVERT: A 449 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7867 (tp-100) REVERT: A 458 GLU cc_start: 0.7720 (pp20) cc_final: 0.7485 (tm-30) REVERT: A 487 ASP cc_start: 0.8290 (m-30) cc_final: 0.8029 (m-30) REVERT: A 565 HIS cc_start: 0.7423 (t-90) cc_final: 0.7086 (t-170) REVERT: A 566 LEU cc_start: 0.8897 (mt) cc_final: 0.8686 (mm) REVERT: A 607 TRP cc_start: 0.8351 (t-100) cc_final: 0.7808 (t60) REVERT: A 608 ASP cc_start: 0.7965 (t0) cc_final: 0.7504 (t0) REVERT: A 610 PHE cc_start: 0.7938 (m-80) cc_final: 0.7582 (m-80) REVERT: A 750 PHE cc_start: 0.7136 (m-80) cc_final: 0.6581 (m-80) REVERT: A 758 ASN cc_start: 0.7916 (m-40) cc_final: 0.7435 (t0) REVERT: A 812 MET cc_start: 0.7453 (mpp) cc_final: 0.7134 (mpp) REVERT: A 816 LEU cc_start: 0.8441 (tp) cc_final: 0.8114 (tp) REVERT: A 821 LEU cc_start: 0.8351 (mt) cc_final: 0.8082 (mt) REVERT: A 832 ASP cc_start: 0.8012 (t0) cc_final: 0.7423 (t0) REVERT: A 853 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7743 (mtp85) REVERT: A 877 MET cc_start: 0.7127 (mmm) cc_final: 0.6767 (tpp) REVERT: A 893 SER cc_start: 0.7305 (t) cc_final: 0.6686 (p) REVERT: A 919 MET cc_start: 0.7622 (mtt) cc_final: 0.7252 (mmp) REVERT: A 922 GLN cc_start: 0.7399 (tt0) cc_final: 0.6602 (tp-100) REVERT: A 934 LYS cc_start: 0.8345 (mmpt) cc_final: 0.8116 (mmtt) REVERT: A 981 LYS cc_start: 0.8254 (tttt) cc_final: 0.7699 (tppt) REVERT: A 1057 MET cc_start: 0.7785 (ppp) cc_final: 0.7569 (ppp) REVERT: A 1060 LYS cc_start: 0.8152 (tptp) cc_final: 0.7712 (tptp) REVERT: A 1062 GLU cc_start: 0.7871 (pt0) cc_final: 0.7616 (mt-10) REVERT: A 1111 LEU cc_start: 0.8611 (mt) cc_final: 0.8376 (mt) REVERT: A 1112 MET cc_start: 0.8436 (mtm) cc_final: 0.8123 (mtp) REVERT: A 1126 ASP cc_start: 0.6426 (m-30) cc_final: 0.6224 (m-30) REVERT: A 1137 VAL cc_start: 0.8301 (t) cc_final: 0.7819 (p) REVERT: A 1145 ASP cc_start: 0.6287 (m-30) cc_final: 0.6031 (m-30) REVERT: A 1148 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7475 (ttp-170) REVERT: A 1207 GLU cc_start: 0.7308 (pm20) cc_final: 0.7068 (pm20) REVERT: A 1219 ASP cc_start: 0.8028 (t70) cc_final: 0.7685 (t0) REVERT: A 1222 GLN cc_start: 0.8523 (mp10) cc_final: 0.7881 (mp10) REVERT: B 77 HIS cc_start: 0.6914 (m-70) cc_final: 0.6680 (m170) REVERT: B 83 LYS cc_start: 0.8723 (ptmt) cc_final: 0.8440 (ptpp) REVERT: B 85 GLN cc_start: 0.7451 (mt0) cc_final: 0.6890 (mt0) REVERT: B 88 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.7703 (ptp90) REVERT: B 108 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7806 (ttmm) REVERT: B 113 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6742 (mm-30) REVERT: B 123 GLU cc_start: 0.7541 (pt0) cc_final: 0.7214 (pt0) REVERT: B 131 LEU cc_start: 0.7844 (mt) cc_final: 0.7605 (mp) REVERT: B 134 LYS cc_start: 0.8393 (mtmt) cc_final: 0.7915 (mtmt) REVERT: B 180 LYS cc_start: 0.8342 (ptmt) cc_final: 0.7560 (ptmt) REVERT: B 183 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6889 (mt-10) REVERT: B 191 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7119 (mt-10) REVERT: B 192 HIS cc_start: 0.8145 (m90) cc_final: 0.7727 (m-70) REVERT: B 201 ASN cc_start: 0.7815 (m110) cc_final: 0.7506 (m110) REVERT: B 288 LYS cc_start: 0.7071 (mttt) cc_final: 0.6388 (mtpt) REVERT: B 289 LEU cc_start: 0.7879 (mt) cc_final: 0.7554 (mt) REVERT: B 304 TRP cc_start: 0.7814 (m100) cc_final: 0.7406 (m100) REVERT: B 310 GLU cc_start: 0.7585 (mp0) cc_final: 0.7347 (mp0) REVERT: B 315 TYR cc_start: 0.7852 (m-80) cc_final: 0.7562 (m-80) REVERT: B 339 ASN cc_start: 0.7052 (t0) cc_final: 0.6502 (t0) REVERT: B 352 ASP cc_start: 0.7275 (t0) cc_final: 0.6923 (t0) REVERT: B 378 LEU cc_start: 0.8379 (mp) cc_final: 0.8051 (mt) REVERT: B 396 ARG cc_start: 0.7570 (ttm170) cc_final: 0.7170 (ttm110) REVERT: B 400 GLN cc_start: 0.7687 (tt0) cc_final: 0.7468 (tp40) REVERT: B 412 SER cc_start: 0.8276 (t) cc_final: 0.7792 (p) REVERT: B 427 GLN cc_start: 0.8286 (pt0) cc_final: 0.7557 (pm20) REVERT: B 431 LYS cc_start: 0.8344 (tttt) cc_final: 0.7948 (tppt) REVERT: B 435 MET cc_start: 0.7207 (mtp) cc_final: 0.6946 (mtp) REVERT: B 449 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7339 (mt-10) REVERT: B 457 SER cc_start: 0.7900 (t) cc_final: 0.7569 (p) REVERT: B 460 THR cc_start: 0.8529 (p) cc_final: 0.8157 (p) REVERT: B 461 THR cc_start: 0.8227 (p) cc_final: 0.7956 (t) REVERT: B 462 MET cc_start: 0.7867 (mmt) cc_final: 0.7602 (mmt) REVERT: B 465 MET cc_start: 0.7557 (mtm) cc_final: 0.7135 (mtm) REVERT: B 466 MET cc_start: 0.7356 (mtp) cc_final: 0.7038 (ttp) REVERT: B 467 HIS cc_start: 0.8113 (t-90) cc_final: 0.7905 (t70) REVERT: C 71 GLU cc_start: 0.8314 (tt0) cc_final: 0.8094 (tt0) REVERT: C 75 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7667 (mtp85) REVERT: C 80 SER cc_start: 0.8553 (t) cc_final: 0.8152 (m) REVERT: C 89 ASP cc_start: 0.8004 (m-30) cc_final: 0.7684 (m-30) REVERT: C 92 LEU cc_start: 0.8628 (mt) cc_final: 0.8361 (mm) REVERT: C 107 ARG cc_start: 0.7472 (ttm170) cc_final: 0.7195 (ttp80) REVERT: C 146 ARG cc_start: 0.7322 (mmt-90) cc_final: 0.6879 (mmt180) REVERT: C 183 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6451 (mt-10) REVERT: C 194 VAL cc_start: 0.7924 (m) cc_final: 0.7717 (p) REVERT: C 231 ILE cc_start: 0.7921 (mt) cc_final: 0.7713 (mm) REVERT: C 233 GLU cc_start: 0.6577 (mt-10) cc_final: 0.6231 (mt-10) REVERT: C 234 LYS cc_start: 0.8111 (mttt) cc_final: 0.7655 (mttt) REVERT: C 242 PHE cc_start: 0.6948 (m-10) cc_final: 0.6603 (m-10) REVERT: C 243 THR cc_start: 0.7886 (t) cc_final: 0.7571 (p) REVERT: C 256 LEU cc_start: 0.8473 (tp) cc_final: 0.8186 (tp) REVERT: C 259 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7341 (mtp85) REVERT: C 262 TRP cc_start: 0.7870 (t60) cc_final: 0.7225 (t60) REVERT: C 287 ASN cc_start: 0.7157 (t0) cc_final: 0.6872 (t0) REVERT: C 288 LYS cc_start: 0.8285 (mttt) cc_final: 0.7714 (mttt) REVERT: C 291 TYR cc_start: 0.8084 (t80) cc_final: 0.7844 (t80) REVERT: C 301 GLU cc_start: 0.7367 (tt0) cc_final: 0.6635 (tt0) REVERT: C 305 ASN cc_start: 0.7530 (t0) cc_final: 0.7283 (t0) REVERT: C 306 LEU cc_start: 0.8315 (mt) cc_final: 0.7934 (mm) REVERT: C 336 LEU cc_start: 0.8371 (mt) cc_final: 0.8022 (mt) REVERT: C 346 MET cc_start: 0.7017 (tmm) cc_final: 0.6332 (tmm) REVERT: C 371 VAL cc_start: 0.8218 (p) cc_final: 0.7984 (m) REVERT: C 373 LYS cc_start: 0.8263 (mttt) cc_final: 0.7630 (ptpp) REVERT: C 396 ARG cc_start: 0.7822 (ttm170) cc_final: 0.6875 (ttm170) REVERT: C 400 GLN cc_start: 0.7709 (mt0) cc_final: 0.7330 (mt0) REVERT: C 415 PRO cc_start: 0.8693 (Cg_endo) cc_final: 0.8452 (Cg_exo) REVERT: C 421 MET cc_start: 0.6494 (mtt) cc_final: 0.6238 (mtt) REVERT: C 426 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 427 GLN cc_start: 0.8236 (mt0) cc_final: 0.7753 (mt0) REVERT: C 430 SER cc_start: 0.8464 (t) cc_final: 0.8006 (p) REVERT: C 431 LYS cc_start: 0.8367 (tttt) cc_final: 0.8155 (tttt) REVERT: C 434 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7619 (mt-10) REVERT: C 466 MET cc_start: 0.6959 (ttm) cc_final: 0.6722 (ttm) REVERT: C 470 LYS cc_start: 0.8559 (mttt) cc_final: 0.8177 (mttt) REVERT: C 478 TYR cc_start: 0.8062 (t80) cc_final: 0.7774 (t80) outliers start: 0 outliers final: 0 residues processed: 567 average time/residue: 0.1278 time to fit residues: 104.1597 Evaluate side-chains 527 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 0.0870 chunk 124 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 398 GLN A 468 ASN A 564 GLN A 906 HIS ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 305 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094094 restraints weight = 66613.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099548 restraints weight = 27210.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103225 restraints weight = 14513.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105630 restraints weight = 9013.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107238 restraints weight = 6307.580| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16209 Z= 0.135 Angle : 0.569 8.672 22166 Z= 0.302 Chirality : 0.042 0.185 2406 Planarity : 0.005 0.055 2692 Dihedral : 14.774 89.406 2496 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 0.19 % Allowed : 1.44 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1837 helix: 1.79 (0.19), residues: 782 sheet: 0.11 (0.34), residues: 234 loop : -0.51 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1071 TYR 0.024 0.002 TYR B 315 PHE 0.027 0.002 PHE A 273 TRP 0.032 0.002 TRP A 490 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (16209) covalent geometry : angle 0.56894 / 0.30 (22166) hydrogen bonds : bond 0.03966 / 2.71 ( 767) hydrogen bonds : angle 4.73630 / 3.35 ( 2137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 578 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8057 (mt) cc_final: 0.7830 (mp) REVERT: A 159 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6601 (pp30) REVERT: A 189 ILE cc_start: 0.7691 (pt) cc_final: 0.7489 (pt) REVERT: A 191 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 193 ARG cc_start: 0.7403 (ttm170) cc_final: 0.7157 (ttp-110) REVERT: A 264 GLN cc_start: 0.7556 (pm20) cc_final: 0.7259 (pm20) REVERT: A 295 MET cc_start: 0.7662 (ttm) cc_final: 0.6875 (ttm) REVERT: A 299 MET cc_start: 0.7270 (mmm) cc_final: 0.6875 (tpt) REVERT: A 354 ASN cc_start: 0.7405 (m-40) cc_final: 0.6852 (m-40) REVERT: A 355 SER cc_start: 0.7495 (t) cc_final: 0.7291 (t) REVERT: A 358 GLU cc_start: 0.7682 (mp0) cc_final: 0.7341 (mp0) REVERT: A 374 ARG cc_start: 0.8104 (ttt180) cc_final: 0.7806 (ttt180) REVERT: A 393 MET cc_start: 0.7276 (ttm) cc_final: 0.6954 (ttm) REVERT: A 405 GLU cc_start: 0.7579 (pp20) cc_final: 0.7365 (pp20) REVERT: A 443 ARG cc_start: 0.6829 (ttt-90) cc_final: 0.6349 (ttt-90) REVERT: A 458 GLU cc_start: 0.7755 (pp20) cc_final: 0.7523 (tm-30) REVERT: A 487 ASP cc_start: 0.8298 (m-30) cc_final: 0.8030 (m-30) REVERT: A 552 LEU cc_start: 0.8950 (mm) cc_final: 0.8743 (mt) REVERT: A 565 HIS cc_start: 0.7703 (t-90) cc_final: 0.7035 (t-170) REVERT: A 566 LEU cc_start: 0.8929 (mt) cc_final: 0.8646 (mm) REVERT: A 607 TRP cc_start: 0.8347 (t-100) cc_final: 0.7810 (t60) REVERT: A 608 ASP cc_start: 0.7911 (t0) cc_final: 0.7446 (t0) REVERT: A 610 PHE cc_start: 0.7912 (m-80) cc_final: 0.7540 (m-80) REVERT: A 758 ASN cc_start: 0.7927 (m-40) cc_final: 0.7412 (t0) REVERT: A 774 MET cc_start: 0.7342 (tpt) cc_final: 0.7134 (tpt) REVERT: A 812 MET cc_start: 0.7489 (mpp) cc_final: 0.7149 (mpp) REVERT: A 816 LEU cc_start: 0.8437 (tp) cc_final: 0.8100 (tp) REVERT: A 821 LEU cc_start: 0.8333 (mt) cc_final: 0.8116 (mt) REVERT: A 823 ARG cc_start: 0.7607 (tmt170) cc_final: 0.6591 (tmt-80) REVERT: A 832 ASP cc_start: 0.7988 (t0) cc_final: 0.7345 (t0) REVERT: A 853 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7674 (mtp85) REVERT: A 858 THR cc_start: 0.7492 (t) cc_final: 0.7205 (t) REVERT: A 873 GLU cc_start: 0.7649 (pm20) cc_final: 0.7220 (pm20) REVERT: A 877 MET cc_start: 0.7034 (mmm) cc_final: 0.6721 (tpp) REVERT: A 893 SER cc_start: 0.7249 (t) cc_final: 0.6555 (p) REVERT: A 906 HIS cc_start: 0.8282 (t70) cc_final: 0.8070 (t-90) REVERT: A 919 MET cc_start: 0.7589 (mtt) cc_final: 0.7218 (mmp) REVERT: A 922 GLN cc_start: 0.7398 (tt0) cc_final: 0.6601 (tp-100) REVERT: A 934 LYS cc_start: 0.8286 (mmpt) cc_final: 0.8010 (mmtt) REVERT: A 981 LYS cc_start: 0.8239 (tttt) cc_final: 0.7703 (tppt) REVERT: A 1057 MET cc_start: 0.7781 (ppp) cc_final: 0.7579 (ppp) REVERT: A 1060 LYS cc_start: 0.8162 (tptp) cc_final: 0.7731 (tptp) REVERT: A 1062 GLU cc_start: 0.7855 (pt0) cc_final: 0.7601 (mt-10) REVERT: A 1084 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7471 (mm-30) REVERT: A 1109 LEU cc_start: 0.8826 (tp) cc_final: 0.8625 (tt) REVERT: A 1112 MET cc_start: 0.8436 (mtm) cc_final: 0.8106 (mtp) REVERT: A 1126 ASP cc_start: 0.6463 (m-30) cc_final: 0.6190 (m-30) REVERT: A 1144 GLU cc_start: 0.6977 (pm20) cc_final: 0.6745 (pm20) REVERT: A 1145 ASP cc_start: 0.6327 (m-30) cc_final: 0.5712 (m-30) REVERT: A 1207 GLU cc_start: 0.7310 (pm20) cc_final: 0.7030 (pm20) REVERT: A 1219 ASP cc_start: 0.7959 (t70) cc_final: 0.7502 (t0) REVERT: A 1222 GLN cc_start: 0.8505 (mp10) cc_final: 0.7909 (mp10) REVERT: B 77 HIS cc_start: 0.6883 (m-70) cc_final: 0.6673 (m170) REVERT: B 85 GLN cc_start: 0.7444 (mt0) cc_final: 0.6929 (mt0) REVERT: B 88 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.7706 (ptp90) REVERT: B 108 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7871 (ttmm) REVERT: B 113 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6716 (mm-30) REVERT: B 123 GLU cc_start: 0.7513 (pt0) cc_final: 0.7205 (pt0) REVERT: B 131 LEU cc_start: 0.7824 (mt) cc_final: 0.7561 (mp) REVERT: B 134 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7949 (mtmt) REVERT: B 180 LYS cc_start: 0.8323 (ptmt) cc_final: 0.7628 (ptmt) REVERT: B 183 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6951 (mt-10) REVERT: B 191 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 201 ASN cc_start: 0.7811 (m110) cc_final: 0.7475 (m110) REVERT: B 210 GLN cc_start: 0.7643 (tt0) cc_final: 0.7277 (tt0) REVERT: B 246 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7304 (ptp90) REVERT: B 257 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7406 (mtp85) REVERT: B 288 LYS cc_start: 0.7151 (mttt) cc_final: 0.6446 (mtpt) REVERT: B 289 LEU cc_start: 0.7892 (mt) cc_final: 0.7544 (mt) REVERT: B 304 TRP cc_start: 0.7788 (m100) cc_final: 0.7392 (m100) REVERT: B 310 GLU cc_start: 0.7585 (mp0) cc_final: 0.7343 (mp0) REVERT: B 315 TYR cc_start: 0.7860 (m-80) cc_final: 0.7553 (m-80) REVERT: B 339 ASN cc_start: 0.7056 (t0) cc_final: 0.6352 (t0) REVERT: B 352 ASP cc_start: 0.7208 (t0) cc_final: 0.6888 (t0) REVERT: B 353 SER cc_start: 0.8084 (p) cc_final: 0.7873 (p) REVERT: B 396 ARG cc_start: 0.7553 (ttm170) cc_final: 0.7138 (ttm110) REVERT: B 400 GLN cc_start: 0.7694 (tt0) cc_final: 0.7463 (tp40) REVERT: B 412 SER cc_start: 0.8265 (t) cc_final: 0.7740 (p) REVERT: B 427 GLN cc_start: 0.8246 (pt0) cc_final: 0.7516 (pm20) REVERT: B 431 LYS cc_start: 0.8303 (tttt) cc_final: 0.7923 (tppt) REVERT: B 435 MET cc_start: 0.7120 (mtp) cc_final: 0.6845 (mtp) REVERT: B 446 THR cc_start: 0.8225 (m) cc_final: 0.7939 (m) REVERT: B 449 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 457 SER cc_start: 0.7911 (t) cc_final: 0.7567 (p) REVERT: B 460 THR cc_start: 0.8501 (p) cc_final: 0.8162 (p) REVERT: B 461 THR cc_start: 0.8198 (p) cc_final: 0.7927 (t) REVERT: B 462 MET cc_start: 0.7821 (mmt) cc_final: 0.7601 (mmt) REVERT: B 465 MET cc_start: 0.7509 (mtm) cc_final: 0.7069 (mtm) REVERT: B 466 MET cc_start: 0.7264 (mtp) cc_final: 0.7012 (ttp) REVERT: C 71 GLU cc_start: 0.8292 (tt0) cc_final: 0.8086 (tt0) REVERT: C 75 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7636 (mtp85) REVERT: C 80 SER cc_start: 0.8461 (t) cc_final: 0.8106 (m) REVERT: C 89 ASP cc_start: 0.7965 (m-30) cc_final: 0.7659 (m-30) REVERT: C 92 LEU cc_start: 0.8622 (mt) cc_final: 0.8361 (mm) REVERT: C 146 ARG cc_start: 0.7341 (mmt-90) cc_final: 0.6959 (mmt180) REVERT: C 183 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6429 (mt-10) REVERT: C 190 LEU cc_start: 0.8650 (mt) cc_final: 0.8398 (mm) REVERT: C 194 VAL cc_start: 0.7900 (m) cc_final: 0.7538 (p) REVERT: C 203 ARG cc_start: 0.7485 (ttt180) cc_final: 0.7277 (ttt180) REVERT: C 234 LYS cc_start: 0.8071 (mttt) cc_final: 0.7586 (mttt) REVERT: C 235 THR cc_start: 0.6986 (p) cc_final: 0.6554 (p) REVERT: C 242 PHE cc_start: 0.6959 (m-10) cc_final: 0.6584 (m-10) REVERT: C 243 THR cc_start: 0.7868 (t) cc_final: 0.7541 (p) REVERT: C 256 LEU cc_start: 0.8463 (tp) cc_final: 0.8186 (tp) REVERT: C 259 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7274 (mtp85) REVERT: C 262 TRP cc_start: 0.7796 (t60) cc_final: 0.7117 (t60) REVERT: C 279 GLN cc_start: 0.7301 (tt0) cc_final: 0.6897 (tm-30) REVERT: C 287 ASN cc_start: 0.7120 (t0) cc_final: 0.6805 (t0) REVERT: C 288 LYS cc_start: 0.8276 (mttt) cc_final: 0.7709 (mttt) REVERT: C 291 TYR cc_start: 0.8139 (t80) cc_final: 0.7836 (t80) REVERT: C 301 GLU cc_start: 0.7366 (tt0) cc_final: 0.6622 (tt0) REVERT: C 305 ASN cc_start: 0.7528 (t0) cc_final: 0.7278 (t0) REVERT: C 306 LEU cc_start: 0.8290 (mt) cc_final: 0.7935 (mm) REVERT: C 336 LEU cc_start: 0.8356 (mt) cc_final: 0.7959 (mt) REVERT: C 343 ASP cc_start: 0.6923 (m-30) cc_final: 0.6450 (m-30) REVERT: C 347 LEU cc_start: 0.8242 (mm) cc_final: 0.7092 (mm) REVERT: C 354 PHE cc_start: 0.7849 (t80) cc_final: 0.7454 (t80) REVERT: C 371 VAL cc_start: 0.8202 (p) cc_final: 0.7995 (m) REVERT: C 373 LYS cc_start: 0.8185 (mttt) cc_final: 0.7496 (ptpp) REVERT: C 396 ARG cc_start: 0.7808 (ttm170) cc_final: 0.6862 (ttm170) REVERT: C 400 GLN cc_start: 0.7887 (mt0) cc_final: 0.7312 (mt0) REVERT: C 415 PRO cc_start: 0.8686 (Cg_endo) cc_final: 0.8454 (Cg_exo) REVERT: C 421 MET cc_start: 0.6404 (mtt) cc_final: 0.6157 (mtt) REVERT: C 427 GLN cc_start: 0.8230 (mt0) cc_final: 0.7226 (mt0) REVERT: C 430 SER cc_start: 0.8426 (t) cc_final: 0.7905 (p) REVERT: C 431 LYS cc_start: 0.8366 (tttt) cc_final: 0.8140 (tttt) REVERT: C 434 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 466 MET cc_start: 0.6974 (ttm) cc_final: 0.6742 (ttm) REVERT: C 470 LYS cc_start: 0.8532 (mttt) cc_final: 0.8167 (mttt) REVERT: C 478 TYR cc_start: 0.7988 (t80) cc_final: 0.7718 (t80) outliers start: 1 outliers final: 0 residues processed: 578 average time/residue: 0.1257 time to fit residues: 104.2534 Evaluate side-chains 526 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 165 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 564 GLN A 811 GLN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 261 GLN B 409 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093627 restraints weight = 67475.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099073 restraints weight = 27247.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102661 restraints weight = 14552.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105046 restraints weight = 9147.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106649 restraints weight = 6433.805| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16209 Z= 0.147 Angle : 0.579 8.798 22166 Z= 0.307 Chirality : 0.043 0.200 2406 Planarity : 0.005 0.076 2692 Dihedral : 14.753 89.395 2496 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.13 % Allowed : 0.81 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.20), residues: 1837 helix: 1.84 (0.19), residues: 778 sheet: 0.24 (0.34), residues: 239 loop : -0.46 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 823 TYR 0.029 0.002 TYR A 233 PHE 0.021 0.002 PHE B 254 TRP 0.025 0.002 TRP A 572 HIS 0.011 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (16209) covalent geometry : angle 0.57923 / 0.31 (22166) hydrogen bonds : bond 0.03979 / 2.73 ( 767) hydrogen bonds : angle 4.72481 / 3.34 ( 2137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8469 (mm) cc_final: 0.8200 (mm) REVERT: A 79 LEU cc_start: 0.8061 (mt) cc_final: 0.7835 (mp) REVERT: A 152 GLU cc_start: 0.7803 (pp20) cc_final: 0.7135 (pp20) REVERT: A 159 GLN cc_start: 0.7119 (tm-30) cc_final: 0.6586 (pp30) REVERT: A 189 ILE cc_start: 0.7690 (pt) cc_final: 0.7481 (pt) REVERT: A 191 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 193 ARG cc_start: 0.7390 (ttm170) cc_final: 0.7127 (ttm-80) REVERT: A 197 PHE cc_start: 0.7468 (t80) cc_final: 0.6968 (t80) REVERT: A 264 GLN cc_start: 0.7538 (pm20) cc_final: 0.7312 (pm20) REVERT: A 295 MET cc_start: 0.7676 (ttm) cc_final: 0.6898 (ttm) REVERT: A 299 MET cc_start: 0.7246 (mmm) cc_final: 0.6851 (tpt) REVERT: A 308 GLN cc_start: 0.7806 (mt0) cc_final: 0.7299 (mt0) REVERT: A 354 ASN cc_start: 0.7377 (m-40) cc_final: 0.6780 (m-40) REVERT: A 355 SER cc_start: 0.7495 (t) cc_final: 0.7239 (t) REVERT: A 358 GLU cc_start: 0.7722 (mp0) cc_final: 0.7403 (mp0) REVERT: A 393 MET cc_start: 0.7247 (ttm) cc_final: 0.6934 (ttm) REVERT: A 405 GLU cc_start: 0.7624 (pp20) cc_final: 0.7370 (pp20) REVERT: A 439 GLN cc_start: 0.8236 (pm20) cc_final: 0.8033 (pm20) REVERT: A 443 ARG cc_start: 0.6842 (ttt-90) cc_final: 0.6408 (ttt-90) REVERT: A 487 ASP cc_start: 0.8323 (m-30) cc_final: 0.8061 (m-30) REVERT: A 565 HIS cc_start: 0.7688 (t-90) cc_final: 0.7154 (t-170) REVERT: A 566 LEU cc_start: 0.8901 (mt) cc_final: 0.8645 (mm) REVERT: A 607 TRP cc_start: 0.8320 (t-100) cc_final: 0.7728 (t60) REVERT: A 608 ASP cc_start: 0.7889 (t0) cc_final: 0.7332 (t0) REVERT: A 610 PHE cc_start: 0.7938 (m-80) cc_final: 0.7546 (m-80) REVERT: A 750 PHE cc_start: 0.7163 (m-80) cc_final: 0.6618 (m-80) REVERT: A 758 ASN cc_start: 0.7938 (m-40) cc_final: 0.7426 (t0) REVERT: A 774 MET cc_start: 0.7380 (tpt) cc_final: 0.6908 (tpt) REVERT: A 812 MET cc_start: 0.7456 (mpp) cc_final: 0.7129 (mpp) REVERT: A 816 LEU cc_start: 0.8457 (tp) cc_final: 0.8113 (tp) REVERT: A 821 LEU cc_start: 0.8295 (mt) cc_final: 0.8088 (mt) REVERT: A 832 ASP cc_start: 0.8073 (t0) cc_final: 0.7379 (t0) REVERT: A 853 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7697 (mtp85) REVERT: A 873 GLU cc_start: 0.7701 (pm20) cc_final: 0.7387 (pm20) REVERT: A 893 SER cc_start: 0.7223 (t) cc_final: 0.6522 (p) REVERT: A 906 HIS cc_start: 0.8219 (t70) cc_final: 0.8016 (t-170) REVERT: A 919 MET cc_start: 0.7575 (mtt) cc_final: 0.7211 (mmp) REVERT: A 922 GLN cc_start: 0.7335 (tt0) cc_final: 0.6543 (tp-100) REVERT: A 934 LYS cc_start: 0.8267 (mmpt) cc_final: 0.7996 (mmtt) REVERT: A 981 LYS cc_start: 0.8234 (tttt) cc_final: 0.7673 (tppt) REVERT: A 1057 MET cc_start: 0.7803 (ppp) cc_final: 0.7578 (ppp) REVERT: A 1060 LYS cc_start: 0.8154 (tptp) cc_final: 0.7759 (tptp) REVERT: A 1062 GLU cc_start: 0.7853 (pt0) cc_final: 0.7597 (mt-10) REVERT: A 1084 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 1112 MET cc_start: 0.8405 (mtm) cc_final: 0.8074 (mtp) REVERT: A 1126 ASP cc_start: 0.6364 (m-30) cc_final: 0.6113 (m-30) REVERT: A 1207 GLU cc_start: 0.7297 (pm20) cc_final: 0.7018 (pm20) REVERT: A 1219 ASP cc_start: 0.7972 (t70) cc_final: 0.7486 (t0) REVERT: A 1222 GLN cc_start: 0.8530 (mp10) cc_final: 0.7936 (mp10) REVERT: B 77 HIS cc_start: 0.6859 (m-70) cc_final: 0.6603 (m170) REVERT: B 85 GLN cc_start: 0.7472 (mt0) cc_final: 0.6971 (mt0) REVERT: B 88 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.7726 (ptp90) REVERT: B 108 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7845 (ttmm) REVERT: B 113 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6751 (mm-30) REVERT: B 123 GLU cc_start: 0.7523 (pt0) cc_final: 0.7159 (pt0) REVERT: B 134 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8013 (mtmt) REVERT: B 180 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7576 (ptmt) REVERT: B 183 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7018 (mt-10) REVERT: B 191 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7172 (mt-10) REVERT: B 192 HIS cc_start: 0.8161 (m90) cc_final: 0.7751 (m-70) REVERT: B 201 ASN cc_start: 0.7766 (m110) cc_final: 0.7454 (m110) REVERT: B 210 GLN cc_start: 0.7638 (tt0) cc_final: 0.7307 (tt0) REVERT: B 246 ARG cc_start: 0.7598 (ptt180) cc_final: 0.7281 (ptp90) REVERT: B 257 ARG cc_start: 0.7644 (ttm110) cc_final: 0.7413 (mtp85) REVERT: B 288 LYS cc_start: 0.7150 (mttt) cc_final: 0.6430 (mtpt) REVERT: B 289 LEU cc_start: 0.7866 (mt) cc_final: 0.7517 (mt) REVERT: B 304 TRP cc_start: 0.7799 (m100) cc_final: 0.7389 (m100) REVERT: B 310 GLU cc_start: 0.7584 (mp0) cc_final: 0.7359 (mp0) REVERT: B 315 TYR cc_start: 0.7882 (m-80) cc_final: 0.7609 (m-80) REVERT: B 339 ASN cc_start: 0.7090 (t0) cc_final: 0.6363 (t0) REVERT: B 352 ASP cc_start: 0.7238 (t0) cc_final: 0.6909 (t0) REVERT: B 353 SER cc_start: 0.8133 (p) cc_final: 0.7919 (p) REVERT: B 396 ARG cc_start: 0.7565 (ttm170) cc_final: 0.7111 (ttm110) REVERT: B 400 GLN cc_start: 0.7706 (tt0) cc_final: 0.7489 (tp40) REVERT: B 412 SER cc_start: 0.8284 (t) cc_final: 0.7761 (p) REVERT: B 427 GLN cc_start: 0.8260 (pt0) cc_final: 0.7519 (pm20) REVERT: B 431 LYS cc_start: 0.8328 (tttt) cc_final: 0.7918 (tppt) REVERT: B 435 MET cc_start: 0.7107 (mtp) cc_final: 0.6862 (mtp) REVERT: B 439 PHE cc_start: 0.8099 (m-80) cc_final: 0.7897 (m-80) REVERT: B 457 SER cc_start: 0.7906 (t) cc_final: 0.7547 (p) REVERT: B 460 THR cc_start: 0.8519 (p) cc_final: 0.8142 (p) REVERT: B 461 THR cc_start: 0.8193 (p) cc_final: 0.7921 (t) REVERT: B 462 MET cc_start: 0.7777 (mmt) cc_final: 0.7523 (mmt) REVERT: B 465 MET cc_start: 0.7513 (mtm) cc_final: 0.7047 (mtm) REVERT: B 466 MET cc_start: 0.7295 (mtp) cc_final: 0.7004 (ttp) REVERT: B 467 HIS cc_start: 0.8102 (t-90) cc_final: 0.7902 (t70) REVERT: C 67 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7829 (mm-30) REVERT: C 75 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7635 (mtp85) REVERT: C 80 SER cc_start: 0.8473 (t) cc_final: 0.7962 (p) REVERT: C 89 ASP cc_start: 0.7993 (m-30) cc_final: 0.7692 (m-30) REVERT: C 92 LEU cc_start: 0.8630 (mt) cc_final: 0.8369 (mm) REVERT: C 183 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6386 (mt-10) REVERT: C 194 VAL cc_start: 0.7898 (m) cc_final: 0.7529 (p) REVERT: C 216 HIS cc_start: 0.7994 (m90) cc_final: 0.7128 (m-70) REVERT: C 234 LYS cc_start: 0.8094 (mttt) cc_final: 0.7683 (mttt) REVERT: C 242 PHE cc_start: 0.6935 (m-10) cc_final: 0.6615 (m-10) REVERT: C 243 THR cc_start: 0.7862 (t) cc_final: 0.7532 (p) REVERT: C 256 LEU cc_start: 0.8487 (tp) cc_final: 0.8197 (tp) REVERT: C 262 TRP cc_start: 0.7775 (t60) cc_final: 0.7108 (t60) REVERT: C 265 LYS cc_start: 0.8251 (tttt) cc_final: 0.8046 (tttt) REVERT: C 279 GLN cc_start: 0.7299 (tt0) cc_final: 0.6890 (tm-30) REVERT: C 287 ASN cc_start: 0.7176 (t0) cc_final: 0.6844 (t0) REVERT: C 288 LYS cc_start: 0.8290 (mttt) cc_final: 0.7708 (mttt) REVERT: C 291 TYR cc_start: 0.8119 (t80) cc_final: 0.7900 (t80) REVERT: C 301 GLU cc_start: 0.7369 (tt0) cc_final: 0.6915 (tt0) REVERT: C 305 ASN cc_start: 0.7536 (t0) cc_final: 0.7254 (t0) REVERT: C 306 LEU cc_start: 0.8286 (mt) cc_final: 0.7983 (mm) REVERT: C 336 LEU cc_start: 0.8424 (mt) cc_final: 0.8031 (mt) REVERT: C 346 MET cc_start: 0.6935 (tmm) cc_final: 0.6570 (tmm) REVERT: C 354 PHE cc_start: 0.7865 (t80) cc_final: 0.7457 (t80) REVERT: C 372 LEU cc_start: 0.8581 (mt) cc_final: 0.8321 (mt) REVERT: C 382 LYS cc_start: 0.8291 (mttp) cc_final: 0.8090 (mmtp) REVERT: C 396 ARG cc_start: 0.7796 (ttm170) cc_final: 0.6840 (ttm170) REVERT: C 400 GLN cc_start: 0.7882 (mt0) cc_final: 0.6917 (mt0) REVERT: C 404 ASN cc_start: 0.8041 (m-40) cc_final: 0.7455 (m110) REVERT: C 415 PRO cc_start: 0.8680 (Cg_endo) cc_final: 0.8455 (Cg_exo) REVERT: C 426 GLU cc_start: 0.7512 (pp20) cc_final: 0.7250 (pp20) REVERT: C 427 GLN cc_start: 0.8096 (mt0) cc_final: 0.7497 (mt0) REVERT: C 430 SER cc_start: 0.8442 (t) cc_final: 0.7962 (p) REVERT: C 431 LYS cc_start: 0.8372 (tttt) cc_final: 0.8145 (tttt) REVERT: C 434 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 466 MET cc_start: 0.6952 (ttm) cc_final: 0.6665 (ttm) REVERT: C 470 LYS cc_start: 0.8517 (mttt) cc_final: 0.8139 (mttt) REVERT: C 471 LEU cc_start: 0.8055 (tp) cc_final: 0.7822 (tt) REVERT: C 478 TYR cc_start: 0.7976 (t80) cc_final: 0.7701 (t80) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.1356 time to fit residues: 114.0887 Evaluate side-chains 526 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 130 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 129 optimal weight: 0.0670 chunk 170 optimal weight: 0.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 398 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 564 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 305 ASN B 404 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.120994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.094547 restraints weight = 63675.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099975 restraints weight = 26204.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103508 restraints weight = 14021.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105813 restraints weight = 8789.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107511 restraints weight = 6212.135| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16209 Z= 0.124 Angle : 0.578 8.916 22166 Z= 0.305 Chirality : 0.042 0.194 2406 Planarity : 0.005 0.075 2692 Dihedral : 14.732 89.333 2496 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 0.19 % Allowed : 0.50 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1837 helix: 1.84 (0.19), residues: 781 sheet: 0.29 (0.34), residues: 239 loop : -0.43 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 823 TYR 0.025 0.002 TYR C 193 PHE 0.026 0.002 PHE A 949 TRP 0.041 0.002 TRP A 235 HIS 0.012 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (16209) covalent geometry : angle 0.57753 / 0.30 (22166) hydrogen bonds : bond 0.03796 / 2.59 ( 767) hydrogen bonds : angle 4.70791 / 3.31 ( 2137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 565 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8527 (mm) cc_final: 0.8180 (mm) REVERT: A 121 PRO cc_start: 0.7966 (Cg_exo) cc_final: 0.7631 (Cg_endo) REVERT: A 159 GLN cc_start: 0.7103 (tm-30) cc_final: 0.6546 (pp30) REVERT: A 169 TRP cc_start: 0.7903 (m-90) cc_final: 0.7695 (m-90) REVERT: A 193 ARG cc_start: 0.7400 (ttm170) cc_final: 0.7161 (ttm-80) REVERT: A 232 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7626 (mtm110) REVERT: A 264 GLN cc_start: 0.7480 (pm20) cc_final: 0.7204 (pm20) REVERT: A 289 MET cc_start: 0.7164 (ttm) cc_final: 0.6958 (ttm) REVERT: A 295 MET cc_start: 0.7698 (ttm) cc_final: 0.6891 (ttm) REVERT: A 299 MET cc_start: 0.7324 (mmm) cc_final: 0.6894 (tpt) REVERT: A 308 GLN cc_start: 0.7793 (mt0) cc_final: 0.7309 (mt0) REVERT: A 354 ASN cc_start: 0.7346 (m-40) cc_final: 0.6784 (m-40) REVERT: A 355 SER cc_start: 0.7468 (t) cc_final: 0.7219 (t) REVERT: A 393 MET cc_start: 0.7238 (ttm) cc_final: 0.6963 (ttm) REVERT: A 405 GLU cc_start: 0.7635 (pp20) cc_final: 0.7409 (pp20) REVERT: A 410 GLN cc_start: 0.7945 (tt0) cc_final: 0.7708 (tt0) REVERT: A 430 MET cc_start: 0.7703 (tpp) cc_final: 0.7185 (mmm) REVERT: A 443 ARG cc_start: 0.6818 (ttt-90) cc_final: 0.6369 (ttt-90) REVERT: A 445 LEU cc_start: 0.8036 (mp) cc_final: 0.7795 (mm) REVERT: A 458 GLU cc_start: 0.7742 (pp20) cc_final: 0.7339 (tm-30) REVERT: A 487 ASP cc_start: 0.8316 (m-30) cc_final: 0.8072 (m-30) REVERT: A 565 HIS cc_start: 0.7716 (t-90) cc_final: 0.7122 (t-170) REVERT: A 566 LEU cc_start: 0.8907 (mt) cc_final: 0.8670 (mm) REVERT: A 574 ARG cc_start: 0.8309 (ptp90) cc_final: 0.7935 (ptp90) REVERT: A 607 TRP cc_start: 0.8311 (t-100) cc_final: 0.7751 (t60) REVERT: A 608 ASP cc_start: 0.7842 (t0) cc_final: 0.7379 (t0) REVERT: A 610 PHE cc_start: 0.7922 (m-80) cc_final: 0.7542 (m-80) REVERT: A 750 PHE cc_start: 0.7165 (m-80) cc_final: 0.6614 (m-80) REVERT: A 758 ASN cc_start: 0.7942 (m-40) cc_final: 0.7398 (t0) REVERT: A 774 MET cc_start: 0.7385 (tpt) cc_final: 0.7098 (mmm) REVERT: A 812 MET cc_start: 0.7409 (mpp) cc_final: 0.7120 (mpp) REVERT: A 816 LEU cc_start: 0.8457 (tp) cc_final: 0.8086 (tp) REVERT: A 832 ASP cc_start: 0.8061 (t0) cc_final: 0.7438 (t0) REVERT: A 893 SER cc_start: 0.7226 (t) cc_final: 0.6917 (t) REVERT: A 919 MET cc_start: 0.7557 (mtt) cc_final: 0.7207 (mmp) REVERT: A 922 GLN cc_start: 0.7336 (tt0) cc_final: 0.6534 (tp-100) REVERT: A 934 LYS cc_start: 0.8247 (mmpt) cc_final: 0.7963 (mmtt) REVERT: A 981 LYS cc_start: 0.8234 (tttt) cc_final: 0.7689 (tppt) REVERT: A 985 MET cc_start: 0.7452 (ttp) cc_final: 0.7228 (ttp) REVERT: A 1057 MET cc_start: 0.7829 (ppp) cc_final: 0.7623 (ppp) REVERT: A 1060 LYS cc_start: 0.8197 (tptp) cc_final: 0.7799 (tptp) REVERT: A 1062 GLU cc_start: 0.7839 (pt0) cc_final: 0.7536 (mt-10) REVERT: A 1102 GLN cc_start: 0.7399 (mp10) cc_final: 0.6459 (mp10) REVERT: A 1112 MET cc_start: 0.8329 (mtm) cc_final: 0.8104 (mtp) REVERT: A 1126 ASP cc_start: 0.6447 (m-30) cc_final: 0.6159 (m-30) REVERT: A 1219 ASP cc_start: 0.7984 (t70) cc_final: 0.7545 (t0) REVERT: A 1222 GLN cc_start: 0.8534 (mp10) cc_final: 0.7931 (mp10) REVERT: B 71 GLU cc_start: 0.7935 (pp20) cc_final: 0.7672 (tm-30) REVERT: B 85 GLN cc_start: 0.7456 (mt0) cc_final: 0.6972 (mt0) REVERT: B 88 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7702 (ptp90) REVERT: B 108 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7826 (ttmm) REVERT: B 113 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6764 (mm-30) REVERT: B 123 GLU cc_start: 0.7542 (pt0) cc_final: 0.7149 (pt0) REVERT: B 134 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7997 (mtmt) REVERT: B 180 LYS cc_start: 0.8257 (ptmt) cc_final: 0.7541 (ptmt) REVERT: B 183 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 191 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7203 (mt-10) REVERT: B 210 GLN cc_start: 0.7598 (tt0) cc_final: 0.7288 (tt0) REVERT: B 246 ARG cc_start: 0.7607 (ptt180) cc_final: 0.7361 (ptt-90) REVERT: B 257 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7396 (mtp85) REVERT: B 288 LYS cc_start: 0.7130 (mttt) cc_final: 0.6359 (mtpt) REVERT: B 289 LEU cc_start: 0.7853 (mt) cc_final: 0.7466 (mt) REVERT: B 304 TRP cc_start: 0.7763 (m100) cc_final: 0.7484 (m100) REVERT: B 310 GLU cc_start: 0.7600 (mp0) cc_final: 0.7372 (mp0) REVERT: B 315 TYR cc_start: 0.7891 (m-80) cc_final: 0.7638 (m-80) REVERT: B 352 ASP cc_start: 0.7193 (t0) cc_final: 0.6897 (t0) REVERT: B 353 SER cc_start: 0.8105 (p) cc_final: 0.7891 (p) REVERT: B 396 ARG cc_start: 0.7485 (ttm170) cc_final: 0.7064 (ttm110) REVERT: B 412 SER cc_start: 0.8263 (t) cc_final: 0.7735 (p) REVERT: B 427 GLN cc_start: 0.8254 (pt0) cc_final: 0.7541 (pm20) REVERT: B 431 LYS cc_start: 0.8299 (tttt) cc_final: 0.7896 (tppt) REVERT: B 439 PHE cc_start: 0.8097 (m-80) cc_final: 0.7873 (m-80) REVERT: B 457 SER cc_start: 0.7916 (t) cc_final: 0.7524 (p) REVERT: B 460 THR cc_start: 0.8508 (p) cc_final: 0.8170 (p) REVERT: B 461 THR cc_start: 0.8206 (p) cc_final: 0.7958 (t) REVERT: B 462 MET cc_start: 0.7744 (mmt) cc_final: 0.7499 (mmt) REVERT: B 465 MET cc_start: 0.7501 (mtm) cc_final: 0.6997 (mtm) REVERT: B 466 MET cc_start: 0.7242 (mtp) cc_final: 0.6951 (ttp) REVERT: C 75 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7589 (mtp85) REVERT: C 80 SER cc_start: 0.8463 (t) cc_final: 0.8126 (m) REVERT: C 89 ASP cc_start: 0.7978 (m-30) cc_final: 0.7660 (m-30) REVERT: C 92 LEU cc_start: 0.8644 (mt) cc_final: 0.8352 (mm) REVERT: C 180 LYS cc_start: 0.7892 (pttt) cc_final: 0.7674 (ptmt) REVERT: C 183 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6399 (mt-10) REVERT: C 185 LEU cc_start: 0.8987 (mt) cc_final: 0.8667 (mt) REVERT: C 194 VAL cc_start: 0.7839 (m) cc_final: 0.7489 (p) REVERT: C 216 HIS cc_start: 0.7986 (m90) cc_final: 0.7140 (m-70) REVERT: C 234 LYS cc_start: 0.8183 (mttt) cc_final: 0.7631 (mttt) REVERT: C 235 THR cc_start: 0.7802 (t) cc_final: 0.7023 (p) REVERT: C 242 PHE cc_start: 0.6953 (m-10) cc_final: 0.6636 (m-10) REVERT: C 243 THR cc_start: 0.7842 (t) cc_final: 0.7507 (p) REVERT: C 256 LEU cc_start: 0.8481 (tp) cc_final: 0.8179 (tp) REVERT: C 259 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7259 (mtp85) REVERT: C 262 TRP cc_start: 0.7718 (t60) cc_final: 0.7179 (t60) REVERT: C 265 LYS cc_start: 0.8260 (tttt) cc_final: 0.8054 (tttt) REVERT: C 279 GLN cc_start: 0.7258 (tt0) cc_final: 0.6840 (tm-30) REVERT: C 287 ASN cc_start: 0.7152 (t0) cc_final: 0.6813 (t0) REVERT: C 288 LYS cc_start: 0.8278 (mttt) cc_final: 0.7709 (mttt) REVERT: C 301 GLU cc_start: 0.7390 (tt0) cc_final: 0.6651 (tt0) REVERT: C 305 ASN cc_start: 0.7542 (t0) cc_final: 0.7279 (t0) REVERT: C 306 LEU cc_start: 0.8324 (mt) cc_final: 0.7981 (mm) REVERT: C 336 LEU cc_start: 0.8410 (mt) cc_final: 0.7997 (mt) REVERT: C 346 MET cc_start: 0.6911 (tmm) cc_final: 0.6548 (tmm) REVERT: C 354 PHE cc_start: 0.7842 (t80) cc_final: 0.7420 (t80) REVERT: C 382 LYS cc_start: 0.8260 (mttp) cc_final: 0.8055 (mmtp) REVERT: C 396 ARG cc_start: 0.7814 (ttm170) cc_final: 0.6789 (ttm170) REVERT: C 400 GLN cc_start: 0.7885 (mt0) cc_final: 0.6893 (mt0) REVERT: C 404 ASN cc_start: 0.8077 (m-40) cc_final: 0.7459 (m110) REVERT: C 415 PRO cc_start: 0.8670 (Cg_endo) cc_final: 0.8468 (Cg_exo) REVERT: C 426 GLU cc_start: 0.7494 (pp20) cc_final: 0.7266 (pp20) REVERT: C 427 GLN cc_start: 0.8068 (mt0) cc_final: 0.7510 (mt0) REVERT: C 430 SER cc_start: 0.8415 (t) cc_final: 0.7928 (p) REVERT: C 434 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7570 (mt-10) REVERT: C 466 MET cc_start: 0.6950 (ttm) cc_final: 0.6707 (ttm) REVERT: C 470 LYS cc_start: 0.8492 (mttt) cc_final: 0.8107 (mttt) REVERT: C 478 TYR cc_start: 0.7975 (t80) cc_final: 0.7732 (t80) outliers start: 1 outliers final: 0 residues processed: 565 average time/residue: 0.1424 time to fit residues: 115.4491 Evaluate side-chains 522 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 34 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 111 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 169 optimal weight: 0.4980 chunk 128 optimal weight: 0.7980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 564 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 132 HIS B 192 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 261 GLN B 404 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.094268 restraints weight = 74148.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099917 restraints weight = 28667.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103677 restraints weight = 15001.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106154 restraints weight = 9239.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107802 restraints weight = 6434.256| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16209 Z= 0.116 Angle : 0.582 13.048 22166 Z= 0.302 Chirality : 0.042 0.183 2406 Planarity : 0.005 0.065 2692 Dihedral : 14.667 89.275 2496 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 0.13 % Allowed : 0.56 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1837 helix: 1.87 (0.19), residues: 784 sheet: 0.21 (0.33), residues: 241 loop : -0.38 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 823 TYR 0.023 0.002 TYR B 315 PHE 0.023 0.002 PHE B 254 TRP 0.052 0.002 TRP A 235 HIS 0.009 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (16209) covalent geometry : angle 0.58180 / 0.30 (22166) hydrogen bonds : bond 0.03615 / 2.45 ( 767) hydrogen bonds : angle 4.61883 / 3.26 ( 2137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8550 (mm) cc_final: 0.8268 (mm) REVERT: A 121 PRO cc_start: 0.8000 (Cg_exo) cc_final: 0.7694 (Cg_endo) REVERT: A 159 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6526 (pp30) REVERT: A 193 ARG cc_start: 0.7410 (ttm170) cc_final: 0.7175 (ttm-80) REVERT: A 213 VAL cc_start: 0.7511 (m) cc_final: 0.7164 (p) REVERT: A 264 GLN cc_start: 0.7503 (pm20) cc_final: 0.7225 (pm20) REVERT: A 295 MET cc_start: 0.7656 (ttm) cc_final: 0.6819 (ttm) REVERT: A 297 MET cc_start: 0.7621 (mtt) cc_final: 0.7399 (mtp) REVERT: A 299 MET cc_start: 0.7266 (mmm) cc_final: 0.6902 (tpt) REVERT: A 354 ASN cc_start: 0.7252 (m-40) cc_final: 0.6801 (m-40) REVERT: A 393 MET cc_start: 0.7283 (ttm) cc_final: 0.6971 (ttm) REVERT: A 410 GLN cc_start: 0.7885 (tt0) cc_final: 0.7369 (tt0) REVERT: A 427 MET cc_start: 0.7613 (ttm) cc_final: 0.7325 (mtp) REVERT: A 430 MET cc_start: 0.7620 (tpp) cc_final: 0.7198 (mmm) REVERT: A 443 ARG cc_start: 0.6746 (ttt-90) cc_final: 0.6321 (ttt-90) REVERT: A 445 LEU cc_start: 0.8035 (mp) cc_final: 0.7793 (mm) REVERT: A 458 GLU cc_start: 0.7813 (pp20) cc_final: 0.7509 (tm-30) REVERT: A 487 ASP cc_start: 0.8321 (m-30) cc_final: 0.8067 (m-30) REVERT: A 565 HIS cc_start: 0.7704 (t-90) cc_final: 0.7125 (t-170) REVERT: A 566 LEU cc_start: 0.8921 (mt) cc_final: 0.8714 (mm) REVERT: A 574 ARG cc_start: 0.8320 (ptp90) cc_final: 0.7920 (ptp90) REVERT: A 607 TRP cc_start: 0.8299 (t-100) cc_final: 0.7736 (t60) REVERT: A 608 ASP cc_start: 0.7797 (t0) cc_final: 0.7422 (t0) REVERT: A 610 PHE cc_start: 0.7887 (m-80) cc_final: 0.7522 (m-80) REVERT: A 750 PHE cc_start: 0.7146 (m-80) cc_final: 0.6621 (m-80) REVERT: A 758 ASN cc_start: 0.7942 (m-40) cc_final: 0.7396 (t0) REVERT: A 774 MET cc_start: 0.7366 (tpt) cc_final: 0.7116 (mmm) REVERT: A 812 MET cc_start: 0.7390 (mpp) cc_final: 0.7154 (mpp) REVERT: A 816 LEU cc_start: 0.8472 (tp) cc_final: 0.8106 (tp) REVERT: A 832 ASP cc_start: 0.8063 (t0) cc_final: 0.7390 (t0) REVERT: A 870 VAL cc_start: 0.8290 (m) cc_final: 0.8056 (p) REVERT: A 877 MET cc_start: 0.7080 (mmp) cc_final: 0.6777 (tpp) REVERT: A 893 SER cc_start: 0.7135 (t) cc_final: 0.6816 (t) REVERT: A 919 MET cc_start: 0.7547 (mtt) cc_final: 0.7173 (mmp) REVERT: A 922 GLN cc_start: 0.7296 (tt0) cc_final: 0.6860 (tp40) REVERT: A 934 LYS cc_start: 0.8217 (mmpt) cc_final: 0.7941 (mmtt) REVERT: A 981 LYS cc_start: 0.8218 (tttt) cc_final: 0.7637 (tppt) REVERT: A 1060 LYS cc_start: 0.8221 (tptp) cc_final: 0.7767 (tptp) REVERT: A 1112 MET cc_start: 0.8265 (mtm) cc_final: 0.8040 (mtp) REVERT: A 1126 ASP cc_start: 0.6466 (m-30) cc_final: 0.6148 (m-30) REVERT: A 1219 ASP cc_start: 0.7948 (t70) cc_final: 0.7406 (t70) REVERT: A 1222 GLN cc_start: 0.8506 (mp10) cc_final: 0.7687 (mp10) REVERT: B 71 GLU cc_start: 0.7940 (pp20) cc_final: 0.7669 (tm-30) REVERT: B 85 GLN cc_start: 0.7442 (mt0) cc_final: 0.6992 (mt0) REVERT: B 88 ARG cc_start: 0.7946 (ptp-170) cc_final: 0.7710 (ptp90) REVERT: B 108 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7810 (ttmm) REVERT: B 113 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 123 GLU cc_start: 0.7552 (pt0) cc_final: 0.7137 (pt0) REVERT: B 134 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8016 (mtmt) REVERT: B 180 LYS cc_start: 0.8275 (ptmt) cc_final: 0.7555 (ptmt) REVERT: B 183 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 191 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 192 HIS cc_start: 0.8176 (m90) cc_final: 0.7678 (m-70) REVERT: B 210 GLN cc_start: 0.7568 (tt0) cc_final: 0.7272 (tt0) REVERT: B 246 ARG cc_start: 0.7621 (ptt180) cc_final: 0.7323 (ptp90) REVERT: B 257 ARG cc_start: 0.7647 (ttm110) cc_final: 0.7341 (mtp85) REVERT: B 288 LYS cc_start: 0.7134 (mttt) cc_final: 0.6463 (mtmt) REVERT: B 289 LEU cc_start: 0.7818 (mt) cc_final: 0.7451 (mt) REVERT: B 304 TRP cc_start: 0.7759 (m100) cc_final: 0.7482 (m100) REVERT: B 310 GLU cc_start: 0.7593 (mp0) cc_final: 0.7348 (mp0) REVERT: B 315 TYR cc_start: 0.7882 (m-80) cc_final: 0.7633 (m-80) REVERT: B 352 ASP cc_start: 0.7162 (t0) cc_final: 0.6874 (t0) REVERT: B 353 SER cc_start: 0.8083 (p) cc_final: 0.7881 (p) REVERT: B 396 ARG cc_start: 0.7397 (ttm170) cc_final: 0.7017 (ttm110) REVERT: B 412 SER cc_start: 0.8275 (t) cc_final: 0.7723 (p) REVERT: B 427 GLN cc_start: 0.8116 (pt0) cc_final: 0.7519 (pm20) REVERT: B 431 LYS cc_start: 0.8344 (tttt) cc_final: 0.7840 (tppt) REVERT: B 439 PHE cc_start: 0.8076 (m-80) cc_final: 0.7850 (m-80) REVERT: B 457 SER cc_start: 0.7892 (t) cc_final: 0.7571 (p) REVERT: B 460 THR cc_start: 0.8547 (p) cc_final: 0.8204 (p) REVERT: B 461 THR cc_start: 0.8197 (p) cc_final: 0.7962 (t) REVERT: B 462 MET cc_start: 0.7725 (mmt) cc_final: 0.7478 (mmt) REVERT: B 465 MET cc_start: 0.7455 (mtm) cc_final: 0.6954 (mpp) REVERT: B 466 MET cc_start: 0.7182 (mtp) cc_final: 0.6894 (ttp) REVERT: C 80 SER cc_start: 0.8488 (t) cc_final: 0.8044 (p) REVERT: C 92 LEU cc_start: 0.8626 (mt) cc_final: 0.8388 (mm) REVERT: C 180 LYS cc_start: 0.7825 (pttt) cc_final: 0.7612 (ptmt) REVERT: C 183 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6366 (mt-10) REVERT: C 185 LEU cc_start: 0.8986 (mt) cc_final: 0.8640 (mt) REVERT: C 194 VAL cc_start: 0.7849 (m) cc_final: 0.7459 (p) REVERT: C 216 HIS cc_start: 0.7908 (m90) cc_final: 0.7081 (m-70) REVERT: C 234 LYS cc_start: 0.8184 (mttt) cc_final: 0.7725 (mttt) REVERT: C 242 PHE cc_start: 0.6922 (m-10) cc_final: 0.6592 (m-10) REVERT: C 243 THR cc_start: 0.7831 (t) cc_final: 0.7488 (p) REVERT: C 256 LEU cc_start: 0.8485 (tp) cc_final: 0.8179 (tp) REVERT: C 259 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7250 (mtp85) REVERT: C 262 TRP cc_start: 0.7656 (t60) cc_final: 0.7144 (t60) REVERT: C 279 GLN cc_start: 0.7199 (tt0) cc_final: 0.6809 (tm-30) REVERT: C 287 ASN cc_start: 0.7158 (t0) cc_final: 0.6818 (t0) REVERT: C 288 LYS cc_start: 0.8306 (mttt) cc_final: 0.7746 (mttt) REVERT: C 301 GLU cc_start: 0.7373 (tt0) cc_final: 0.6629 (tt0) REVERT: C 305 ASN cc_start: 0.7558 (t0) cc_final: 0.7301 (t0) REVERT: C 306 LEU cc_start: 0.8311 (mt) cc_final: 0.7960 (mm) REVERT: C 323 HIS cc_start: 0.6356 (m170) cc_final: 0.6150 (m170) REVERT: C 336 LEU cc_start: 0.8454 (mt) cc_final: 0.8028 (mt) REVERT: C 346 MET cc_start: 0.6801 (tmm) cc_final: 0.6588 (tmm) REVERT: C 354 PHE cc_start: 0.7877 (t80) cc_final: 0.7458 (t80) REVERT: C 382 LYS cc_start: 0.8247 (mttp) cc_final: 0.8038 (mmtp) REVERT: C 396 ARG cc_start: 0.7769 (ttm170) cc_final: 0.6789 (ttm170) REVERT: C 400 GLN cc_start: 0.7861 (mt0) cc_final: 0.6872 (mt0) REVERT: C 404 ASN cc_start: 0.8049 (m-40) cc_final: 0.7430 (m110) REVERT: C 415 PRO cc_start: 0.8687 (Cg_endo) cc_final: 0.8459 (Cg_exo) REVERT: C 426 GLU cc_start: 0.7499 (pp20) cc_final: 0.7260 (pp20) REVERT: C 427 GLN cc_start: 0.8091 (mt0) cc_final: 0.7533 (mt0) REVERT: C 430 SER cc_start: 0.8412 (t) cc_final: 0.7922 (p) REVERT: C 434 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7521 (mt-10) REVERT: C 466 MET cc_start: 0.6954 (ttm) cc_final: 0.6723 (ttm) REVERT: C 470 LYS cc_start: 0.8471 (mttt) cc_final: 0.8068 (mttt) REVERT: C 478 TYR cc_start: 0.7971 (t80) cc_final: 0.7723 (t80) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.1439 time to fit residues: 115.4754 Evaluate side-chains 520 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 107 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 156 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 HIS A 398 GLN A 410 GLN A 468 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN B 261 GLN B 305 ASN B 400 GLN B 404 ASN B 409 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091560 restraints weight = 75143.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097183 restraints weight = 29092.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100864 restraints weight = 15267.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103330 restraints weight = 9481.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104965 restraints weight = 6620.467| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16209 Z= 0.205 Angle : 0.622 11.153 22166 Z= 0.329 Chirality : 0.044 0.187 2406 Planarity : 0.005 0.064 2692 Dihedral : 14.775 89.895 2496 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1837 helix: 1.73 (0.18), residues: 784 sheet: 0.15 (0.33), residues: 241 loop : -0.51 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 823 TYR 0.023 0.002 TYR B 315 PHE 0.025 0.002 PHE B 254 TRP 0.036 0.002 TRP A 235 HIS 0.008 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.21 (16209) covalent geometry : angle 0.62244 / 0.33 (22166) hydrogen bonds : bond 0.04285 / 2.97 ( 767) hydrogen bonds : angle 4.80857 / 3.43 ( 2137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.99 seconds wall clock time: 56 minutes 7.87 seconds (3367.87 seconds total)