Starting phenix.real_space_refine on Sun Aug 24 00:25:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v54_42979/08_2025/8v54_42979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v54_42979/08_2025/8v54_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_2025/8v54_42979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v54_42979/08_2025/8v54_42979.map" model { file = "/net/cci-nas-00/data/ceres_data/8v54_42979/08_2025/8v54_42979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v54_42979/08_2025/8v54_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.19, 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: 1.11 Conformation dependent library (CDL) restraints added in 720.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.70 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: 2.51 Time building geometry restraints manager: 1.51 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=" C1' DC P 27 " pdb=" N1 DC P 27 " ideal model delta sigma weight residual 1.490 1.448 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CA PRO A 783 " pdb=" CB PRO A 783 " ideal model delta sigma weight residual 1.531 1.523 0.008 6.20e-03 2.60e+04 1.61e+00 bond pdb=" C4' DT T 8 " pdb=" O4' DT T 8 " ideal model delta sigma weight residual 1.450 1.430 0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" C4' DG T 3 " pdb=" O4' DG T 3 " ideal model delta sigma weight residual 1.450 1.430 0.020 2.00e-02 2.50e+03 9.92e-01 bond pdb=" CA GLY A 784 " pdb=" C GLY A 784 " ideal model delta sigma weight residual 1.512 1.523 -0.011 1.15e-02 7.56e+03 9.90e-01 ... (remaining 16204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 21743 1.39 - 2.77: 343 2.77 - 4.16: 66 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=" CA TRP A 859 " pdb=" CB TRP A 859 " pdb=" CG TRP A 859 " ideal model delta sigma weight residual 113.60 109.35 4.25 1.90e+00 2.77e-01 5.00e+00 angle pdb=" CA LEU C 312 " pdb=" CB LEU C 312 " pdb=" CG LEU C 312 " ideal model delta sigma weight residual 116.30 123.18 -6.88 3.50e+00 8.16e-02 3.86e+00 angle pdb=" C3' DC T 6 " pdb=" C2' DC T 6 " pdb=" C1' DC T 6 " ideal model delta sigma weight residual 101.60 104.40 -2.80 1.50e+00 4.44e-01 3.49e+00 angle pdb=" C GLU A 557 " pdb=" N LEU A 558 " pdb=" CA LEU A 558 " ideal model delta sigma weight residual 122.84 126.20 -3.36 1.81e+00 3.05e-01 3.44e+00 ... (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: 1970 0.049 - 0.099: 361 0.099 - 0.148: 74 0.148 - 0.197: 0 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=" 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 chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-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: 1.990 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.900 Find NCS groups from input model: 0.150 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16209 Z= 0.167 Angle : 0.475 6.926 22166 Z= 0.263 Chirality : 0.039 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 aren 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 covalent geometry : bond 0.00333 (16209) covalent geometry : angle 0.47523 (22166) hydrogen bonds : bond 0.18405 ( 767) hydrogen bonds : angle 6.77645 ( 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 : 0.401 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: 0.7540 (p0) REVERT: A 76 ILE cc_start: 0.8480 (mm) cc_final: 0.8040 (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: 0.7761 (tptp) REVERT: A 159 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6827 (pp30) REVERT: A 193 ARG cc_start: 0.7768 (ttt180) cc_final: 0.7417 (tpp80) REVERT: A 234 SER cc_start: 0.7462 (p) cc_final: 0.7093 (m) REVERT: A 264 GLN cc_start: 0.8109 (pt0) cc_final: 0.7444 (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: 0.7760 (pt0) REVERT: A 443 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6640 (ttt-90) REVERT: A 447 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 457 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7579 (ttp-170) REVERT: A 459 MET cc_start: 0.7138 (tpp) cc_final: 0.6875 (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: 0.7587 (m100) REVERT: A 566 LEU cc_start: 0.8884 (mt) cc_final: 0.8670 (mm) REVERT: A 579 ARG cc_start: 0.6395 (mtt180) cc_final: 0.5889 (mtt180) REVERT: A 593 SER cc_start: 0.8180 (m) cc_final: 0.7933 (p) REVERT: A 607 TRP cc_start: 0.8168 (t-100) cc_final: 0.7854 (t-100) REVERT: A 755 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8280 (mmtt) REVERT: A 758 ASN cc_start: 0.8006 (m-40) cc_final: 0.7548 (t0) REVERT: A 769 ASP cc_start: 0.7989 (p0) cc_final: 0.7478 (p0) REVERT: A 772 PRO cc_start: 0.8905 (Cg_exo) cc_final: 0.8237 (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: 0.8248 (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: 0.7277 (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: 0.7390 (t0) REVERT: A 893 SER cc_start: 0.7045 (t) cc_final: 0.6489 (p) REVERT: A 916 PHE cc_start: 0.7696 (t80) cc_final: 0.7082 (t80) REVERT: A 920 THR cc_start: 0.7677 (m) cc_final: 0.7466 (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: 0.8150 (mmpt) REVERT: A 981 LYS cc_start: 0.8262 (tttt) cc_final: 0.7818 (tptt) REVERT: A 985 MET cc_start: 0.7327 (ttp) cc_final: 0.6932 (ttp) REVERT: A 1057 MET cc_start: 0.7831 (ppp) cc_final: 0.7488 (ppp) REVERT: A 1060 LYS cc_start: 0.8049 (tptp) cc_final: 0.7598 (tptp) REVERT: A 1062 GLU cc_start: 0.7997 (pt0) cc_final: 0.7594 (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 1110 HIS cc_start: 0.8477 (m-70) cc_final: 0.8277 (m-70) 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: 0.7973 (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: 0.6294 (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: 0.6195 (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: 0.7092 (ttm) REVERT: A 1202 ASN cc_start: 0.7687 (m-40) cc_final: 0.6732 (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: 0.7579 (t0) REVERT: A 1222 GLN cc_start: 0.8552 (mp10) cc_final: 0.8033 (mp10) REVERT: B 71 GLU cc_start: 0.7981 (tt0) cc_final: 0.7781 (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: 0.6963 (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: 0.8081 (mtmt) REVERT: B 180 LYS cc_start: 0.8312 (ptmt) cc_final: 0.7650 (ptmt) REVERT: B 183 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6786 (mt-10) REVERT: B 191 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7404 (mt-10) REVERT: B 192 HIS cc_start: 0.7908 (m90) cc_final: 0.7517 (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: 0.7524 (p) REVERT: B 288 LYS cc_start: 0.7379 (mttt) cc_final: 0.6882 (mtpt) REVERT: B 291 TYR cc_start: 0.7454 (t80) cc_final: 0.7250 (t80) REVERT: B 292 ASN cc_start: 0.7980 (t0) cc_final: 0.7775 (t0) REVERT: B 310 GLU cc_start: 0.7555 (mp0) cc_final: 0.7240 (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: 0.7182 (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: 0.8138 (p) REVERT: B 426 GLU cc_start: 0.7950 (pp20) cc_final: 0.7427 (tm-30) REVERT: B 431 LYS cc_start: 0.8553 (tttt) cc_final: 0.8162 (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: 0.7624 (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: 0.5966 (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: 0.8152 (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: 0.7608 (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: 0.7401 (m-70) REVERT: C 234 LYS cc_start: 0.7994 (mttt) cc_final: 0.7765 (mttt) REVERT: C 256 LEU cc_start: 0.8493 (tp) cc_final: 0.8205 (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: 0.7610 (t60) REVERT: C 280 ASP cc_start: 0.6503 (p0) cc_final: 0.6058 (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: 0.7719 (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: 0.6713 (tt0) REVERT: C 305 ASN cc_start: 0.7749 (t0) cc_final: 0.7524 (t0) REVERT: C 306 LEU cc_start: 0.8778 (mt) cc_final: 0.8324 (mm) REVERT: C 328 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7678 (mtt180) REVERT: C 336 LEU cc_start: 0.8469 (mt) cc_final: 0.8030 (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: 0.8271 (m) REVERT: C 372 LEU cc_start: 0.8617 (mt) cc_final: 0.8341 (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: 0.6499 (mtt) REVERT: C 426 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7869 (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: 0.7515 (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: 0.1272 time to fit residues: 112.2129 Evaluate side-chains 565 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 559 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 410 GLN A 497 GLN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091518 restraints weight = 61881.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096683 restraints weight = 26556.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100163 restraints weight = 14719.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102558 restraints weight = 9401.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104148 restraints weight = 6659.212| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 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 = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 16209 Z= 0.343 Angle : 0.680 12.678 22166 Z= 0.369 Chirality : 0.048 0.208 2406 Planarity : 0.005 0.057 2692 Dihedral : 15.023 88.075 2496 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.13 % Allowed : 1.88 % Favored : 98.00 % 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 aren not related in a simple way. whole: 0.38 (0.19), residues: 1837 helix: 1.25 (0.18), residues: 786 sheet: -0.10 (0.32), residues: 241 loop : -0.57 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1128 TYR 0.042 0.003 TYR B 315 PHE 0.023 0.002 PHE B 403 TRP 0.038 0.003 TRP A 486 HIS 0.016 0.002 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00685 (16209) covalent geometry : angle 0.67990 (22166) hydrogen bonds : bond 0.05803 ( 767) hydrogen bonds : angle 5.68341 ( 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 579 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 0.522 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: 0.8462 (mm) cc_final: 0.8151 (mm) REVERT: A 79 LEU cc_start: 0.8103 (mt) cc_final: 0.7810 (mp) REVERT: A 145 LYS cc_start: 0.8221 (tptp) cc_final: 0.7800 (tptp) REVERT: A 159 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6690 (pp30) REVERT: A 264 GLN cc_start: 0.7894 (pt0) cc_final: 0.7614 (pm20) REVERT: A 280 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 289 MET cc_start: 0.7446 (ttm) cc_final: 0.6580 (ttm) REVERT: A 295 MET cc_start: 0.7310 (ttt) cc_final: 0.6876 (ttp) REVERT: A 354 ASN cc_start: 0.7730 (m-40) cc_final: 0.7283 (m-40) REVERT: A 358 GLU cc_start: 0.7617 (mp0) cc_final: 0.7397 (mp0) REVERT: A 375 GLU cc_start: 0.7439 (pt0) cc_final: 0.7068 (pt0) REVERT: A 393 MET cc_start: 0.7128 (ttm) cc_final: 0.6764 (ttm) REVERT: A 405 GLU cc_start: 0.7609 (tp30) cc_final: 0.7080 (tm-30) REVERT: A 439 GLN cc_start: 0.7799 (pt0) cc_final: 0.7596 (pt0) REVERT: A 443 ARG cc_start: 0.6995 (ttt-90) cc_final: 0.6422 (ttt-90) REVERT: A 449 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7827 (tp-100) REVERT: A 453 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7509 (mm-30) REVERT: A 457 ARG cc_start: 0.7738 (ttp-170) cc_final: 0.7535 (ttp-170) REVERT: A 479 TYR cc_start: 0.7874 (p90) cc_final: 0.7615 (p90) REVERT: A 484 TRP cc_start: 0.8153 (m-90) cc_final: 0.7519 (m-90) REVERT: A 487 ASP cc_start: 0.8349 (m-30) cc_final: 0.8100 (m-30) REVERT: A 565 HIS cc_start: 0.7741 (t70) cc_final: 0.7209 (t70) REVERT: A 566 LEU cc_start: 0.8879 (mt) cc_final: 0.8514 (mm) REVERT: A 572 TRP cc_start: 0.8535 (p-90) cc_final: 0.8261 (p-90) REVERT: A 593 SER cc_start: 0.7877 (m) cc_final: 0.7565 (p) REVERT: A 607 TRP cc_start: 0.8233 (t-100) cc_final: 0.7741 (t-100) REVERT: A 617 ARG cc_start: 0.7023 (ttt90) cc_final: 0.6813 (mtp85) REVERT: A 755 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8253 (mmtt) REVERT: A 758 ASN cc_start: 0.7972 (m-40) cc_final: 0.7538 (t0) REVERT: A 769 ASP cc_start: 0.7493 (p0) cc_final: 0.6981 (p0) REVERT: A 797 MET cc_start: 0.7688 (mtt) cc_final: 0.7449 (tpp) REVERT: A 816 LEU cc_start: 0.8487 (tp) cc_final: 0.8153 (tp) REVERT: A 821 LEU cc_start: 0.8393 (mt) cc_final: 0.8141 (mt) REVERT: A 826 ILE cc_start: 0.8026 (mt) cc_final: 0.7783 (pt) REVERT: A 832 ASP cc_start: 0.8132 (t0) cc_final: 0.7794 (t0) REVERT: A 841 LEU cc_start: 0.8166 (mp) cc_final: 0.7962 (mt) REVERT: A 877 MET cc_start: 0.7266 (mmm) cc_final: 0.6994 (mmm) REVERT: A 893 SER cc_start: 0.7286 (t) cc_final: 0.6753 (p) REVERT: A 916 PHE cc_start: 0.8026 (t80) cc_final: 0.7506 (t80) REVERT: A 920 THR cc_start: 0.7915 (m) cc_final: 0.7696 (p) REVERT: A 922 GLN cc_start: 0.7504 (tt0) cc_final: 0.6810 (tp-100) REVERT: A 944 GLU cc_start: 0.8371 (pm20) cc_final: 0.7956 (pm20) REVERT: A 981 LYS cc_start: 0.8254 (tttt) cc_final: 0.7772 (tppt) REVERT: A 985 MET cc_start: 0.7068 (ttp) cc_final: 0.6685 (ttp) REVERT: A 1057 MET cc_start: 0.7794 (ppp) cc_final: 0.7541 (ppp) REVERT: A 1060 LYS cc_start: 0.8113 (tptp) cc_final: 0.7620 (tptp) REVERT: A 1062 GLU cc_start: 0.7899 (pt0) cc_final: 0.7654 (mt-10) REVERT: A 1093 MET cc_start: 0.7225 (pmm) cc_final: 0.6737 (pmm) REVERT: A 1109 LEU cc_start: 0.8817 (tp) cc_final: 0.8575 (tt) REVERT: A 1111 LEU cc_start: 0.8752 (mt) cc_final: 0.8525 (mt) REVERT: A 1112 MET cc_start: 0.8495 (mtm) cc_final: 0.8129 (mtp) REVERT: A 1113 LEU cc_start: 0.8621 (mp) cc_final: 0.8364 (mm) REVERT: A 1116 MET cc_start: 0.7428 (tpt) cc_final: 0.6486 (tpt) REVERT: A 1120 PHE cc_start: 0.8094 (m-10) cc_final: 0.7767 (m-80) REVERT: A 1126 ASP cc_start: 0.6560 (m-30) cc_final: 0.6169 (m-30) REVERT: A 1148 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7714 (ttp-170) REVERT: A 1154 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7893 (mm-40) REVERT: A 1168 LEU cc_start: 0.8733 (mt) cc_final: 0.8461 (mt) REVERT: A 1188 CYS cc_start: 0.8023 (p) cc_final: 0.7758 (p) REVERT: A 1222 GLN cc_start: 0.8475 (mp10) cc_final: 0.8075 (mp10) REVERT: B 72 ILE cc_start: 0.8381 (mm) cc_final: 0.7978 (mm) REVERT: B 77 HIS cc_start: 0.6930 (m-70) cc_final: 0.6556 (m-70) REVERT: B 80 SER cc_start: 0.7507 (m) cc_final: 0.7243 (m) REVERT: B 88 ARG cc_start: 0.8084 (ptp-170) cc_final: 0.7718 (ptp90) REVERT: B 108 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7861 (ttmm) REVERT: B 113 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6735 (mm-30) REVERT: B 123 GLU cc_start: 0.7575 (pt0) cc_final: 0.7269 (pt0) REVERT: B 134 LYS cc_start: 0.8469 (mtmt) cc_final: 0.7965 (mtmt) REVERT: B 180 LYS cc_start: 0.8349 (ptmt) cc_final: 0.7686 (ptmt) REVERT: B 183 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6942 (mt-10) REVERT: B 191 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 192 HIS cc_start: 0.8189 (m90) cc_final: 0.7783 (m-70) REVERT: B 201 ASN cc_start: 0.7898 (m110) cc_final: 0.7474 (m110) REVERT: B 235 THR cc_start: 0.8268 (m) cc_final: 0.8033 (m) REVERT: B 262 TRP cc_start: 0.7968 (t60) cc_final: 0.6736 (t60) REVERT: B 288 LYS cc_start: 0.6994 (mttt) cc_final: 0.6422 (mtpt) REVERT: B 304 TRP cc_start: 0.7973 (m100) cc_final: 0.7726 (m100) REVERT: B 310 GLU cc_start: 0.7570 (mp0) cc_final: 0.7233 (mp0) REVERT: B 315 TYR cc_start: 0.7796 (m-80) cc_final: 0.7418 (m-80) REVERT: B 339 ASN cc_start: 0.7060 (t0) cc_final: 0.6729 (t0) REVERT: B 349 TYR cc_start: 0.8319 (m-10) cc_final: 0.7910 (m-10) REVERT: B 352 ASP cc_start: 0.7352 (t0) cc_final: 0.7023 (t0) REVERT: B 353 SER cc_start: 0.8311 (p) cc_final: 0.8055 (p) REVERT: B 378 LEU cc_start: 0.8355 (mp) cc_final: 0.8087 (mt) REVERT: B 396 ARG cc_start: 0.7584 (ttm170) cc_final: 0.7178 (ttm110) REVERT: B 412 SER cc_start: 0.8260 (t) cc_final: 0.7804 (p) REVERT: B 431 LYS cc_start: 0.8432 (tttt) cc_final: 0.8122 (tppt) REVERT: B 435 MET cc_start: 0.7341 (mtp) cc_final: 0.7073 (mtp) REVERT: B 446 THR cc_start: 0.8298 (m) cc_final: 0.7883 (m) REVERT: B 449 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7300 (mt-10) REVERT: B 457 SER cc_start: 0.7868 (t) cc_final: 0.7527 (p) REVERT: B 460 THR cc_start: 0.8641 (p) cc_final: 0.8099 (p) REVERT: B 462 MET cc_start: 0.8014 (mmt) cc_final: 0.7724 (mmt) REVERT: B 465 MET cc_start: 0.7544 (mtm) cc_final: 0.7221 (mtm) REVERT: B 466 MET cc_start: 0.7378 (mtp) cc_final: 0.7064 (ttm) REVERT: B 467 HIS cc_start: 0.8231 (t-90) cc_final: 0.7889 (t70) REVERT: B 470 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7600 (mtpp) REVERT: C 69 LEU cc_start: 0.8605 (tt) cc_final: 0.8314 (tt) REVERT: C 75 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7636 (mtp85) REVERT: C 80 SER cc_start: 0.8540 (t) cc_final: 0.8053 (p) REVERT: C 92 LEU cc_start: 0.8600 (mt) cc_final: 0.8343 (mm) REVERT: C 109 ASN cc_start: 0.7954 (m-40) cc_final: 0.7754 (m-40) REVERT: C 183 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6482 (mt-10) REVERT: C 199 LEU cc_start: 0.8312 (tp) cc_final: 0.8061 (tt) REVERT: C 203 ARG cc_start: 0.7514 (ttt180) cc_final: 0.7139 (ttt180) REVERT: C 235 THR cc_start: 0.7001 (p) cc_final: 0.6538 (p) REVERT: C 256 LEU cc_start: 0.8531 (tp) cc_final: 0.8280 (tp) REVERT: C 259 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7370 (mtp85) REVERT: C 262 TRP cc_start: 0.7946 (t60) cc_final: 0.7477 (t60) REVERT: C 288 LYS cc_start: 0.8208 (mttt) cc_final: 0.7715 (mttt) REVERT: C 291 TYR cc_start: 0.8057 (t80) cc_final: 0.7825 (t80) REVERT: C 301 GLU cc_start: 0.7404 (tt0) cc_final: 0.6688 (tt0) REVERT: C 306 LEU cc_start: 0.8450 (mt) cc_final: 0.7987 (mm) REVERT: C 336 LEU cc_start: 0.8329 (mt) cc_final: 0.8023 (mt) REVERT: C 346 MET cc_start: 0.7167 (tmm) cc_final: 0.6501 (tmm) REVERT: C 354 PHE cc_start: 0.7823 (t80) cc_final: 0.7551 (t80) REVERT: C 371 VAL cc_start: 0.8412 (p) cc_final: 0.8135 (m) REVERT: C 421 MET cc_start: 0.6441 (mtt) cc_final: 0.6227 (mtt) REVERT: C 427 GLN cc_start: 0.8268 (mt0) cc_final: 0.7731 (mt0) REVERT: C 430 SER cc_start: 0.8517 (t) cc_final: 0.8100 (p) REVERT: C 431 LYS cc_start: 0.8447 (tttt) cc_final: 0.8155 (tttt) REVERT: C 434 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7766 (mt-10) REVERT: C 466 MET cc_start: 0.6979 (ttm) cc_final: 0.6716 (ttm) REVERT: C 470 LYS cc_start: 0.8665 (mttt) cc_final: 0.8251 (mttt) outliers start: 0 outliers final: 0 residues processed: 579 average time/residue: 0.1290 time to fit residues: 106.7187 Evaluate side-chains 542 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.092089 restraints weight = 63582.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097396 restraints weight = 26787.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100952 restraints weight = 14650.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103353 restraints weight = 9324.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104951 restraints weight = 6615.522| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16209 Z= 0.248 Angle : 0.611 10.451 22166 Z= 0.326 Chirality : 0.045 0.178 2406 Planarity : 0.005 0.061 2692 Dihedral : 14.948 88.546 2496 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.19 % Allowed : 2.63 % Favored : 97.18 % 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 aren not related in a simple way. whole: 0.41 (0.20), residues: 1837 helix: 1.29 (0.18), residues: 792 sheet: -0.07 (0.34), residues: 232 loop : -0.59 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 126 TYR 0.033 0.002 TYR B 315 PHE 0.031 0.002 PHE A 139 TRP 0.023 0.002 TRP A 486 HIS 0.005 0.001 HIS A1110 Details of bonding type rmsd covalent geometry : bond 0.00501 (16209) covalent geometry : angle 0.61052 (22166) hydrogen bonds : bond 0.04868 ( 767) hydrogen bonds : angle 5.29867 ( 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 573 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 572 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: A 79 LEU cc_start: 0.8119 (mt) cc_final: 0.7832 (mp) REVERT: A 110 HIS cc_start: 0.7397 (m90) cc_final: 0.6632 (m90) REVERT: A 145 LYS cc_start: 0.8196 (tptp) cc_final: 0.7674 (tptp) REVERT: A 159 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6705 (pp30) REVERT: A 193 ARG cc_start: 0.7343 (ttp-110) cc_final: 0.6972 (ptm160) REVERT: A 264 GLN cc_start: 0.7892 (pt0) cc_final: 0.7538 (pm20) REVERT: A 275 ARG cc_start: 0.8279 (ttt180) cc_final: 0.8077 (ttt180) REVERT: A 280 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 289 MET cc_start: 0.7199 (ttm) cc_final: 0.6282 (ttm) REVERT: A 354 ASN cc_start: 0.7682 (m-40) cc_final: 0.7400 (m-40) REVERT: A 355 SER cc_start: 0.7847 (t) cc_final: 0.7617 (t) REVERT: A 358 GLU cc_start: 0.7615 (mp0) cc_final: 0.7251 (mp0) REVERT: A 375 GLU cc_start: 0.7405 (pt0) cc_final: 0.7001 (pt0) REVERT: A 393 MET cc_start: 0.7183 (ttm) cc_final: 0.6881 (ttm) REVERT: A 405 GLU cc_start: 0.7601 (tp30) cc_final: 0.7227 (tm-30) REVERT: A 443 ARG cc_start: 0.6969 (ttt-90) cc_final: 0.6400 (ttt-90) REVERT: A 449 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7823 (tp-100) REVERT: A 453 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7499 (mm-30) REVERT: A 457 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7548 (ttp-170) REVERT: A 484 TRP cc_start: 0.8168 (m-90) cc_final: 0.7561 (m-90) REVERT: A 487 ASP cc_start: 0.8355 (m-30) cc_final: 0.8154 (m-30) REVERT: A 537 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7699 (tm-30) REVERT: A 565 HIS cc_start: 0.7587 (t70) cc_final: 0.7234 (t-90) REVERT: A 566 LEU cc_start: 0.8896 (mt) cc_final: 0.8614 (mm) REVERT: A 586 THR cc_start: 0.8227 (t) cc_final: 0.7906 (p) REVERT: A 593 SER cc_start: 0.7917 (m) cc_final: 0.7599 (p) REVERT: A 607 TRP cc_start: 0.8208 (t-100) cc_final: 0.7703 (t60) REVERT: A 617 ARG cc_start: 0.6990 (ttt90) cc_final: 0.6789 (mtp85) REVERT: A 755 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8145 (mmtt) REVERT: A 758 ASN cc_start: 0.7970 (m-40) cc_final: 0.7509 (t0) REVERT: A 769 ASP cc_start: 0.7461 (p0) cc_final: 0.6928 (p0) REVERT: A 797 MET cc_start: 0.7675 (mtt) cc_final: 0.7453 (ttm) REVERT: A 806 LYS cc_start: 0.7917 (mmmm) cc_final: 0.7692 (mmmm) REVERT: A 816 LEU cc_start: 0.8465 (tp) cc_final: 0.8081 (tp) REVERT: A 821 LEU cc_start: 0.8385 (mt) cc_final: 0.8127 (mt) REVERT: A 832 ASP cc_start: 0.8097 (t0) cc_final: 0.7878 (t70) REVERT: A 877 MET cc_start: 0.7236 (mmm) cc_final: 0.6954 (mmm) REVERT: A 893 SER cc_start: 0.7351 (t) cc_final: 0.6792 (p) REVERT: A 916 PHE cc_start: 0.8003 (t80) cc_final: 0.7365 (t80) REVERT: A 922 GLN cc_start: 0.7436 (tt0) cc_final: 0.7022 (tp40) REVERT: A 981 LYS cc_start: 0.8240 (tttt) cc_final: 0.7756 (tppt) REVERT: A 1057 MET cc_start: 0.7809 (ppp) cc_final: 0.7524 (ppp) REVERT: A 1060 LYS cc_start: 0.8109 (tptp) cc_final: 0.7590 (tptp) REVERT: A 1093 MET cc_start: 0.7127 (pmm) cc_final: 0.6585 (pmm) REVERT: A 1110 HIS cc_start: 0.8635 (m-70) cc_final: 0.8368 (m-70) REVERT: A 1112 MET cc_start: 0.8503 (mtm) cc_final: 0.8246 (mtp) REVERT: A 1116 MET cc_start: 0.7264 (tpt) cc_final: 0.6455 (tpt) REVERT: A 1119 LEU cc_start: 0.8169 (mt) cc_final: 0.7927 (mt) REVERT: A 1126 ASP cc_start: 0.6502 (m-30) cc_final: 0.6256 (m-30) REVERT: A 1137 VAL cc_start: 0.8365 (t) cc_final: 0.8017 (p) REVERT: A 1148 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7471 (ttp-170) REVERT: A 1222 GLN cc_start: 0.8464 (mp10) cc_final: 0.7815 (mp10) REVERT: B 77 HIS cc_start: 0.7031 (m-70) cc_final: 0.6735 (m-70) REVERT: B 80 SER cc_start: 0.7428 (m) cc_final: 0.7208 (m) REVERT: B 83 LYS cc_start: 0.8728 (ptmt) cc_final: 0.8491 (ptpp) REVERT: B 88 ARG cc_start: 0.8048 (ptp-170) cc_final: 0.7660 (ptp90) REVERT: B 108 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7888 (ttmm) REVERT: B 113 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6663 (mm-30) REVERT: B 123 GLU cc_start: 0.7569 (pt0) cc_final: 0.7187 (pt0) REVERT: B 134 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7893 (mtmt) REVERT: B 180 LYS cc_start: 0.8301 (ptmt) cc_final: 0.7645 (ptmt) REVERT: B 183 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6906 (mt-10) REVERT: B 191 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7310 (mt-10) REVERT: B 192 HIS cc_start: 0.8156 (m90) cc_final: 0.7756 (m-70) REVERT: B 201 ASN cc_start: 0.7889 (m110) cc_final: 0.7470 (m110) REVERT: B 235 THR cc_start: 0.8252 (m) cc_final: 0.8046 (m) REVERT: B 257 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7376 (mtp85) REVERT: B 263 TRP cc_start: 0.7880 (m100) cc_final: 0.7137 (m100) REVERT: B 288 LYS cc_start: 0.7069 (mttt) cc_final: 0.6334 (mtpt) REVERT: B 289 LEU cc_start: 0.7917 (mt) cc_final: 0.7621 (mt) REVERT: B 304 TRP cc_start: 0.7933 (m100) cc_final: 0.7562 (m100) REVERT: B 310 GLU cc_start: 0.7569 (mp0) cc_final: 0.7259 (mp0) REVERT: B 315 TYR cc_start: 0.7830 (m-80) cc_final: 0.7423 (m-80) REVERT: B 352 ASP cc_start: 0.7342 (t0) cc_final: 0.6982 (t0) REVERT: B 372 LEU cc_start: 0.7809 (mp) cc_final: 0.7589 (mt) REVERT: B 396 ARG cc_start: 0.7558 (ttm170) cc_final: 0.7154 (ttm110) REVERT: B 400 GLN cc_start: 0.7742 (tt0) cc_final: 0.7503 (tp40) REVERT: B 412 SER cc_start: 0.8246 (t) cc_final: 0.7738 (p) REVERT: B 427 GLN cc_start: 0.8343 (pt0) cc_final: 0.7443 (pm20) REVERT: B 431 LYS cc_start: 0.8348 (tttt) cc_final: 0.8036 (tppt) REVERT: B 435 MET cc_start: 0.7258 (mtp) cc_final: 0.6970 (mtp) REVERT: B 446 THR cc_start: 0.8356 (m) cc_final: 0.7914 (m) REVERT: B 449 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 457 SER cc_start: 0.7876 (t) cc_final: 0.7525 (p) REVERT: B 460 THR cc_start: 0.8553 (p) cc_final: 0.8116 (p) REVERT: B 461 THR cc_start: 0.8252 (p) cc_final: 0.7914 (t) REVERT: B 462 MET cc_start: 0.7954 (mmt) cc_final: 0.7687 (mmt) REVERT: B 465 MET cc_start: 0.7559 (mtm) cc_final: 0.7185 (mtm) REVERT: B 466 MET cc_start: 0.7376 (mtp) cc_final: 0.6984 (ttp) REVERT: B 467 HIS cc_start: 0.8192 (t-90) cc_final: 0.7829 (t70) REVERT: B 483 LYS cc_start: 0.6481 (mtpp) cc_final: 0.6118 (mtpp) REVERT: C 69 LEU cc_start: 0.8616 (tt) cc_final: 0.8326 (tt) REVERT: C 75 ARG cc_start: 0.7951 (mtp85) cc_final: 0.7532 (mtp85) REVERT: C 80 SER cc_start: 0.8584 (t) cc_final: 0.8191 (m) REVERT: C 89 ASP cc_start: 0.8013 (m-30) cc_final: 0.7735 (m-30) REVERT: C 92 LEU cc_start: 0.8558 (mt) cc_final: 0.8336 (mm) REVERT: C 107 ARG cc_start: 0.7505 (ttm170) cc_final: 0.7160 (ttp80) REVERT: C 109 ASN cc_start: 0.7992 (m-40) cc_final: 0.7780 (m-40) REVERT: C 110 LEU cc_start: 0.7918 (tt) cc_final: 0.7701 (tp) REVERT: C 183 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6416 (mt-10) REVERT: C 194 VAL cc_start: 0.7927 (m) cc_final: 0.7699 (p) REVERT: C 203 ARG cc_start: 0.7515 (ttt180) cc_final: 0.7160 (ttt180) REVERT: C 233 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6277 (mp0) REVERT: C 234 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7665 (mtmm) REVERT: C 235 THR cc_start: 0.7087 (p) cc_final: 0.6533 (p) REVERT: C 256 LEU cc_start: 0.8424 (tp) cc_final: 0.8219 (tp) REVERT: C 259 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7334 (mtp85) REVERT: C 262 TRP cc_start: 0.7892 (t60) cc_final: 0.7290 (t60) REVERT: C 288 LYS cc_start: 0.8247 (mttt) cc_final: 0.7746 (mttt) REVERT: C 291 TYR cc_start: 0.8091 (t80) cc_final: 0.7800 (t80) REVERT: C 301 GLU cc_start: 0.7380 (tt0) cc_final: 0.6643 (tt0) REVERT: C 305 ASN cc_start: 0.7572 (t0) cc_final: 0.7349 (t0) REVERT: C 306 LEU cc_start: 0.8331 (mt) cc_final: 0.7974 (mm) REVERT: C 336 LEU cc_start: 0.8342 (mt) cc_final: 0.7946 (mt) REVERT: C 343 ASP cc_start: 0.7050 (m-30) cc_final: 0.6827 (m-30) REVERT: C 346 MET cc_start: 0.7070 (tmm) cc_final: 0.6375 (tmm) REVERT: C 354 PHE cc_start: 0.7907 (t80) cc_final: 0.7484 (t80) REVERT: C 371 VAL cc_start: 0.8368 (p) cc_final: 0.8033 (m) REVERT: C 421 MET cc_start: 0.6528 (mtt) cc_final: 0.6297 (mtt) REVERT: C 427 GLN cc_start: 0.8247 (mt0) cc_final: 0.7755 (mt0) REVERT: C 430 SER cc_start: 0.8487 (t) cc_final: 0.8019 (p) REVERT: C 431 LYS cc_start: 0.8406 (tttt) cc_final: 0.8155 (tttt) REVERT: C 434 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7729 (mt-10) REVERT: C 466 MET cc_start: 0.6915 (ttm) cc_final: 0.6685 (ttm) REVERT: C 470 LYS cc_start: 0.8630 (mttt) cc_final: 0.8235 (mttt) outliers start: 1 outliers final: 0 residues processed: 572 average time/residue: 0.1285 time to fit residues: 104.8945 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 : 0.333 ------------------------------------------------------------------------------- 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: 0.9990 chunk 123 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 440 ASN A 468 ASN A 565 HIS ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 HIS ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.092743 restraints weight = 63378.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098042 restraints weight = 26416.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101597 restraints weight = 14366.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103971 restraints weight = 9092.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105408 restraints weight = 6449.878| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16209 Z= 0.203 Angle : 0.586 8.288 22166 Z= 0.312 Chirality : 0.043 0.192 2406 Planarity : 0.005 0.055 2692 Dihedral : 14.867 89.134 2496 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.19 % Allowed : 1.81 % Favored : 98.00 % 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 aren not related in a simple way. whole: 0.50 (0.20), residues: 1837 helix: 1.47 (0.18), residues: 783 sheet: -0.11 (0.33), residues: 246 loop : -0.61 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 275 TYR 0.028 0.002 TYR B 315 PHE 0.032 0.002 PHE C 242 TRP 0.021 0.002 TRP A 572 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00414 (16209) covalent geometry : angle 0.58641 (22166) hydrogen bonds : bond 0.04470 ( 767) hydrogen bonds : angle 5.08970 ( 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 572 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 571 time to evaluate : 0.456 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: A 76 ILE cc_start: 0.8469 (mm) cc_final: 0.8180 (mm) REVERT: A 79 LEU cc_start: 0.8079 (mt) cc_final: 0.7816 (mp) REVERT: A 110 HIS cc_start: 0.7297 (m90) cc_final: 0.6577 (m90) REVERT: A 133 ASP cc_start: 0.6641 (p0) cc_final: 0.6435 (m-30) REVERT: A 145 LYS cc_start: 0.8172 (tptp) cc_final: 0.7797 (tptp) REVERT: A 159 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6711 (pp30) REVERT: A 193 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6920 (ptm160) REVERT: A 264 GLN cc_start: 0.7838 (pt0) cc_final: 0.7466 (pm20) REVERT: A 280 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 289 MET cc_start: 0.6836 (ttm) cc_final: 0.6560 (ttm) REVERT: A 354 ASN cc_start: 0.7680 (m-40) cc_final: 0.7177 (m-40) REVERT: A 358 GLU cc_start: 0.7559 (mp0) cc_final: 0.7218 (mp0) REVERT: A 375 GLU cc_start: 0.7362 (pt0) cc_final: 0.6987 (pm20) REVERT: A 379 LYS cc_start: 0.7707 (ptpp) cc_final: 0.7390 (mtmt) REVERT: A 393 MET cc_start: 0.7261 (ttm) cc_final: 0.6941 (ttm) REVERT: A 405 GLU cc_start: 0.7610 (tp30) cc_final: 0.7280 (tm-30) REVERT: A 410 GLN cc_start: 0.7712 (tt0) cc_final: 0.7277 (tt0) REVERT: A 427 MET cc_start: 0.7642 (ttm) cc_final: 0.7383 (ttm) REVERT: A 439 GLN cc_start: 0.7882 (pt0) cc_final: 0.7645 (pt0) REVERT: A 443 ARG cc_start: 0.6950 (ttt-90) cc_final: 0.6391 (ttt-90) REVERT: A 453 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7499 (mm-30) REVERT: A 487 ASP cc_start: 0.8342 (m-30) cc_final: 0.8055 (m-30) REVERT: A 565 HIS cc_start: 0.7533 (t-90) cc_final: 0.7197 (t70) REVERT: A 566 LEU cc_start: 0.8875 (mt) cc_final: 0.8635 (mm) REVERT: A 586 THR cc_start: 0.8012 (t) cc_final: 0.7747 (p) REVERT: A 593 SER cc_start: 0.7964 (m) cc_final: 0.7611 (p) REVERT: A 607 TRP cc_start: 0.8169 (t-100) cc_final: 0.7702 (t60) REVERT: A 617 ARG cc_start: 0.6981 (ttt90) cc_final: 0.6763 (mtp85) REVERT: A 755 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8132 (mmtt) REVERT: A 758 ASN cc_start: 0.7970 (m-40) cc_final: 0.7533 (t0) REVERT: A 769 ASP cc_start: 0.7469 (p0) cc_final: 0.6986 (p0) REVERT: A 774 MET cc_start: 0.7262 (tpt) cc_final: 0.6997 (tpt) REVERT: A 806 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7650 (mmmm) REVERT: A 812 MET cc_start: 0.7456 (mpp) cc_final: 0.7214 (mpp) REVERT: A 816 LEU cc_start: 0.8472 (tp) cc_final: 0.8103 (tp) REVERT: A 821 LEU cc_start: 0.8400 (mt) cc_final: 0.8129 (mt) REVERT: A 823 ARG cc_start: 0.7699 (tmt170) cc_final: 0.7059 (tmt170) REVERT: A 827 ARG cc_start: 0.7390 (ttp80) cc_final: 0.6955 (ttp80) REVERT: A 877 MET cc_start: 0.7178 (mmm) cc_final: 0.6803 (tpp) REVERT: A 893 SER cc_start: 0.7335 (t) cc_final: 0.6724 (p) REVERT: A 916 PHE cc_start: 0.8088 (t80) cc_final: 0.7552 (t80) REVERT: A 922 GLN cc_start: 0.7318 (tt0) cc_final: 0.7031 (tt0) REVERT: A 981 LYS cc_start: 0.8249 (tttt) cc_final: 0.7734 (tppt) REVERT: A 1057 MET cc_start: 0.7842 (ppp) cc_final: 0.7553 (ppp) REVERT: A 1060 LYS cc_start: 0.8137 (tptp) cc_final: 0.7621 (tptp) REVERT: A 1093 MET cc_start: 0.7062 (pmm) cc_final: 0.6655 (pmm) REVERT: A 1109 LEU cc_start: 0.8809 (tp) cc_final: 0.8517 (tt) REVERT: A 1111 LEU cc_start: 0.8635 (mt) cc_final: 0.8376 (mt) REVERT: A 1112 MET cc_start: 0.8445 (mtm) cc_final: 0.8098 (mtp) REVERT: A 1113 LEU cc_start: 0.8551 (mp) cc_final: 0.8248 (mm) REVERT: A 1116 MET cc_start: 0.7233 (tpt) cc_final: 0.6489 (tpt) REVERT: A 1137 VAL cc_start: 0.8287 (t) cc_final: 0.7803 (p) REVERT: A 1148 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7418 (ttp-170) REVERT: A 1222 GLN cc_start: 0.8454 (mp10) cc_final: 0.7850 (mp10) REVERT: B 77 HIS cc_start: 0.7023 (m-70) cc_final: 0.6730 (m170) REVERT: B 83 LYS cc_start: 0.8742 (ptmt) cc_final: 0.8491 (ptpp) REVERT: B 88 ARG cc_start: 0.8028 (ptp-170) cc_final: 0.7663 (ptp90) REVERT: B 108 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7973 (ttmm) REVERT: B 113 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 123 GLU cc_start: 0.7542 (pt0) cc_final: 0.7182 (pt0) REVERT: B 134 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7880 (mtmt) REVERT: B 180 LYS cc_start: 0.8321 (ptmt) cc_final: 0.7636 (ptmt) REVERT: B 183 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6873 (mt-10) REVERT: B 191 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7210 (mt-10) REVERT: B 192 HIS cc_start: 0.8117 (m90) cc_final: 0.7690 (m-70) REVERT: B 201 ASN cc_start: 0.7894 (m110) cc_final: 0.7492 (m110) REVERT: B 257 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7434 (mtp85) REVERT: B 263 TRP cc_start: 0.7851 (m100) cc_final: 0.7017 (m100) REVERT: B 288 LYS cc_start: 0.7061 (mttt) cc_final: 0.6344 (mtpt) REVERT: B 289 LEU cc_start: 0.7900 (mt) cc_final: 0.7542 (mt) REVERT: B 304 TRP cc_start: 0.7904 (m100) cc_final: 0.7515 (m100) REVERT: B 310 GLU cc_start: 0.7571 (mp0) cc_final: 0.7231 (mp0) REVERT: B 315 TYR cc_start: 0.7857 (m-80) cc_final: 0.7453 (m-80) REVERT: B 339 ASN cc_start: 0.7024 (t0) cc_final: 0.6486 (t0) REVERT: B 346 MET cc_start: 0.7607 (tmm) cc_final: 0.7395 (tmm) REVERT: B 352 ASP cc_start: 0.7278 (t0) cc_final: 0.6919 (t0) REVERT: B 372 LEU cc_start: 0.7830 (mp) cc_final: 0.7606 (mt) REVERT: B 378 LEU cc_start: 0.8385 (mp) cc_final: 0.8064 (mt) REVERT: B 387 VAL cc_start: 0.8067 (t) cc_final: 0.7860 (m) REVERT: B 396 ARG cc_start: 0.7555 (ttm170) cc_final: 0.7146 (ttm110) REVERT: B 400 GLN cc_start: 0.7709 (tt0) cc_final: 0.7502 (tp40) REVERT: B 412 SER cc_start: 0.8248 (t) cc_final: 0.7737 (p) REVERT: B 427 GLN cc_start: 0.8346 (pt0) cc_final: 0.7517 (pm20) REVERT: B 431 LYS cc_start: 0.8382 (tttt) cc_final: 0.8003 (tppt) REVERT: B 435 MET cc_start: 0.7154 (mtp) cc_final: 0.6929 (mtp) REVERT: B 446 THR cc_start: 0.8345 (m) cc_final: 0.7946 (m) REVERT: B 449 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7271 (mt-10) REVERT: B 457 SER cc_start: 0.8003 (t) cc_final: 0.7638 (p) REVERT: B 461 THR cc_start: 0.8263 (p) cc_final: 0.7935 (t) REVERT: B 462 MET cc_start: 0.7890 (mmt) cc_final: 0.7600 (mmt) REVERT: B 465 MET cc_start: 0.7548 (mtm) cc_final: 0.7146 (mtm) REVERT: B 466 MET cc_start: 0.7368 (mtp) cc_final: 0.6937 (ttp) REVERT: C 71 GLU cc_start: 0.8369 (tt0) cc_final: 0.8141 (tt0) REVERT: C 75 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7590 (mtp85) REVERT: C 80 SER cc_start: 0.8527 (t) cc_final: 0.8043 (m) REVERT: C 89 ASP cc_start: 0.8002 (m-30) cc_final: 0.7702 (m-30) REVERT: C 107 ARG cc_start: 0.7483 (ttm170) cc_final: 0.7186 (ttp80) REVERT: C 183 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6373 (mt-10) REVERT: C 194 VAL cc_start: 0.8001 (m) cc_final: 0.7778 (p) REVERT: C 203 ARG cc_start: 0.7499 (ttt180) cc_final: 0.7146 (ttt180) REVERT: C 231 ILE cc_start: 0.7978 (mt) cc_final: 0.7767 (mm) REVERT: C 233 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6287 (mp0) REVERT: C 234 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7662 (mtmm) REVERT: C 235 THR cc_start: 0.7024 (p) cc_final: 0.6599 (p) REVERT: C 242 PHE cc_start: 0.6883 (m-10) cc_final: 0.6620 (m-10) REVERT: C 243 THR cc_start: 0.7863 (t) cc_final: 0.7557 (p) REVERT: C 256 LEU cc_start: 0.8446 (tp) cc_final: 0.8139 (tp) REVERT: C 259 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7337 (mtp85) REVERT: C 262 TRP cc_start: 0.7875 (t60) cc_final: 0.7213 (t60) REVERT: C 280 ASP cc_start: 0.6410 (p0) cc_final: 0.6097 (p0) REVERT: C 287 ASN cc_start: 0.7275 (t0) cc_final: 0.7025 (t0) REVERT: C 288 LYS cc_start: 0.8235 (mttt) cc_final: 0.7735 (mttt) REVERT: C 299 LEU cc_start: 0.8515 (tp) cc_final: 0.8264 (tt) REVERT: C 301 GLU cc_start: 0.7410 (tt0) cc_final: 0.6627 (tt0) REVERT: C 305 ASN cc_start: 0.7559 (t0) cc_final: 0.7317 (t0) REVERT: C 306 LEU cc_start: 0.8397 (mt) cc_final: 0.7975 (mm) REVERT: C 336 LEU cc_start: 0.8353 (mt) cc_final: 0.7998 (mt) REVERT: C 343 ASP cc_start: 0.6989 (m-30) cc_final: 0.6481 (m-30) REVERT: C 347 LEU cc_start: 0.8318 (mm) cc_final: 0.7304 (mm) REVERT: C 371 VAL cc_start: 0.8215 (p) cc_final: 0.7989 (m) REVERT: C 396 ARG cc_start: 0.7791 (ttm170) cc_final: 0.6826 (ttm170) REVERT: C 400 GLN cc_start: 0.7799 (mt0) cc_final: 0.7148 (mt0) REVERT: C 415 PRO cc_start: 0.8676 (Cg_endo) cc_final: 0.8453 (Cg_exo) REVERT: C 421 MET cc_start: 0.6503 (mtt) cc_final: 0.6284 (mtt) REVERT: C 427 GLN cc_start: 0.8247 (mt0) cc_final: 0.7755 (mt0) REVERT: C 430 SER cc_start: 0.8464 (t) cc_final: 0.7982 (p) REVERT: C 431 LYS cc_start: 0.8389 (tttt) cc_final: 0.8173 (tttt) REVERT: C 434 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 466 MET cc_start: 0.6963 (ttm) cc_final: 0.6628 (ttm) REVERT: C 470 LYS cc_start: 0.8603 (mttt) cc_final: 0.8197 (mttt) outliers start: 1 outliers final: 1 residues processed: 571 average time/residue: 0.1295 time to fit residues: 104.5307 Evaluate side-chains 537 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 536 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 0.9980 chunk 94 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 102 optimal weight: 0.0040 chunk 76 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 440 ASN A 468 ASN A 906 HIS B 409 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.120578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094389 restraints weight = 58894.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099580 restraints weight = 25028.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103052 restraints weight = 13646.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105244 restraints weight = 8649.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106851 restraints weight = 6228.758| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16209 Z= 0.146 Angle : 0.547 8.450 22166 Z= 0.289 Chirality : 0.042 0.187 2406 Planarity : 0.004 0.055 2692 Dihedral : 14.711 89.803 2496 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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 aren not related in a simple way. whole: 0.80 (0.20), residues: 1837 helix: 1.75 (0.19), residues: 780 sheet: 0.08 (0.32), residues: 253 loop : -0.50 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 417 TYR 0.025 0.001 TYR B 315 PHE 0.023 0.002 PHE C 242 TRP 0.025 0.002 TRP A 490 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00304 (16209) covalent geometry : angle 0.54653 (22166) hydrogen bonds : bond 0.03930 ( 767) hydrogen bonds : angle 4.78273 ( 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 571 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 0.542 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 76 ILE cc_start: 0.8475 (mm) cc_final: 0.8222 (mm) REVERT: A 79 LEU cc_start: 0.8101 (mt) cc_final: 0.7851 (mp) REVERT: A 110 HIS cc_start: 0.7248 (m90) cc_final: 0.6565 (m90) REVERT: A 159 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6649 (pp30) REVERT: A 193 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.6947 (ptm160) REVERT: A 197 PHE cc_start: 0.7363 (t80) cc_final: 0.6852 (t80) REVERT: A 264 GLN cc_start: 0.7881 (pt0) cc_final: 0.7577 (pm20) REVERT: A 280 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7022 (mm-30) REVERT: A 289 MET cc_start: 0.7088 (ttm) cc_final: 0.6550 (ttm) REVERT: A 293 ASP cc_start: 0.5295 (t0) cc_final: 0.5094 (t0) REVERT: A 308 GLN cc_start: 0.7852 (mt0) cc_final: 0.7408 (tt0) REVERT: A 354 ASN cc_start: 0.7584 (m-40) cc_final: 0.7227 (m-40) REVERT: A 355 SER cc_start: 0.7635 (t) cc_final: 0.7386 (t) REVERT: A 358 GLU cc_start: 0.7570 (mp0) cc_final: 0.7196 (mp0) REVERT: A 375 GLU cc_start: 0.7336 (pt0) cc_final: 0.6940 (pm20) REVERT: A 379 LYS cc_start: 0.7720 (ptpp) cc_final: 0.7390 (mtmt) REVERT: A 393 MET cc_start: 0.7251 (ttm) cc_final: 0.6899 (ttm) REVERT: A 405 GLU cc_start: 0.7525 (tp30) cc_final: 0.7278 (tm-30) REVERT: A 427 MET cc_start: 0.7615 (ttm) cc_final: 0.7231 (ttm) REVERT: A 443 ARG cc_start: 0.6893 (ttt-90) cc_final: 0.6374 (ttt-90) REVERT: A 453 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7509 (mm-30) REVERT: A 487 ASP cc_start: 0.8365 (m-30) cc_final: 0.8087 (m-30) REVERT: A 537 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7655 (tm-30) REVERT: A 579 ARG cc_start: 0.6382 (mtt180) cc_final: 0.6063 (mtt90) REVERT: A 586 THR cc_start: 0.8023 (t) cc_final: 0.7706 (p) REVERT: A 593 SER cc_start: 0.7919 (m) cc_final: 0.7583 (p) REVERT: A 607 TRP cc_start: 0.8155 (t-100) cc_final: 0.7653 (t60) REVERT: A 758 ASN cc_start: 0.7925 (m-40) cc_final: 0.7476 (t0) REVERT: A 769 ASP cc_start: 0.7480 (p0) cc_final: 0.6985 (p0) REVERT: A 806 LYS cc_start: 0.7931 (mmmm) cc_final: 0.7636 (mmmm) REVERT: A 812 MET cc_start: 0.7434 (mpp) cc_final: 0.7232 (mpp) REVERT: A 816 LEU cc_start: 0.8471 (tp) cc_final: 0.8077 (tp) REVERT: A 821 LEU cc_start: 0.8360 (mt) cc_final: 0.8139 (mt) REVERT: A 823 ARG cc_start: 0.7730 (tmt170) cc_final: 0.7196 (tmt170) REVERT: A 827 ARG cc_start: 0.7340 (ttp80) cc_final: 0.6788 (ttp80) REVERT: A 877 MET cc_start: 0.7161 (mmm) cc_final: 0.6759 (tpp) REVERT: A 893 SER cc_start: 0.7293 (t) cc_final: 0.6679 (p) REVERT: A 919 MET cc_start: 0.7518 (mtt) cc_final: 0.7186 (mpp) REVERT: A 922 GLN cc_start: 0.7291 (tt0) cc_final: 0.6425 (tp-100) REVERT: A 934 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8152 (mmtt) REVERT: A 981 LYS cc_start: 0.8249 (tttt) cc_final: 0.7699 (tppt) REVERT: A 1057 MET cc_start: 0.7796 (ppp) cc_final: 0.7596 (ppp) REVERT: A 1060 LYS cc_start: 0.8142 (tptp) cc_final: 0.7668 (tptp) REVERT: A 1093 MET cc_start: 0.6843 (pmm) cc_final: 0.6561 (pmm) REVERT: A 1109 LEU cc_start: 0.8791 (tp) cc_final: 0.8578 (tt) REVERT: A 1110 HIS cc_start: 0.8483 (m90) cc_final: 0.8193 (m-70) REVERT: A 1111 LEU cc_start: 0.8579 (mt) cc_final: 0.8275 (mt) REVERT: A 1112 MET cc_start: 0.8398 (mtm) cc_final: 0.8028 (mtp) REVERT: A 1113 LEU cc_start: 0.8552 (mp) cc_final: 0.8223 (mm) REVERT: A 1116 MET cc_start: 0.7194 (tpt) cc_final: 0.6423 (tpt) REVERT: A 1137 VAL cc_start: 0.8279 (t) cc_final: 0.7767 (p) REVERT: A 1148 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7451 (ttm-80) REVERT: A 1219 ASP cc_start: 0.8059 (t70) cc_final: 0.7553 (t70) REVERT: A 1222 GLN cc_start: 0.8491 (mp10) cc_final: 0.7780 (mp10) REVERT: B 77 HIS cc_start: 0.6987 (m-70) cc_final: 0.6764 (m170) REVERT: B 83 LYS cc_start: 0.8708 (ptmt) cc_final: 0.8443 (ptpp) REVERT: B 85 GLN cc_start: 0.7457 (mt0) cc_final: 0.6950 (mt0) REVERT: B 88 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7725 (ptp90) REVERT: B 108 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7818 (ttmm) REVERT: B 113 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6740 (mm-30) REVERT: B 123 GLU cc_start: 0.7519 (pt0) cc_final: 0.7175 (pt0) REVERT: B 134 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7890 (mtmt) REVERT: B 180 LYS cc_start: 0.8308 (ptmt) cc_final: 0.7608 (ptmt) REVERT: B 183 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6924 (mt-10) REVERT: B 191 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7262 (mt-10) REVERT: B 192 HIS cc_start: 0.8125 (m90) cc_final: 0.7648 (m-70) REVERT: B 201 ASN cc_start: 0.7858 (m110) cc_final: 0.7505 (m110) REVERT: B 210 GLN cc_start: 0.7662 (tt0) cc_final: 0.7315 (tt0) REVERT: B 288 LYS cc_start: 0.7128 (mttt) cc_final: 0.6462 (mtpt) REVERT: B 289 LEU cc_start: 0.7871 (mt) cc_final: 0.7567 (mt) REVERT: B 304 TRP cc_start: 0.7849 (m100) cc_final: 0.7479 (m100) REVERT: B 310 GLU cc_start: 0.7565 (mp0) cc_final: 0.7180 (mp0) REVERT: B 311 LEU cc_start: 0.8121 (tp) cc_final: 0.6855 (tp) REVERT: B 314 MET cc_start: 0.6728 (ppp) cc_final: 0.6291 (ppp) REVERT: B 315 TYR cc_start: 0.7891 (m-80) cc_final: 0.7644 (m-80) REVERT: B 339 ASN cc_start: 0.7025 (t0) cc_final: 0.6312 (t0) REVERT: B 352 ASP cc_start: 0.7256 (t0) cc_final: 0.6916 (t0) REVERT: B 353 SER cc_start: 0.8230 (p) cc_final: 0.7998 (p) REVERT: B 378 LEU cc_start: 0.8385 (mp) cc_final: 0.8080 (mt) REVERT: B 396 ARG cc_start: 0.7552 (ttm170) cc_final: 0.7150 (ttm110) REVERT: B 400 GLN cc_start: 0.7677 (tt0) cc_final: 0.7404 (tp40) REVERT: B 407 LEU cc_start: 0.8003 (mt) cc_final: 0.7777 (mm) REVERT: B 412 SER cc_start: 0.8263 (t) cc_final: 0.7742 (p) REVERT: B 427 GLN cc_start: 0.8353 (pt0) cc_final: 0.7524 (pm20) REVERT: B 431 LYS cc_start: 0.8361 (tttt) cc_final: 0.7929 (tppt) REVERT: B 446 THR cc_start: 0.8315 (m) cc_final: 0.7959 (m) REVERT: B 449 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 457 SER cc_start: 0.7914 (t) cc_final: 0.7604 (p) REVERT: B 460 THR cc_start: 0.8483 (p) cc_final: 0.8114 (p) REVERT: B 462 MET cc_start: 0.7828 (mmt) cc_final: 0.7588 (mmt) REVERT: B 465 MET cc_start: 0.7548 (mtm) cc_final: 0.7087 (mtm) REVERT: B 466 MET cc_start: 0.7345 (mtp) cc_final: 0.6928 (ttp) REVERT: B 467 HIS cc_start: 0.8118 (t-90) cc_final: 0.7857 (t70) REVERT: C 71 GLU cc_start: 0.8349 (tt0) cc_final: 0.8110 (tt0) REVERT: C 75 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7656 (mtp85) REVERT: C 80 SER cc_start: 0.8490 (t) cc_final: 0.8019 (m) REVERT: C 107 ARG cc_start: 0.7462 (ttm170) cc_final: 0.7198 (ttp80) REVERT: C 183 GLU cc_start: 0.6533 (mt-10) cc_final: 0.6298 (mt-10) REVERT: C 185 LEU cc_start: 0.8912 (mt) cc_final: 0.8589 (mt) REVERT: C 233 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6405 (mp0) REVERT: C 235 THR cc_start: 0.7037 (p) cc_final: 0.6482 (p) REVERT: C 243 THR cc_start: 0.7831 (t) cc_final: 0.7516 (p) REVERT: C 259 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7344 (mtp85) REVERT: C 262 TRP cc_start: 0.7847 (t60) cc_final: 0.7135 (t60) REVERT: C 291 TYR cc_start: 0.8170 (t80) cc_final: 0.7887 (t80) REVERT: C 297 LYS cc_start: 0.7869 (mttp) cc_final: 0.7635 (mttp) REVERT: C 301 GLU cc_start: 0.7326 (tt0) cc_final: 0.6692 (tt0) REVERT: C 305 ASN cc_start: 0.7555 (t0) cc_final: 0.7300 (t0) REVERT: C 306 LEU cc_start: 0.8330 (mt) cc_final: 0.7945 (mm) REVERT: C 328 ARG cc_start: 0.7517 (mtt-85) cc_final: 0.7274 (mtt-85) REVERT: C 336 LEU cc_start: 0.8370 (mt) cc_final: 0.7967 (mt) REVERT: C 343 ASP cc_start: 0.6871 (m-30) cc_final: 0.6660 (m-30) REVERT: C 346 MET cc_start: 0.6986 (tmm) cc_final: 0.6586 (tmm) REVERT: C 371 VAL cc_start: 0.8229 (p) cc_final: 0.7973 (m) REVERT: C 373 LYS cc_start: 0.8276 (mttt) cc_final: 0.7602 (ptpp) REVERT: C 396 ARG cc_start: 0.7798 (ttm170) cc_final: 0.6816 (ttm170) REVERT: C 400 GLN cc_start: 0.7786 (mt0) cc_final: 0.7168 (mt0) REVERT: C 405 GLU cc_start: 0.7311 (tt0) cc_final: 0.7096 (tt0) REVERT: C 415 PRO cc_start: 0.8678 (Cg_endo) cc_final: 0.8449 (Cg_exo) REVERT: C 430 SER cc_start: 0.8457 (t) cc_final: 0.7919 (p) REVERT: C 431 LYS cc_start: 0.8390 (tttt) cc_final: 0.8159 (tttt) REVERT: C 434 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 466 MET cc_start: 0.6966 (ttm) cc_final: 0.6660 (ttm) REVERT: C 470 LYS cc_start: 0.8555 (mttt) cc_final: 0.8153 (mttt) outliers start: 0 outliers final: 0 residues processed: 571 average time/residue: 0.1197 time to fit residues: 98.3444 Evaluate side-chains 531 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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: 5.9990 chunk 110 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 201 ASN B 305 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.088530 restraints weight = 90573.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094356 restraints weight = 33198.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098219 restraints weight = 17112.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100880 restraints weight = 10487.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102619 restraints weight = 7269.449| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 16209 Z= 0.342 Angle : 0.683 10.411 22166 Z= 0.368 Chirality : 0.048 0.185 2406 Planarity : 0.005 0.061 2692 Dihedral : 14.976 88.887 2496 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.19 % Allowed : 2.07 % Favored : 97.75 % 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 aren not related in a simple way. whole: 0.22 (0.20), residues: 1837 helix: 1.22 (0.18), residues: 785 sheet: -0.18 (0.33), residues: 251 loop : -0.78 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 275 TYR 0.023 0.002 TYR B 315 PHE 0.029 0.003 PHE C 474 TRP 0.027 0.003 TRP A 572 HIS 0.009 0.002 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00685 (16209) covalent geometry : angle 0.68288 (22166) hydrogen bonds : bond 0.05357 ( 767) hydrogen bonds : angle 5.32667 ( 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 571 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 570 time to evaluate : 0.327 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: A 76 ILE cc_start: 0.8455 (mm) cc_final: 0.8247 (mm) REVERT: A 145 LYS cc_start: 0.8225 (tptp) cc_final: 0.7679 (tptp) REVERT: A 159 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6753 (pp30) REVERT: A 193 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6802 (ttp-170) REVERT: A 213 VAL cc_start: 0.7959 (m) cc_final: 0.7549 (p) REVERT: A 264 GLN cc_start: 0.7934 (pt0) cc_final: 0.7706 (pm20) REVERT: A 280 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 295 MET cc_start: 0.7617 (ttp) cc_final: 0.7136 (ttm) REVERT: A 304 LEU cc_start: 0.8368 (mt) cc_final: 0.7359 (mt) REVERT: A 308 GLN cc_start: 0.7845 (mt0) cc_final: 0.7553 (tt0) REVERT: A 354 ASN cc_start: 0.7762 (m-40) cc_final: 0.7375 (m-40) REVERT: A 355 SER cc_start: 0.7775 (t) cc_final: 0.7288 (t) REVERT: A 358 GLU cc_start: 0.7646 (mp0) cc_final: 0.7015 (mp0) REVERT: A 375 GLU cc_start: 0.7390 (pt0) cc_final: 0.6999 (pm20) REVERT: A 379 LYS cc_start: 0.7801 (ptpp) cc_final: 0.7450 (mtmt) REVERT: A 393 MET cc_start: 0.7197 (ttm) cc_final: 0.6878 (ttm) REVERT: A 405 GLU cc_start: 0.7641 (tp30) cc_final: 0.7281 (tm-30) REVERT: A 443 ARG cc_start: 0.6935 (ttt-90) cc_final: 0.6421 (ttt-90) REVERT: A 453 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7484 (mm-30) REVERT: A 484 TRP cc_start: 0.8167 (m-90) cc_final: 0.7550 (m-90) REVERT: A 487 ASP cc_start: 0.8341 (m-30) cc_final: 0.8087 (m-30) REVERT: A 537 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7746 (tm-30) REVERT: A 564 GLN cc_start: 0.7382 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 565 HIS cc_start: 0.7511 (t70) cc_final: 0.7268 (t70) REVERT: A 586 THR cc_start: 0.7953 (t) cc_final: 0.7659 (p) REVERT: A 593 SER cc_start: 0.7894 (m) cc_final: 0.7584 (p) REVERT: A 607 TRP cc_start: 0.8162 (t-100) cc_final: 0.7642 (t60) REVERT: A 758 ASN cc_start: 0.8035 (m-40) cc_final: 0.7540 (t0) REVERT: A 812 MET cc_start: 0.7550 (mpp) cc_final: 0.7255 (mpp) REVERT: A 816 LEU cc_start: 0.8475 (tp) cc_final: 0.8140 (tp) REVERT: A 821 LEU cc_start: 0.8454 (mt) cc_final: 0.8187 (mt) REVERT: A 823 ARG cc_start: 0.7803 (tmt170) cc_final: 0.7558 (tmt170) REVERT: A 832 ASP cc_start: 0.8077 (t0) cc_final: 0.7767 (t0) REVERT: A 877 MET cc_start: 0.7148 (mmm) cc_final: 0.6859 (mmm) REVERT: A 890 ASP cc_start: 0.7029 (t0) cc_final: 0.6789 (t0) REVERT: A 893 SER cc_start: 0.7402 (t) cc_final: 0.6807 (p) REVERT: A 906 HIS cc_start: 0.8332 (t70) cc_final: 0.8125 (t-90) REVERT: A 919 MET cc_start: 0.7684 (mtt) cc_final: 0.7335 (mpp) REVERT: A 922 GLN cc_start: 0.7258 (tt0) cc_final: 0.6527 (tp-100) REVERT: A 934 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8209 (mmtt) REVERT: A 981 LYS cc_start: 0.8199 (tttt) cc_final: 0.7708 (tppt) REVERT: A 1057 MET cc_start: 0.7807 (ppp) cc_final: 0.7587 (ppp) REVERT: A 1060 LYS cc_start: 0.8092 (tptp) cc_final: 0.7677 (tptp) REVERT: A 1074 VAL cc_start: 0.8617 (m) cc_final: 0.8317 (t) REVERT: A 1093 MET cc_start: 0.7057 (pmm) cc_final: 0.6713 (pmm) REVERT: A 1107 ASP cc_start: 0.7149 (m-30) cc_final: 0.6709 (t0) REVERT: A 1110 HIS cc_start: 0.8480 (m90) cc_final: 0.8199 (m-70) REVERT: A 1111 LEU cc_start: 0.8724 (mt) cc_final: 0.8454 (mt) REVERT: A 1112 MET cc_start: 0.8438 (mtm) cc_final: 0.8136 (mtp) REVERT: A 1116 MET cc_start: 0.7307 (tpt) cc_final: 0.6536 (tpt) REVERT: A 1137 VAL cc_start: 0.8371 (t) cc_final: 0.7951 (p) REVERT: A 1163 MET cc_start: 0.7874 (tpp) cc_final: 0.7461 (tpp) REVERT: A 1219 ASP cc_start: 0.8106 (t70) cc_final: 0.7480 (t0) REVERT: A 1222 GLN cc_start: 0.8482 (mp10) cc_final: 0.7750 (mp10) REVERT: B 83 LYS cc_start: 0.8731 (ptmt) cc_final: 0.8482 (ptpp) REVERT: B 85 GLN cc_start: 0.7487 (mt0) cc_final: 0.6927 (mt0) REVERT: B 88 ARG cc_start: 0.8087 (ptp-170) cc_final: 0.7699 (ptp90) REVERT: B 108 LYS cc_start: 0.8288 (ttmm) cc_final: 0.8053 (ttmm) REVERT: B 113 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6762 (mm-30) REVERT: B 123 GLU cc_start: 0.7532 (pt0) cc_final: 0.7278 (pt0) REVERT: B 134 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8001 (mtpt) REVERT: B 180 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7903 (ptmt) REVERT: B 183 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6965 (mt-10) REVERT: B 191 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7235 (mt-10) REVERT: B 192 HIS cc_start: 0.8202 (m90) cc_final: 0.7809 (m-70) REVERT: B 236 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7320 (mt-10) REVERT: B 246 ARG cc_start: 0.7965 (ttp-110) cc_final: 0.7711 (ttp80) REVERT: B 257 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7335 (mtp85) REVERT: B 262 TRP cc_start: 0.7992 (t60) cc_final: 0.6746 (t60) REVERT: B 263 TRP cc_start: 0.7857 (m100) cc_final: 0.6905 (m100) REVERT: B 288 LYS cc_start: 0.6997 (mttt) cc_final: 0.6336 (mtpt) REVERT: B 289 LEU cc_start: 0.7885 (mt) cc_final: 0.7580 (mt) REVERT: B 310 GLU cc_start: 0.7545 (mp0) cc_final: 0.7202 (mp0) REVERT: B 314 MET cc_start: 0.6698 (ppp) cc_final: 0.6313 (ppp) REVERT: B 315 TYR cc_start: 0.7878 (m-80) cc_final: 0.7669 (m-80) REVERT: B 339 ASN cc_start: 0.7218 (t0) cc_final: 0.6068 (t0) REVERT: B 352 ASP cc_start: 0.7389 (t0) cc_final: 0.7026 (t0) REVERT: B 353 SER cc_start: 0.8359 (p) cc_final: 0.8100 (p) REVERT: B 378 LEU cc_start: 0.8419 (mp) cc_final: 0.8118 (mt) REVERT: B 396 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7210 (ttm110) REVERT: B 400 GLN cc_start: 0.7714 (tt0) cc_final: 0.7490 (tp40) REVERT: B 412 SER cc_start: 0.8248 (t) cc_final: 0.7832 (p) REVERT: B 427 GLN cc_start: 0.8327 (pt0) cc_final: 0.7501 (pm20) REVERT: B 431 LYS cc_start: 0.8430 (tttt) cc_final: 0.8030 (tppt) REVERT: B 449 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 457 SER cc_start: 0.7829 (t) cc_final: 0.7401 (p) REVERT: B 460 THR cc_start: 0.8575 (p) cc_final: 0.8108 (p) REVERT: B 461 THR cc_start: 0.8245 (p) cc_final: 0.7942 (t) REVERT: B 465 MET cc_start: 0.7500 (mtm) cc_final: 0.7121 (mtm) REVERT: B 466 MET cc_start: 0.7462 (mtp) cc_final: 0.6956 (ttp) REVERT: C 75 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7593 (mtp85) REVERT: C 80 SER cc_start: 0.8530 (t) cc_final: 0.7949 (p) REVERT: C 89 ASP cc_start: 0.8004 (m-30) cc_final: 0.7697 (m-30) REVERT: C 183 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6225 (mt-10) REVERT: C 185 LEU cc_start: 0.8895 (mt) cc_final: 0.8610 (mt) REVERT: C 203 ARG cc_start: 0.7430 (ttt180) cc_final: 0.7205 (ttt180) REVERT: C 210 GLN cc_start: 0.7737 (tt0) cc_final: 0.7165 (tt0) REVERT: C 233 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6243 (mp0) REVERT: C 234 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7534 (mtmm) REVERT: C 242 PHE cc_start: 0.6970 (m-10) cc_final: 0.6730 (m-10) REVERT: C 243 THR cc_start: 0.7929 (t) cc_final: 0.7660 (p) REVERT: C 262 TRP cc_start: 0.7888 (t60) cc_final: 0.7329 (t60) REVERT: C 272 ASN cc_start: 0.7837 (m110) cc_final: 0.7522 (t0) REVERT: C 273 PHE cc_start: 0.7425 (m-80) cc_final: 0.7200 (m-10) REVERT: C 280 ASP cc_start: 0.6663 (p0) cc_final: 0.6382 (p0) REVERT: C 287 ASN cc_start: 0.7743 (t0) cc_final: 0.7117 (t0) REVERT: C 291 TYR cc_start: 0.8275 (t80) cc_final: 0.7167 (t80) REVERT: C 297 LYS cc_start: 0.7838 (mttp) cc_final: 0.7516 (mttp) REVERT: C 299 LEU cc_start: 0.8623 (tp) cc_final: 0.8314 (tt) REVERT: C 301 GLU cc_start: 0.7331 (tt0) cc_final: 0.6683 (tt0) REVERT: C 305 ASN cc_start: 0.7555 (t0) cc_final: 0.7342 (t0) REVERT: C 306 LEU cc_start: 0.8387 (mt) cc_final: 0.7959 (mm) REVERT: C 336 LEU cc_start: 0.8370 (mt) cc_final: 0.8003 (mt) REVERT: C 346 MET cc_start: 0.7175 (tmm) cc_final: 0.6758 (tmm) REVERT: C 371 VAL cc_start: 0.8224 (p) cc_final: 0.7991 (m) REVERT: C 372 LEU cc_start: 0.8544 (mt) cc_final: 0.8336 (tp) REVERT: C 373 LYS cc_start: 0.8244 (mttt) cc_final: 0.7633 (ptpp) REVERT: C 400 GLN cc_start: 0.7814 (mt0) cc_final: 0.7237 (mt0) REVERT: C 427 GLN cc_start: 0.8510 (tt0) cc_final: 0.8067 (tt0) REVERT: C 430 SER cc_start: 0.8501 (t) cc_final: 0.8062 (p) REVERT: C 431 LYS cc_start: 0.8400 (tttt) cc_final: 0.8193 (tttt) REVERT: C 434 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7764 (mt-10) REVERT: C 437 ILE cc_start: 0.7767 (mt) cc_final: 0.7554 (mt) REVERT: C 466 MET cc_start: 0.6956 (ttm) cc_final: 0.6707 (ttm) REVERT: C 470 LYS cc_start: 0.8650 (mttt) cc_final: 0.8193 (mttt) REVERT: C 471 LEU cc_start: 0.8240 (tp) cc_final: 0.8017 (tt) REVERT: C 478 TYR cc_start: 0.8111 (t80) cc_final: 0.7866 (t80) outliers start: 1 outliers final: 0 residues processed: 570 average time/residue: 0.1205 time to fit residues: 98.3345 Evaluate side-chains 536 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 3.9990 chunk 129 optimal weight: 0.0470 chunk 44 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 77 optimal weight: 0.0370 chunk 89 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 277 HIS A 398 GLN A 410 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.094543 restraints weight = 67006.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100063 restraints weight = 27088.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103698 restraints weight = 14478.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106117 restraints weight = 9086.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107722 restraints weight = 6403.829| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 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 = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16209 Z= 0.121 Angle : 0.561 9.724 22166 Z= 0.293 Chirality : 0.041 0.182 2406 Planarity : 0.005 0.053 2692 Dihedral : 14.655 89.650 2496 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.13 % Allowed : 1.06 % Favored : 98.81 % 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 aren not related in a simple way. whole: 0.79 (0.20), residues: 1837 helix: 1.71 (0.19), residues: 785 sheet: 0.11 (0.33), residues: 249 loop : -0.49 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1071 TYR 0.025 0.002 TYR A 233 PHE 0.019 0.002 PHE C 474 TRP 0.039 0.002 TRP A 486 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00260 (16209) covalent geometry : angle 0.56052 (22166) hydrogen bonds : bond 0.03690 ( 767) hydrogen bonds : angle 4.69328 ( 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 576 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 0.555 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: 0.8430 (mm) cc_final: 0.8186 (mm) REVERT: A 79 LEU cc_start: 0.8097 (mt) cc_final: 0.7862 (mp) REVERT: A 159 GLN cc_start: 0.7133 (tm-30) cc_final: 0.6602 (pp30) REVERT: A 193 ARG cc_start: 0.7317 (ttp-110) cc_final: 0.6859 (ptm160) REVERT: A 280 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6991 (mm-30) REVERT: A 289 MET cc_start: 0.7189 (ttm) cc_final: 0.6342 (ttm) REVERT: A 354 ASN cc_start: 0.7571 (m-40) cc_final: 0.7220 (m-40) REVERT: A 355 SER cc_start: 0.7496 (t) cc_final: 0.7236 (t) REVERT: A 358 GLU cc_start: 0.7608 (mp0) cc_final: 0.7275 (mp0) REVERT: A 393 MET cc_start: 0.7302 (ttm) cc_final: 0.6947 (ttm) REVERT: A 405 GLU cc_start: 0.7560 (tp30) cc_final: 0.7007 (tm-30) REVERT: A 438 ASN cc_start: 0.7755 (p0) cc_final: 0.7468 (p0) REVERT: A 443 ARG cc_start: 0.6875 (ttt-90) cc_final: 0.6299 (ttt-90) REVERT: A 453 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7469 (mm-30) REVERT: A 552 LEU cc_start: 0.8937 (mm) cc_final: 0.8735 (mt) REVERT: A 564 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6622 (tm-30) REVERT: A 565 HIS cc_start: 0.7469 (t70) cc_final: 0.7249 (t70) REVERT: A 586 THR cc_start: 0.8100 (t) cc_final: 0.7820 (p) REVERT: A 593 SER cc_start: 0.7973 (m) cc_final: 0.7616 (p) REVERT: A 607 TRP cc_start: 0.8162 (t-100) cc_final: 0.7656 (t60) REVERT: A 751 LYS cc_start: 0.7398 (ttmt) cc_final: 0.7189 (tttm) REVERT: A 758 ASN cc_start: 0.7972 (m-40) cc_final: 0.7379 (t0) REVERT: A 806 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7651 (mmmm) REVERT: A 812 MET cc_start: 0.7454 (mpp) cc_final: 0.7183 (mpp) REVERT: A 816 LEU cc_start: 0.8444 (tp) cc_final: 0.8184 (tp) REVERT: A 821 LEU cc_start: 0.8311 (mt) cc_final: 0.8053 (mt) REVERT: A 823 ARG cc_start: 0.7688 (tmt170) cc_final: 0.7440 (tmt170) REVERT: A 832 ASP cc_start: 0.8050 (t0) cc_final: 0.7314 (t0) REVERT: A 870 VAL cc_start: 0.8365 (m) cc_final: 0.8133 (p) REVERT: A 893 SER cc_start: 0.7169 (t) cc_final: 0.6840 (t) REVERT: A 906 HIS cc_start: 0.8233 (t70) cc_final: 0.8019 (t-90) REVERT: A 922 GLN cc_start: 0.7295 (tt0) cc_final: 0.6510 (tp-100) REVERT: A 981 LYS cc_start: 0.8230 (tttt) cc_final: 0.7659 (tppt) REVERT: A 1057 MET cc_start: 0.7887 (ppp) cc_final: 0.7618 (ppp) REVERT: A 1060 LYS cc_start: 0.8179 (tptp) cc_final: 0.7702 (tptp) REVERT: A 1074 VAL cc_start: 0.8556 (m) cc_final: 0.8178 (t) REVERT: A 1093 MET cc_start: 0.6732 (pmm) cc_final: 0.6156 (pmm) REVERT: A 1102 GLN cc_start: 0.7405 (mp10) cc_final: 0.6567 (mp10) REVERT: A 1110 HIS cc_start: 0.8465 (m90) cc_final: 0.8200 (m-70) REVERT: A 1111 LEU cc_start: 0.8578 (mt) cc_final: 0.8263 (mt) REVERT: A 1116 MET cc_start: 0.7175 (tpt) cc_final: 0.6458 (tpt) REVERT: A 1120 PHE cc_start: 0.7976 (m-80) cc_final: 0.7101 (m-80) REVERT: A 1156 THR cc_start: 0.7793 (m) cc_final: 0.7158 (m) REVERT: A 1222 GLN cc_start: 0.8476 (mp10) cc_final: 0.7784 (mp10) REVERT: B 71 GLU cc_start: 0.8053 (pp20) cc_final: 0.7734 (tm-30) REVERT: B 85 GLN cc_start: 0.7476 (mt0) cc_final: 0.6994 (mt0) REVERT: B 88 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7603 (ptp90) REVERT: B 108 LYS cc_start: 0.8204 (ttmm) cc_final: 0.8003 (ttmm) REVERT: B 123 GLU cc_start: 0.7582 (pt0) cc_final: 0.7213 (pt0) REVERT: B 134 LYS cc_start: 0.8411 (mtmt) cc_final: 0.7944 (mtmt) REVERT: B 180 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7528 (ptmt) REVERT: B 183 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6942 (mt-10) REVERT: B 191 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7181 (mt-10) REVERT: B 192 HIS cc_start: 0.8121 (m90) cc_final: 0.7614 (m-70) REVERT: B 246 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7757 (ttp80) REVERT: B 257 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7374 (mtp85) REVERT: B 288 LYS cc_start: 0.7136 (mttt) cc_final: 0.6473 (mtpt) REVERT: B 289 LEU cc_start: 0.7806 (mt) cc_final: 0.7456 (mt) REVERT: B 304 TRP cc_start: 0.7846 (m100) cc_final: 0.7474 (m100) REVERT: B 310 GLU cc_start: 0.7529 (mp0) cc_final: 0.7206 (mp0) REVERT: B 315 TYR cc_start: 0.7844 (m-80) cc_final: 0.7509 (m-80) REVERT: B 352 ASP cc_start: 0.7202 (t0) cc_final: 0.6887 (t0) REVERT: B 353 SER cc_start: 0.8158 (p) cc_final: 0.7955 (p) REVERT: B 369 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7243 (ttt90) REVERT: B 396 ARG cc_start: 0.7580 (ttm170) cc_final: 0.7156 (ttm110) REVERT: B 412 SER cc_start: 0.8233 (t) cc_final: 0.7734 (p) REVERT: B 431 LYS cc_start: 0.8305 (tttt) cc_final: 0.7831 (tppt) REVERT: B 446 THR cc_start: 0.8230 (m) cc_final: 0.7946 (m) REVERT: B 449 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7270 (mt-10) REVERT: B 457 SER cc_start: 0.7992 (t) cc_final: 0.7678 (p) REVERT: B 460 THR cc_start: 0.8449 (p) cc_final: 0.8160 (p) REVERT: B 463 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8255 (mtmt) REVERT: B 465 MET cc_start: 0.7487 (mtm) cc_final: 0.6962 (mtm) REVERT: B 466 MET cc_start: 0.7350 (mtp) cc_final: 0.6925 (ttp) REVERT: B 467 HIS cc_start: 0.8081 (t-90) cc_final: 0.7871 (t70) REVERT: C 71 GLU cc_start: 0.8312 (tt0) cc_final: 0.8076 (tt0) REVERT: C 75 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7643 (mtp85) REVERT: C 80 SER cc_start: 0.8465 (t) cc_final: 0.7979 (m) REVERT: C 107 ARG cc_start: 0.7377 (ttm170) cc_final: 0.7175 (ttp80) REVERT: C 183 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6277 (mt-10) REVERT: C 185 LEU cc_start: 0.8897 (mt) cc_final: 0.8539 (mt) REVERT: C 233 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6286 (mp0) REVERT: C 235 THR cc_start: 0.7012 (p) cc_final: 0.6479 (p) REVERT: C 259 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7347 (mtp85) REVERT: C 262 TRP cc_start: 0.7797 (t60) cc_final: 0.7215 (t60) REVERT: C 265 LYS cc_start: 0.8227 (tttt) cc_final: 0.7996 (tttt) REVERT: C 269 SER cc_start: 0.8023 (m) cc_final: 0.7760 (p) REVERT: C 287 ASN cc_start: 0.7711 (t0) cc_final: 0.7236 (t0) REVERT: C 297 LYS cc_start: 0.7931 (mttp) cc_final: 0.7598 (mttp) REVERT: C 301 GLU cc_start: 0.7256 (tt0) cc_final: 0.6607 (tt0) REVERT: C 305 ASN cc_start: 0.7503 (t0) cc_final: 0.7240 (t0) REVERT: C 306 LEU cc_start: 0.8327 (mt) cc_final: 0.7944 (mm) REVERT: C 336 LEU cc_start: 0.8353 (mt) cc_final: 0.7932 (mt) REVERT: C 343 ASP cc_start: 0.6823 (m-30) cc_final: 0.6579 (m-30) REVERT: C 344 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7694 (mtm-85) REVERT: C 347 LEU cc_start: 0.8246 (mm) cc_final: 0.7177 (mm) REVERT: C 371 VAL cc_start: 0.8154 (p) cc_final: 0.7940 (m) REVERT: C 373 LYS cc_start: 0.8194 (mttt) cc_final: 0.7474 (ptpp) REVERT: C 396 ARG cc_start: 0.7787 (ttm170) cc_final: 0.6804 (ttm170) REVERT: C 400 GLN cc_start: 0.7748 (mt0) cc_final: 0.6868 (mt0) REVERT: C 404 ASN cc_start: 0.7922 (m110) cc_final: 0.7461 (m110) REVERT: C 415 PRO cc_start: 0.8672 (Cg_endo) cc_final: 0.8438 (Cg_exo) REVERT: C 427 GLN cc_start: 0.8503 (tt0) cc_final: 0.7745 (tt0) REVERT: C 430 SER cc_start: 0.8386 (t) cc_final: 0.7852 (p) REVERT: C 431 LYS cc_start: 0.8361 (tttt) cc_final: 0.8140 (tttt) REVERT: C 434 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 466 MET cc_start: 0.6891 (ttm) cc_final: 0.6686 (ttm) REVERT: C 470 LYS cc_start: 0.8496 (mttt) cc_final: 0.8124 (mttt) REVERT: C 471 LEU cc_start: 0.8087 (tp) cc_final: 0.7871 (tt) REVERT: C 478 TYR cc_start: 0.8007 (t80) cc_final: 0.7785 (t80) outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.1265 time to fit residues: 103.5040 Evaluate side-chains 539 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 0.0770 chunk 72 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 398 GLN A 410 GLN A 468 ASN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 397 GLN B 409 ASN C 216 HIS C 272 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093936 restraints weight = 68190.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099450 restraints weight = 27307.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103089 restraints weight = 14591.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105511 restraints weight = 9138.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107140 restraints weight = 6428.720| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 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 = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16209 Z= 0.130 Angle : 0.578 13.757 22166 Z= 0.296 Chirality : 0.042 0.181 2406 Planarity : 0.004 0.055 2692 Dihedral : 14.542 89.578 2496 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.19 % Allowed : 0.88 % Favored : 98.94 % 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 aren not related in a simple way. whole: 0.87 (0.20), residues: 1837 helix: 1.80 (0.19), residues: 785 sheet: 0.10 (0.32), residues: 255 loop : -0.45 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 232 TYR 0.023 0.001 TYR B 315 PHE 0.021 0.002 PHE B 254 TRP 0.028 0.002 TRP A 486 HIS 0.010 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00280 (16209) covalent geometry : angle 0.57804 (22166) hydrogen bonds : bond 0.03693 ( 767) hydrogen bonds : angle 4.63470 ( 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 569 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 568 time to evaluate : 0.541 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: 0.8487 (mm) cc_final: 0.8238 (mm) REVERT: A 79 LEU cc_start: 0.8093 (mt) cc_final: 0.7831 (mp) REVERT: A 159 GLN cc_start: 0.7108 (tm-30) cc_final: 0.6563 (pp30) REVERT: A 193 ARG cc_start: 0.7306 (ttp-110) cc_final: 0.7095 (ttp-170) REVERT: A 197 PHE cc_start: 0.7331 (t80) cc_final: 0.6920 (t80) REVERT: A 213 VAL cc_start: 0.7589 (m) cc_final: 0.7323 (p) REVERT: A 280 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6970 (mm-30) REVERT: A 293 ASP cc_start: 0.5457 (t0) cc_final: 0.5198 (t0) REVERT: A 308 GLN cc_start: 0.7839 (mt0) cc_final: 0.7498 (mt0) REVERT: A 312 TRP cc_start: 0.8558 (t60) cc_final: 0.8347 (t60) REVERT: A 354 ASN cc_start: 0.7519 (m-40) cc_final: 0.7095 (m-40) REVERT: A 355 SER cc_start: 0.7491 (t) cc_final: 0.7226 (t) REVERT: A 358 GLU cc_start: 0.7623 (mp0) cc_final: 0.7299 (mp0) REVERT: A 393 MET cc_start: 0.7298 (ttm) cc_final: 0.6998 (ttm) REVERT: A 405 GLU cc_start: 0.7566 (tp30) cc_final: 0.7051 (tm-30) REVERT: A 410 GLN cc_start: 0.7668 (tt0) cc_final: 0.7043 (tt0) REVERT: A 443 ARG cc_start: 0.6868 (ttt-90) cc_final: 0.6278 (ttt-90) REVERT: A 445 LEU cc_start: 0.8020 (mm) cc_final: 0.7795 (mp) REVERT: A 453 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7462 (mm-30) REVERT: A 548 CYS cc_start: 0.8406 (t) cc_final: 0.8175 (t) REVERT: A 552 LEU cc_start: 0.8939 (mm) cc_final: 0.8728 (mt) REVERT: A 586 THR cc_start: 0.8158 (t) cc_final: 0.7860 (p) REVERT: A 593 SER cc_start: 0.7978 (m) cc_final: 0.7631 (p) REVERT: A 607 TRP cc_start: 0.8180 (t-100) cc_final: 0.7678 (t60) REVERT: A 751 LYS cc_start: 0.7452 (ttmt) cc_final: 0.7142 (tttt) REVERT: A 758 ASN cc_start: 0.7966 (m-40) cc_final: 0.7374 (t0) REVERT: A 796 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7682 (ttpt) REVERT: A 812 MET cc_start: 0.7399 (mpp) cc_final: 0.7146 (mpp) REVERT: A 816 LEU cc_start: 0.8449 (tp) cc_final: 0.8094 (tp) REVERT: A 823 ARG cc_start: 0.7709 (tmt170) cc_final: 0.7446 (tmt170) REVERT: A 832 ASP cc_start: 0.8048 (t0) cc_final: 0.7469 (t0) REVERT: A 875 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8024 (mtpp) REVERT: A 893 SER cc_start: 0.7154 (t) cc_final: 0.6805 (t) REVERT: A 906 HIS cc_start: 0.8242 (t70) cc_final: 0.8040 (t-90) REVERT: A 922 GLN cc_start: 0.7231 (tt0) cc_final: 0.6741 (tp40) REVERT: A 981 LYS cc_start: 0.8182 (tttt) cc_final: 0.7734 (tppt) REVERT: A 1057 MET cc_start: 0.7817 (ppp) cc_final: 0.7605 (ppp) REVERT: A 1060 LYS cc_start: 0.8203 (tptp) cc_final: 0.7734 (tptp) REVERT: A 1102 GLN cc_start: 0.7511 (mp10) cc_final: 0.6696 (mp10) REVERT: A 1110 HIS cc_start: 0.8501 (m90) cc_final: 0.8266 (m-70) REVERT: A 1116 MET cc_start: 0.7188 (tpt) cc_final: 0.6473 (tpt) REVERT: A 1120 PHE cc_start: 0.7944 (m-80) cc_final: 0.7107 (m-80) REVERT: A 1133 ILE cc_start: 0.6993 (mt) cc_final: 0.6348 (mt) REVERT: A 1136 GLU cc_start: 0.5904 (mt-10) cc_final: 0.5563 (mt-10) REVERT: A 1219 ASP cc_start: 0.8094 (t70) cc_final: 0.7577 (t0) REVERT: A 1222 GLN cc_start: 0.8464 (mp10) cc_final: 0.7748 (mp10) REVERT: B 71 GLU cc_start: 0.8061 (pp20) cc_final: 0.7746 (tm-30) REVERT: B 85 GLN cc_start: 0.7522 (mt0) cc_final: 0.7082 (mt0) REVERT: B 88 ARG cc_start: 0.7990 (ptp-170) cc_final: 0.7736 (ptp90) REVERT: B 123 GLU cc_start: 0.7525 (pt0) cc_final: 0.7180 (pt0) REVERT: B 134 LYS cc_start: 0.8433 (mtmt) cc_final: 0.7939 (mtmt) REVERT: B 180 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7500 (ptmt) REVERT: B 183 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6986 (mt-10) REVERT: B 191 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7253 (mt-10) REVERT: B 192 HIS cc_start: 0.8126 (m90) cc_final: 0.7887 (m90) REVERT: B 246 ARG cc_start: 0.8033 (ttp-110) cc_final: 0.7767 (ttp80) REVERT: B 288 LYS cc_start: 0.7135 (mttt) cc_final: 0.6494 (mtpt) REVERT: B 289 LEU cc_start: 0.7801 (mt) cc_final: 0.7467 (mt) REVERT: B 304 TRP cc_start: 0.7824 (m100) cc_final: 0.7477 (m100) REVERT: B 310 GLU cc_start: 0.7547 (mp0) cc_final: 0.7222 (mp0) REVERT: B 315 TYR cc_start: 0.7853 (m-80) cc_final: 0.7561 (m-80) REVERT: B 352 ASP cc_start: 0.7242 (t0) cc_final: 0.6914 (t0) REVERT: B 353 SER cc_start: 0.8209 (p) cc_final: 0.7985 (p) REVERT: B 396 ARG cc_start: 0.7505 (ttm170) cc_final: 0.7033 (ttm110) REVERT: B 397 GLN cc_start: 0.8159 (tp-100) cc_final: 0.6737 (tp-100) REVERT: B 412 SER cc_start: 0.8252 (t) cc_final: 0.7706 (p) REVERT: B 427 GLN cc_start: 0.8210 (pt0) cc_final: 0.7572 (pm20) REVERT: B 431 LYS cc_start: 0.8369 (tttt) cc_final: 0.7474 (tppt) REVERT: B 435 MET cc_start: 0.7068 (mtm) cc_final: 0.6652 (mtm) REVERT: B 449 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7286 (mt-10) REVERT: B 457 SER cc_start: 0.7910 (t) cc_final: 0.7578 (p) REVERT: B 460 THR cc_start: 0.8475 (p) cc_final: 0.8106 (p) REVERT: B 463 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8178 (mttp) REVERT: B 465 MET cc_start: 0.7407 (mtm) cc_final: 0.6966 (mpp) REVERT: B 466 MET cc_start: 0.7286 (mtp) cc_final: 0.6881 (ttp) REVERT: B 467 HIS cc_start: 0.8106 (t-90) cc_final: 0.7821 (t70) REVERT: C 75 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7619 (mtp85) REVERT: C 78 PHE cc_start: 0.7158 (m-80) cc_final: 0.6934 (m-80) REVERT: C 80 SER cc_start: 0.8475 (t) cc_final: 0.8017 (m) REVERT: C 107 ARG cc_start: 0.7382 (ttm170) cc_final: 0.7163 (ttp80) REVERT: C 183 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6320 (mt-10) REVERT: C 185 LEU cc_start: 0.8881 (mt) cc_final: 0.8589 (mt) REVERT: C 235 THR cc_start: 0.6999 (p) cc_final: 0.6513 (p) REVERT: C 259 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7345 (mtp85) REVERT: C 262 TRP cc_start: 0.7606 (t60) cc_final: 0.7018 (t60) REVERT: C 265 LYS cc_start: 0.8186 (tttt) cc_final: 0.7969 (tttt) REVERT: C 287 ASN cc_start: 0.7733 (t0) cc_final: 0.7196 (t0) REVERT: C 297 LYS cc_start: 0.7897 (mttp) cc_final: 0.7595 (mttp) REVERT: C 301 GLU cc_start: 0.7223 (tt0) cc_final: 0.6675 (tt0) REVERT: C 305 ASN cc_start: 0.7568 (t0) cc_final: 0.7302 (t0) REVERT: C 306 LEU cc_start: 0.8301 (mt) cc_final: 0.7910 (mm) REVERT: C 336 LEU cc_start: 0.8367 (mt) cc_final: 0.8013 (mt) REVERT: C 343 ASP cc_start: 0.6886 (m-30) cc_final: 0.6491 (m-30) REVERT: C 344 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7717 (mtm-85) REVERT: C 347 LEU cc_start: 0.8232 (mm) cc_final: 0.7211 (mm) REVERT: C 354 PHE cc_start: 0.7983 (t80) cc_final: 0.7503 (t80) REVERT: C 371 VAL cc_start: 0.8110 (p) cc_final: 0.7860 (m) REVERT: C 373 LYS cc_start: 0.8154 (mttt) cc_final: 0.7491 (ptpp) REVERT: C 396 ARG cc_start: 0.7753 (ttm170) cc_final: 0.6787 (ttm170) REVERT: C 400 GLN cc_start: 0.7753 (mt0) cc_final: 0.7203 (mt0) REVERT: C 415 PRO cc_start: 0.8673 (Cg_endo) cc_final: 0.8438 (Cg_exo) REVERT: C 426 GLU cc_start: 0.7544 (pp20) cc_final: 0.7316 (pp20) REVERT: C 427 GLN cc_start: 0.8438 (tt0) cc_final: 0.8034 (tt0) REVERT: C 430 SER cc_start: 0.8401 (t) cc_final: 0.7914 (p) REVERT: C 431 LYS cc_start: 0.8360 (tttt) cc_final: 0.8142 (tttt) REVERT: C 434 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 466 MET cc_start: 0.6915 (ttm) cc_final: 0.6689 (ttm) REVERT: C 470 LYS cc_start: 0.8533 (mttt) cc_final: 0.8137 (mttt) REVERT: C 478 TYR cc_start: 0.8006 (t80) cc_final: 0.7760 (t80) outliers start: 1 outliers final: 0 residues processed: 568 average time/residue: 0.1279 time to fit residues: 103.5501 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 : 0.517 ------------------------------------------------------------------------------- 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: 0.0060 chunk 165 optimal weight: 0.0070 chunk 7 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 170 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 398 GLN A 468 ASN A 472 GLN A1098 ASN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN B 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.122218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095740 restraints weight = 60766.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.101002 restraints weight = 25639.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104516 restraints weight = 13823.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106817 restraints weight = 8751.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108392 restraints weight = 6262.448| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 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 = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16209 Z= 0.117 Angle : 0.576 8.755 22166 Z= 0.297 Chirality : 0.041 0.184 2406 Planarity : 0.005 0.056 2692 Dihedral : 14.427 89.229 2496 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.13 % Allowed : 0.69 % Favored : 99.19 % 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 aren not related in a simple way. whole: 0.95 (0.20), residues: 1837 helix: 1.83 (0.19), residues: 786 sheet: 0.16 (0.32), residues: 257 loop : -0.40 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 126 TYR 0.024 0.002 TYR C 193 PHE 0.029 0.002 PHE A 139 TRP 0.029 0.002 TRP A 312 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00258 (16209) covalent geometry : angle 0.57635 (22166) hydrogen bonds : bond 0.03495 ( 767) hydrogen bonds : angle 4.52271 ( 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 565 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 565 time to evaluate : 0.543 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: A 76 ILE cc_start: 0.8504 (mm) cc_final: 0.8287 (mm) REVERT: A 79 LEU cc_start: 0.8108 (mt) cc_final: 0.7887 (mp) REVERT: A 159 GLN cc_start: 0.7057 (tm-30) cc_final: 0.6503 (pp30) REVERT: A 177 ARG cc_start: 0.8149 (ttt90) cc_final: 0.7758 (ttt90) REVERT: A 193 ARG cc_start: 0.7313 (ttp-110) cc_final: 0.7107 (ttp-170) REVERT: A 197 PHE cc_start: 0.7329 (t80) cc_final: 0.7012 (t80) REVERT: A 213 VAL cc_start: 0.7481 (m) cc_final: 0.7249 (p) REVERT: A 280 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6991 (mm-30) REVERT: A 299 MET cc_start: 0.7383 (tpt) cc_final: 0.7032 (tpt) REVERT: A 354 ASN cc_start: 0.7416 (m-40) cc_final: 0.6938 (m-40) REVERT: A 355 SER cc_start: 0.7361 (t) cc_final: 0.6902 (t) REVERT: A 358 GLU cc_start: 0.7675 (mp0) cc_final: 0.7158 (mp0) REVERT: A 393 MET cc_start: 0.7318 (ttm) cc_final: 0.7020 (ttm) REVERT: A 405 GLU cc_start: 0.7525 (tp30) cc_final: 0.7129 (tm-30) REVERT: A 410 GLN cc_start: 0.7485 (tt0) cc_final: 0.6935 (tt0) REVERT: A 441 TRP cc_start: 0.7481 (t-100) cc_final: 0.6458 (t-100) REVERT: A 443 ARG cc_start: 0.6687 (ttt-90) cc_final: 0.6191 (ttt-90) REVERT: A 453 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7457 (mm-30) REVERT: A 551 LYS cc_start: 0.8420 (tptp) cc_final: 0.8160 (ttmm) REVERT: A 552 LEU cc_start: 0.8919 (mm) cc_final: 0.8698 (mt) REVERT: A 586 THR cc_start: 0.8138 (t) cc_final: 0.7918 (p) REVERT: A 593 SER cc_start: 0.7973 (m) cc_final: 0.7183 (p) REVERT: A 607 TRP cc_start: 0.8145 (t-100) cc_final: 0.7677 (t60) REVERT: A 751 LYS cc_start: 0.7463 (ttmt) cc_final: 0.7180 (tttt) REVERT: A 758 ASN cc_start: 0.7974 (m-40) cc_final: 0.7363 (t0) REVERT: A 796 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7566 (ttmm) REVERT: A 812 MET cc_start: 0.7366 (mpp) cc_final: 0.7081 (mpp) REVERT: A 816 LEU cc_start: 0.8467 (tp) cc_final: 0.8089 (tp) REVERT: A 823 ARG cc_start: 0.7683 (tmt170) cc_final: 0.7437 (tmt170) REVERT: A 832 ASP cc_start: 0.8037 (t0) cc_final: 0.7256 (t0) REVERT: A 870 VAL cc_start: 0.8262 (m) cc_final: 0.8013 (p) REVERT: A 875 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7828 (mtpp) REVERT: A 877 MET cc_start: 0.6843 (tpt) cc_final: 0.5939 (tpp) REVERT: A 893 SER cc_start: 0.7107 (t) cc_final: 0.6754 (t) REVERT: A 906 HIS cc_start: 0.8249 (t70) cc_final: 0.8037 (t-90) REVERT: A 919 MET cc_start: 0.7609 (mtt) cc_final: 0.7276 (mpp) REVERT: A 922 GLN cc_start: 0.7269 (tt0) cc_final: 0.6763 (tp40) REVERT: A 981 LYS cc_start: 0.8208 (tttt) cc_final: 0.7721 (tppt) REVERT: A 1060 LYS cc_start: 0.8248 (tptp) cc_final: 0.7794 (tptp) REVERT: A 1110 HIS cc_start: 0.8506 (m90) cc_final: 0.8276 (m-70) REVERT: A 1116 MET cc_start: 0.7125 (tpt) cc_final: 0.6450 (tpt) REVERT: A 1120 PHE cc_start: 0.7939 (m-80) cc_final: 0.6965 (m-80) REVERT: A 1133 ILE cc_start: 0.6885 (mt) cc_final: 0.6379 (mt) REVERT: A 1136 GLU cc_start: 0.5915 (mt-10) cc_final: 0.5652 (mt-10) REVERT: A 1156 THR cc_start: 0.7871 (m) cc_final: 0.7108 (m) REVERT: A 1188 CYS cc_start: 0.8340 (p) cc_final: 0.7923 (p) REVERT: A 1192 GLU cc_start: 0.7770 (mp0) cc_final: 0.7183 (mp0) REVERT: A 1219 ASP cc_start: 0.8103 (t70) cc_final: 0.7835 (t0) REVERT: A 1222 GLN cc_start: 0.8461 (mp10) cc_final: 0.7795 (mp10) REVERT: B 77 HIS cc_start: 0.6887 (m90) cc_final: 0.6678 (m90) REVERT: B 85 GLN cc_start: 0.7524 (mt0) cc_final: 0.7168 (mt0) REVERT: B 88 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7742 (ptp90) REVERT: B 123 GLU cc_start: 0.7545 (pt0) cc_final: 0.7129 (pt0) REVERT: B 134 LYS cc_start: 0.8397 (mtmt) cc_final: 0.7967 (mtmt) REVERT: B 180 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7425 (ptmt) REVERT: B 183 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7018 (mt-10) REVERT: B 191 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 199 LEU cc_start: 0.8214 (tp) cc_final: 0.7873 (tp) REVERT: B 201 ASN cc_start: 0.7953 (t0) cc_final: 0.7735 (t0) REVERT: B 236 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6800 (mt-10) REVERT: B 246 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7797 (ttp80) REVERT: B 288 LYS cc_start: 0.7165 (mttt) cc_final: 0.6518 (mtpt) REVERT: B 289 LEU cc_start: 0.7791 (mt) cc_final: 0.7452 (mt) REVERT: B 304 TRP cc_start: 0.7799 (m100) cc_final: 0.7447 (m100) REVERT: B 310 GLU cc_start: 0.7552 (mp0) cc_final: 0.7254 (mp0) REVERT: B 315 TYR cc_start: 0.7867 (m-80) cc_final: 0.7580 (m-80) REVERT: B 352 ASP cc_start: 0.7155 (t0) cc_final: 0.6871 (t0) REVERT: B 353 SER cc_start: 0.8152 (p) cc_final: 0.7941 (p) REVERT: B 412 SER cc_start: 0.8274 (t) cc_final: 0.7732 (p) REVERT: B 426 GLU cc_start: 0.7796 (pm20) cc_final: 0.7484 (pp20) REVERT: B 427 GLN cc_start: 0.8202 (pt0) cc_final: 0.7696 (pm20) REVERT: B 431 LYS cc_start: 0.8302 (tttt) cc_final: 0.7767 (tppt) REVERT: B 449 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7223 (mt-10) REVERT: B 463 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8176 (mttp) REVERT: B 465 MET cc_start: 0.7337 (mtm) cc_final: 0.6880 (mpp) REVERT: B 466 MET cc_start: 0.7219 (mtp) cc_final: 0.6876 (ttp) REVERT: B 467 HIS cc_start: 0.8046 (t-90) cc_final: 0.7804 (t70) REVERT: C 80 SER cc_start: 0.8472 (t) cc_final: 0.8091 (m) REVERT: C 121 PHE cc_start: 0.7989 (m-80) cc_final: 0.7724 (m-10) REVERT: C 183 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6299 (mt-10) REVERT: C 185 LEU cc_start: 0.8913 (mt) cc_final: 0.8561 (mt) REVERT: C 190 LEU cc_start: 0.8689 (mt) cc_final: 0.8437 (mm) REVERT: C 235 THR cc_start: 0.7021 (p) cc_final: 0.6491 (p) REVERT: C 252 LEU cc_start: 0.7980 (tp) cc_final: 0.7775 (tp) REVERT: C 259 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7326 (mtp85) REVERT: C 262 TRP cc_start: 0.7594 (t60) cc_final: 0.7058 (t60) REVERT: C 272 ASN cc_start: 0.7637 (m110) cc_final: 0.7333 (t0) REVERT: C 297 LYS cc_start: 0.7915 (mttp) cc_final: 0.7487 (mttp) REVERT: C 301 GLU cc_start: 0.7285 (tt0) cc_final: 0.6721 (tt0) REVERT: C 305 ASN cc_start: 0.7537 (t0) cc_final: 0.7305 (t0) REVERT: C 306 LEU cc_start: 0.8245 (mt) cc_final: 0.7849 (mm) REVERT: C 336 LEU cc_start: 0.8415 (mt) cc_final: 0.8013 (mt) REVERT: C 344 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7736 (mtm-85) REVERT: C 347 LEU cc_start: 0.8315 (mm) cc_final: 0.7634 (mt) REVERT: C 354 PHE cc_start: 0.7930 (t80) cc_final: 0.7440 (t80) REVERT: C 373 LYS cc_start: 0.8151 (mttt) cc_final: 0.7486 (ptpp) REVERT: C 396 ARG cc_start: 0.7744 (ttm170) cc_final: 0.6716 (ttm170) REVERT: C 400 GLN cc_start: 0.7810 (mt0) cc_final: 0.7204 (mp10) REVERT: C 415 PRO cc_start: 0.8688 (Cg_endo) cc_final: 0.8474 (Cg_exo) REVERT: C 426 GLU cc_start: 0.7511 (pp20) cc_final: 0.7298 (pp20) REVERT: C 427 GLN cc_start: 0.8426 (tt0) cc_final: 0.8007 (tt0) REVERT: C 430 SER cc_start: 0.8371 (t) cc_final: 0.7874 (p) REVERT: C 431 LYS cc_start: 0.8342 (tttt) cc_final: 0.8137 (tttt) REVERT: C 434 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7494 (mt-10) REVERT: C 466 MET cc_start: 0.6888 (ttm) cc_final: 0.6648 (ttm) REVERT: C 470 LYS cc_start: 0.8492 (mttt) cc_final: 0.8131 (mttt) REVERT: C 471 LEU cc_start: 0.8129 (tp) cc_final: 0.7902 (tt) REVERT: C 478 TYR cc_start: 0.7982 (t80) cc_final: 0.7735 (t80) outliers start: 0 outliers final: 0 residues processed: 565 average time/residue: 0.1257 time to fit residues: 100.7006 Evaluate side-chains 528 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 2.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A 468 ASN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 210 GLN B 258 HIS B 305 ASN B 400 GLN B 404 ASN B 409 ASN C 216 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094026 restraints weight = 70378.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099538 restraints weight = 27943.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103160 restraints weight = 14883.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105548 restraints weight = 9333.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107195 restraints weight = 6591.155| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 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 = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16209 Z= 0.143 Angle : 0.594 12.847 22166 Z= 0.307 Chirality : 0.042 0.180 2406 Planarity : 0.005 0.052 2692 Dihedral : 14.413 89.248 2496 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.19 % Allowed : 0.63 % Favored : 99.19 % 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 aren not related in a simple way. whole: 0.94 (0.20), residues: 1837 helix: 1.83 (0.19), residues: 787 sheet: 0.25 (0.32), residues: 253 loop : -0.43 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 232 TYR 0.022 0.002 TYR B 315 PHE 0.031 0.002 PHE C 242 TRP 0.037 0.002 TRP A 572 HIS 0.006 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00304 (16209) covalent geometry : angle 0.59391 (22166) hydrogen bonds : bond 0.03711 ( 767) hydrogen bonds : angle 4.53718 ( 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 561 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 560 time to evaluate : 0.497 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 72 ASN cc_start: 0.7867 (p0) cc_final: 0.6686 (p0) REVERT: A 76 ILE cc_start: 0.8484 (mm) cc_final: 0.8109 (mm) REVERT: A 79 LEU cc_start: 0.8179 (mt) cc_final: 0.7886 (mp) REVERT: A 159 GLN cc_start: 0.7045 (tm-30) cc_final: 0.6478 (pp30) REVERT: A 177 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7747 (ttt90) REVERT: A 213 VAL cc_start: 0.7543 (m) cc_final: 0.7191 (p) REVERT: A 264 GLN cc_start: 0.7473 (pm20) cc_final: 0.7056 (pm20) REVERT: A 280 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7023 (mm-30) REVERT: A 289 MET cc_start: 0.6973 (ttm) cc_final: 0.6706 (ttm) REVERT: A 299 MET cc_start: 0.7402 (tpt) cc_final: 0.7018 (tpt) REVERT: A 308 GLN cc_start: 0.7832 (mt0) cc_final: 0.7504 (mt0) REVERT: A 354 ASN cc_start: 0.7455 (m-40) cc_final: 0.6959 (m-40) REVERT: A 355 SER cc_start: 0.7442 (t) cc_final: 0.6981 (t) REVERT: A 358 GLU cc_start: 0.7706 (mp0) cc_final: 0.7180 (mp0) REVERT: A 393 MET cc_start: 0.7303 (ttm) cc_final: 0.6990 (ttm) REVERT: A 405 GLU cc_start: 0.7484 (tp30) cc_final: 0.7071 (tm-30) REVERT: A 427 MET cc_start: 0.7637 (ttm) cc_final: 0.7251 (ttm) REVERT: A 441 TRP cc_start: 0.7576 (t-100) cc_final: 0.6565 (t-100) REVERT: A 443 ARG cc_start: 0.6797 (ttt-90) cc_final: 0.6270 (ttt-90) REVERT: A 445 LEU cc_start: 0.8097 (mp) cc_final: 0.7874 (mm) REVERT: A 453 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7450 (mm-30) REVERT: A 484 TRP cc_start: 0.8119 (m-90) cc_final: 0.7482 (m-90) REVERT: A 551 LYS cc_start: 0.8415 (tptp) cc_final: 0.8163 (ttmm) REVERT: A 552 LEU cc_start: 0.8928 (mm) cc_final: 0.8701 (mt) REVERT: A 586 THR cc_start: 0.8111 (t) cc_final: 0.7871 (p) REVERT: A 593 SER cc_start: 0.7860 (m) cc_final: 0.7479 (p) REVERT: A 596 MET cc_start: 0.6701 (mpp) cc_final: 0.6245 (mtm) REVERT: A 601 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7659 (mtmm) REVERT: A 607 TRP cc_start: 0.8157 (t-100) cc_final: 0.7660 (t60) REVERT: A 751 LYS cc_start: 0.7474 (ttmt) cc_final: 0.7151 (tttt) REVERT: A 758 ASN cc_start: 0.7965 (m-40) cc_final: 0.7410 (t0) REVERT: A 774 MET cc_start: 0.7369 (mmm) cc_final: 0.7109 (mmm) REVERT: A 797 MET cc_start: 0.7771 (mtt) cc_final: 0.7554 (ttm) REVERT: A 812 MET cc_start: 0.7373 (mpp) cc_final: 0.7086 (mpp) REVERT: A 816 LEU cc_start: 0.8499 (tp) cc_final: 0.8130 (tp) REVERT: A 823 ARG cc_start: 0.7712 (tmt170) cc_final: 0.7445 (tmt170) REVERT: A 832 ASP cc_start: 0.8054 (t0) cc_final: 0.7310 (t0) REVERT: A 875 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7828 (mtpp) REVERT: A 877 MET cc_start: 0.7094 (tpt) cc_final: 0.6016 (tpp) REVERT: A 890 ASP cc_start: 0.6892 (t0) cc_final: 0.6683 (t0) REVERT: A 893 SER cc_start: 0.7213 (t) cc_final: 0.6848 (t) REVERT: A 919 MET cc_start: 0.7486 (mtt) cc_final: 0.7208 (mpp) REVERT: A 922 GLN cc_start: 0.7241 (tt0) cc_final: 0.6762 (tp40) REVERT: A 934 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7859 (mmtt) REVERT: A 981 LYS cc_start: 0.8181 (tttt) cc_final: 0.7692 (tppt) REVERT: A 1060 LYS cc_start: 0.8259 (tptp) cc_final: 0.7826 (tptp) REVERT: A 1102 GLN cc_start: 0.7490 (mp10) cc_final: 0.6673 (mp10) REVERT: A 1110 HIS cc_start: 0.8457 (m90) cc_final: 0.8230 (m-70) REVERT: A 1111 LEU cc_start: 0.8378 (mt) cc_final: 0.8163 (mt) REVERT: A 1116 MET cc_start: 0.7133 (tpt) cc_final: 0.6462 (tpt) REVERT: A 1120 PHE cc_start: 0.7947 (m-80) cc_final: 0.7059 (m-80) REVERT: A 1136 GLU cc_start: 0.5932 (mt-10) cc_final: 0.5645 (mt-10) REVERT: A 1156 THR cc_start: 0.7885 (m) cc_final: 0.7167 (m) REVERT: A 1219 ASP cc_start: 0.8108 (t70) cc_final: 0.7573 (t0) REVERT: A 1222 GLN cc_start: 0.8469 (mp10) cc_final: 0.7797 (mp10) REVERT: B 71 GLU cc_start: 0.8030 (pp20) cc_final: 0.7701 (tm-30) REVERT: B 77 HIS cc_start: 0.6902 (m90) cc_final: 0.6642 (m90) REVERT: B 85 GLN cc_start: 0.7568 (mt0) cc_final: 0.7190 (mt0) REVERT: B 88 ARG cc_start: 0.7967 (ptp-170) cc_final: 0.7716 (ptp90) REVERT: B 113 GLU cc_start: 0.7262 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 123 GLU cc_start: 0.7492 (pt0) cc_final: 0.7128 (pt0) REVERT: B 134 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7965 (mtmt) REVERT: B 180 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7412 (ptmt) REVERT: B 183 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6984 (mt-10) REVERT: B 186 LEU cc_start: 0.8140 (tt) cc_final: 0.7889 (tt) REVERT: B 191 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7207 (mt-10) REVERT: B 192 HIS cc_start: 0.8162 (m90) cc_final: 0.7667 (m-70) REVERT: B 199 LEU cc_start: 0.8181 (tp) cc_final: 0.7966 (tp) REVERT: B 201 ASN cc_start: 0.7947 (t0) cc_final: 0.7703 (t0) REVERT: B 236 GLU cc_start: 0.7846 (mt-10) cc_final: 0.6691 (mt-10) REVERT: B 246 ARG cc_start: 0.8046 (ttp-110) cc_final: 0.7779 (ttp80) REVERT: B 288 LYS cc_start: 0.7158 (mttt) cc_final: 0.6509 (mtpt) REVERT: B 289 LEU cc_start: 0.7782 (mt) cc_final: 0.7474 (mt) REVERT: B 304 TRP cc_start: 0.7803 (m100) cc_final: 0.7441 (m100) REVERT: B 310 GLU cc_start: 0.7560 (mp0) cc_final: 0.7283 (mp0) REVERT: B 315 TYR cc_start: 0.7847 (m-80) cc_final: 0.7559 (m-80) REVERT: B 352 ASP cc_start: 0.7201 (t0) cc_final: 0.6879 (t0) REVERT: B 353 SER cc_start: 0.8246 (p) cc_final: 0.8040 (p) REVERT: B 412 SER cc_start: 0.8260 (t) cc_final: 0.7726 (p) REVERT: B 427 GLN cc_start: 0.8244 (pt0) cc_final: 0.7638 (pm20) REVERT: B 431 LYS cc_start: 0.8389 (tttt) cc_final: 0.7823 (tppt) REVERT: B 463 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8200 (mttp) REVERT: B 465 MET cc_start: 0.7361 (mtm) cc_final: 0.6908 (mpp) REVERT: B 466 MET cc_start: 0.7266 (mtp) cc_final: 0.6932 (ttp) REVERT: B 467 HIS cc_start: 0.8101 (t-90) cc_final: 0.7844 (t70) REVERT: C 67 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 69 LEU cc_start: 0.8530 (tt) cc_final: 0.8318 (tt) REVERT: C 75 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7512 (mtp85) REVERT: C 80 SER cc_start: 0.8486 (t) cc_final: 0.8003 (m) REVERT: C 121 PHE cc_start: 0.7993 (m-80) cc_final: 0.7768 (m-10) REVERT: C 183 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6307 (mt-10) REVERT: C 185 LEU cc_start: 0.8920 (mt) cc_final: 0.8583 (mt) REVERT: C 235 THR cc_start: 0.6912 (p) cc_final: 0.6640 (p) REVERT: C 259 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7260 (mtp85) REVERT: C 262 TRP cc_start: 0.7553 (t60) cc_final: 0.7054 (t60) REVERT: C 280 ASP cc_start: 0.6191 (p0) cc_final: 0.5457 (p0) REVERT: C 287 ASN cc_start: 0.7679 (t0) cc_final: 0.7328 (t0) REVERT: C 298 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6279 (mp0) REVERT: C 301 GLU cc_start: 0.7297 (tt0) cc_final: 0.6722 (tt0) REVERT: C 323 HIS cc_start: 0.6248 (m90) cc_final: 0.5907 (m90) REVERT: C 336 LEU cc_start: 0.8400 (mt) cc_final: 0.7992 (mt) REVERT: C 343 ASP cc_start: 0.6868 (m-30) cc_final: 0.6379 (m-30) REVERT: C 344 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7800 (mtm-85) REVERT: C 347 LEU cc_start: 0.8292 (mm) cc_final: 0.7373 (mm) REVERT: C 354 PHE cc_start: 0.7969 (t80) cc_final: 0.7493 (t80) REVERT: C 372 LEU cc_start: 0.8608 (tp) cc_final: 0.8364 (tp) REVERT: C 373 LYS cc_start: 0.8156 (mttt) cc_final: 0.7487 (ptpp) REVERT: C 396 ARG cc_start: 0.7735 (ttm170) cc_final: 0.6724 (ttm170) REVERT: C 400 GLN cc_start: 0.7760 (mt0) cc_final: 0.7125 (mp10) REVERT: C 415 PRO cc_start: 0.8679 (Cg_endo) cc_final: 0.8423 (Cg_exo) REVERT: C 426 GLU cc_start: 0.7541 (pp20) cc_final: 0.7320 (pp20) REVERT: C 427 GLN cc_start: 0.8417 (tt0) cc_final: 0.8002 (tt0) REVERT: C 430 SER cc_start: 0.8389 (t) cc_final: 0.7951 (p) REVERT: C 434 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7620 (mt-10) REVERT: C 466 MET cc_start: 0.6912 (ttm) cc_final: 0.6661 (ttm) REVERT: C 470 LYS cc_start: 0.8536 (mttt) cc_final: 0.8118 (mttt) REVERT: C 471 LEU cc_start: 0.8170 (tp) cc_final: 0.7942 (tt) REVERT: C 478 TYR cc_start: 0.7973 (t80) cc_final: 0.7711 (t80) outliers start: 1 outliers final: 0 residues processed: 560 average time/residue: 0.1308 time to fit residues: 103.8321 Evaluate side-chains 533 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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: 4.9990 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 398 GLN A 410 GLN A 468 ASN A 811 GLN A 906 HIS B 210 GLN B 400 GLN B 404 ASN C 216 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093546 restraints weight = 72885.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099080 restraints weight = 28674.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102761 restraints weight = 15096.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105222 restraints weight = 9366.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106775 restraints weight = 6597.700| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 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 = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16209 Z= 0.151 Angle : 0.595 10.426 22166 Z= 0.309 Chirality : 0.043 0.181 2406 Planarity : 0.004 0.051 2692 Dihedral : 14.405 89.512 2496 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 aren not related in a simple way. whole: 0.90 (0.20), residues: 1837 helix: 1.78 (0.19), residues: 796 sheet: 0.20 (0.32), residues: 257 loop : -0.46 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 232 TYR 0.022 0.002 TYR B 315 PHE 0.028 0.002 PHE C 242 TRP 0.034 0.002 TRP A 572 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00321 (16209) covalent geometry : angle 0.59499 (22166) hydrogen bonds : bond 0.03747 ( 767) hydrogen bonds : angle 4.54768 ( 2137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2992.75 seconds wall clock time: 52 minutes 12.00 seconds (3132.00 seconds total)