Starting phenix.real_space_refine on Sat Jun 14 02:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v54_42979/06_2025/8v54_42979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v54_42979/06_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_42979/06_2025/8v54_42979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v54_42979/06_2025/8v54_42979.map" model { file = "/net/cci-nas-00/data/ceres_data/8v54_42979/06_2025/8v54_42979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v54_42979/06_2025/8v54_42979.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG: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: 13.10, per 1000 atoms: 0.83 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: 4.23 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 6.12 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: 6.84 Time building geometry restraints manager: 4.93 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: 98.510 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 48.030 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.320 ------------------------------------------------------------------------------- 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 : 9.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (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 TRP 0.014 0.001 TRP A 859 HIS 0.004 0.001 HIS C 133 PHE 0.014 0.001 PHE C 403 TYR 0.010 0.001 TYR B 478 ARG 0.002 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.18405 ( 767) hydrogen bonds : angle 6.77645 ( 2137) covalent geometry : bond 0.00333 (16209) covalent geometry : angle 0.47523 (22166) *********************** 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 : 1.504 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: 0.3420 time to fit residues: 299.8262 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 : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 0.0060 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 46 optimal weight: 0.0970 chunk 92 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 A 277 HIS A 354 ASN A 388 ASN A 410 GLN A 497 GLN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094038 restraints weight = 75080.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099812 restraints weight = 29542.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103635 restraints weight = 15584.262| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16209 Z= 0.144 Angle : 0.575 10.881 22166 Z= 0.302 Chirality : 0.042 0.186 2406 Planarity : 0.005 0.055 2692 Dihedral : 14.703 89.254 2496 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1837 helix: 1.78 (0.19), residues: 794 sheet: 0.43 (0.33), residues: 247 loop : -0.23 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 486 HIS 0.012 0.001 HIS A 565 PHE 0.017 0.002 PHE A1120 TYR 0.039 0.002 TYR B 315 ARG 0.008 0.001 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 767) hydrogen bonds : angle 5.20917 ( 2137) covalent geometry : bond 0.00312 (16209) covalent geometry : angle 0.57481 (22166) *********************** 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 590 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 2.017 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: 0.8507 (mm) cc_final: 0.8192 (mm) REVERT: A 79 LEU cc_start: 0.8131 (mt) cc_final: 0.7868 (mp) REVERT: A 133 ASP cc_start: 0.6658 (p0) cc_final: 0.6396 (m-30) REVERT: A 136 ASP cc_start: 0.7727 (t70) cc_final: 0.7208 (t0) REVERT: A 145 LYS cc_start: 0.8126 (tptp) cc_final: 0.7684 (tptp) REVERT: A 159 GLN cc_start: 0.7131 (tm-30) cc_final: 0.6607 (pp30) REVERT: A 205 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 280 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7101 (mm-30) REVERT: A 289 MET cc_start: 0.7348 (ttm) cc_final: 0.6695 (ttm) REVERT: A 290 ARG cc_start: 0.7531 (mmt-90) cc_final: 0.7315 (mmp80) REVERT: A 295 MET cc_start: 0.7367 (ttt) cc_final: 0.6761 (ttp) REVERT: A 299 MET cc_start: 0.7389 (tpt) cc_final: 0.6926 (tmm) REVERT: A 308 GLN cc_start: 0.7983 (mt0) cc_final: 0.7239 (mt0) REVERT: A 354 ASN cc_start: 0.7492 (m-40) cc_final: 0.7151 (m-40) REVERT: A 355 SER cc_start: 0.7729 (t) cc_final: 0.7519 (t) REVERT: A 375 GLU cc_start: 0.7381 (pt0) cc_final: 0.7013 (pt0) REVERT: A 393 MET cc_start: 0.7248 (ttm) cc_final: 0.6839 (ttm) REVERT: A 439 GLN cc_start: 0.7761 (pt0) cc_final: 0.7452 (pt0) REVERT: A 443 ARG cc_start: 0.7002 (ttt-90) cc_final: 0.6312 (ttt-90) REVERT: A 453 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7527 (mm-30) REVERT: A 457 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7488 (ttp-170) REVERT: A 484 TRP cc_start: 0.8117 (m-90) cc_final: 0.7434 (m-90) REVERT: A 565 HIS cc_start: 0.7858 (t70) cc_final: 0.7230 (t-170) REVERT: A 566 LEU cc_start: 0.8939 (mt) cc_final: 0.8606 (mm) REVERT: A 572 TRP cc_start: 0.8546 (p-90) cc_final: 0.8241 (p-90) REVERT: A 593 SER cc_start: 0.7919 (m) cc_final: 0.7630 (p) REVERT: A 598 VAL cc_start: 0.7928 (m) cc_final: 0.7694 (p) REVERT: A 607 TRP cc_start: 0.8239 (t-100) cc_final: 0.7701 (t60) REVERT: A 617 ARG cc_start: 0.6897 (ttt90) cc_final: 0.6696 (mtp85) REVERT: A 758 ASN cc_start: 0.7853 (m-40) cc_final: 0.7408 (t0) REVERT: A 769 ASP cc_start: 0.7503 (p0) cc_final: 0.6950 (p0) REVERT: A 806 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7651 (mmmm) REVERT: A 812 MET cc_start: 0.7474 (mpp) cc_final: 0.7191 (mpp) REVERT: A 816 LEU cc_start: 0.8454 (tp) cc_final: 0.8063 (tp) REVERT: A 823 ARG cc_start: 0.7521 (tmt-80) cc_final: 0.7296 (tmt-80) REVERT: A 826 ILE cc_start: 0.8038 (mt) cc_final: 0.7806 (pt) REVERT: A 877 MET cc_start: 0.7197 (mmm) cc_final: 0.6963 (mmm) REVERT: A 893 SER cc_start: 0.7225 (t) cc_final: 0.6631 (p) REVERT: A 916 PHE cc_start: 0.7990 (t80) cc_final: 0.7360 (t80) REVERT: A 922 GLN cc_start: 0.7548 (tt0) cc_final: 0.7040 (tp40) REVERT: A 981 LYS cc_start: 0.8294 (tttt) cc_final: 0.7781 (tptt) REVERT: A 1057 MET cc_start: 0.7762 (ppp) cc_final: 0.7515 (ppp) REVERT: A 1060 LYS cc_start: 0.8176 (tptp) cc_final: 0.7613 (tptp) REVERT: A 1093 MET cc_start: 0.6991 (pmm) cc_final: 0.6624 (pmm) REVERT: A 1111 LEU cc_start: 0.8614 (mt) cc_final: 0.8376 (mt) REVERT: A 1112 MET cc_start: 0.8401 (mtm) cc_final: 0.8063 (mtp) REVERT: A 1113 LEU cc_start: 0.8534 (mp) cc_final: 0.8269 (mm) REVERT: A 1116 MET cc_start: 0.7414 (tpt) cc_final: 0.6603 (tpt) REVERT: A 1126 ASP cc_start: 0.6621 (m-30) cc_final: 0.6289 (m-30) REVERT: A 1188 CYS cc_start: 0.8056 (p) cc_final: 0.7806 (p) REVERT: A 1195 MET cc_start: 0.7338 (ttm) cc_final: 0.7122 (ttm) REVERT: A 1222 GLN cc_start: 0.8442 (mp10) cc_final: 0.7885 (mp10) REVERT: B 72 ILE cc_start: 0.8389 (mm) cc_final: 0.8118 (mm) REVERT: B 77 HIS cc_start: 0.6760 (m-70) cc_final: 0.6445 (m170) REVERT: B 88 ARG cc_start: 0.7901 (ptp-170) cc_final: 0.7672 (ptp90) REVERT: B 113 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6600 (mm-30) REVERT: B 123 GLU cc_start: 0.7562 (pt0) cc_final: 0.7176 (pt0) REVERT: B 134 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8048 (mtmt) REVERT: B 180 LYS cc_start: 0.8298 (ptmt) cc_final: 0.7614 (ptmt) REVERT: B 183 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6856 (mt-10) REVERT: B 191 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7028 (mt-10) REVERT: B 201 ASN cc_start: 0.7830 (m110) cc_final: 0.7405 (m110) REVERT: B 234 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7897 (mtmm) REVERT: B 235 THR cc_start: 0.8177 (m) cc_final: 0.7866 (m) REVERT: B 251 TRP cc_start: 0.7322 (m100) cc_final: 0.6874 (m100) REVERT: B 257 ARG cc_start: 0.7602 (ttm110) cc_final: 0.7321 (mtp85) REVERT: B 288 LYS cc_start: 0.7159 (mttt) cc_final: 0.6471 (mtpt) REVERT: B 289 LEU cc_start: 0.7786 (mt) cc_final: 0.7556 (mt) REVERT: B 304 TRP cc_start: 0.7814 (m100) cc_final: 0.7586 (m100) REVERT: B 310 GLU cc_start: 0.7554 (mp0) cc_final: 0.7214 (mp0) REVERT: B 315 TYR cc_start: 0.7884 (m-80) cc_final: 0.7506 (m-80) REVERT: B 339 ASN cc_start: 0.6939 (t0) cc_final: 0.6283 (t0) REVERT: B 352 ASP cc_start: 0.7199 (t0) cc_final: 0.6880 (t0) REVERT: B 353 SER cc_start: 0.7938 (p) cc_final: 0.7724 (p) REVERT: B 378 LEU cc_start: 0.8364 (mp) cc_final: 0.8023 (mt) REVERT: B 396 ARG cc_start: 0.7556 (ttm170) cc_final: 0.7129 (ttm110) REVERT: B 412 SER cc_start: 0.8328 (t) cc_final: 0.7854 (p) REVERT: B 426 GLU cc_start: 0.7725 (pp20) cc_final: 0.7316 (pp20) REVERT: B 427 GLN cc_start: 0.8219 (pt0) cc_final: 0.8006 (pt0) REVERT: B 431 LYS cc_start: 0.8350 (tttt) cc_final: 0.7962 (tppt) REVERT: B 446 THR cc_start: 0.8196 (m) cc_final: 0.7874 (m) REVERT: B 449 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7255 (mt-10) REVERT: B 457 SER cc_start: 0.7914 (t) cc_final: 0.7589 (p) REVERT: B 460 THR cc_start: 0.8530 (p) cc_final: 0.8066 (p) REVERT: B 461 THR cc_start: 0.8210 (p) cc_final: 0.7931 (t) REVERT: B 462 MET cc_start: 0.8022 (mmt) cc_final: 0.7725 (mmt) REVERT: B 465 MET cc_start: 0.7550 (mtm) cc_final: 0.7123 (mtm) REVERT: B 466 MET cc_start: 0.7269 (mtp) cc_final: 0.7017 (ttp) REVERT: B 483 LYS cc_start: 0.6555 (tttt) cc_final: 0.6326 (ttmm) REVERT: C 75 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7556 (mtp85) REVERT: C 80 SER cc_start: 0.8487 (t) cc_final: 0.8198 (m) REVERT: C 92 LEU cc_start: 0.8620 (mt) cc_final: 0.8335 (mm) REVERT: C 146 ARG cc_start: 0.7435 (mmt-90) cc_final: 0.6991 (mmt180) REVERT: C 183 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6485 (mt-10) REVERT: C 210 GLN cc_start: 0.7627 (tt0) cc_final: 0.7148 (tt0) REVERT: C 211 ILE cc_start: 0.7985 (mt) cc_final: 0.7775 (mt) REVERT: C 215 PHE cc_start: 0.8117 (m-80) cc_final: 0.7862 (m-80) REVERT: C 233 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6268 (mp0) REVERT: C 256 LEU cc_start: 0.8481 (tp) cc_final: 0.8204 (tp) REVERT: C 259 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7392 (mtp85) REVERT: C 262 TRP cc_start: 0.7903 (t60) cc_final: 0.7301 (t60) REVERT: C 287 ASN cc_start: 0.7123 (t0) cc_final: 0.6876 (t0) REVERT: C 288 LYS cc_start: 0.8208 (mttt) cc_final: 0.7693 (mttt) REVERT: C 291 TYR cc_start: 0.8047 (t80) cc_final: 0.7736 (t80) REVERT: C 299 LEU cc_start: 0.8473 (tp) cc_final: 0.8250 (tt) REVERT: C 301 GLU cc_start: 0.7443 (tt0) cc_final: 0.6667 (tt0) REVERT: C 306 LEU cc_start: 0.8398 (mt) cc_final: 0.7904 (mm) REVERT: C 328 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7534 (mtt180) REVERT: C 336 LEU cc_start: 0.8343 (mt) cc_final: 0.8029 (mt) REVERT: C 347 LEU cc_start: 0.8258 (mm) cc_final: 0.7245 (mm) REVERT: C 371 VAL cc_start: 0.8409 (p) cc_final: 0.8046 (m) REVERT: C 400 GLN cc_start: 0.7713 (mt0) cc_final: 0.6858 (mt0) REVERT: C 404 ASN cc_start: 0.7977 (m110) cc_final: 0.7605 (m110) REVERT: C 421 MET cc_start: 0.6522 (mtt) cc_final: 0.6152 (mtt) REVERT: C 427 GLN cc_start: 0.8311 (mt0) cc_final: 0.7796 (mt0) REVERT: C 430 SER cc_start: 0.8440 (t) cc_final: 0.7932 (p) REVERT: C 431 LYS cc_start: 0.8418 (tttt) cc_final: 0.8127 (tttt) REVERT: C 434 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7610 (mt-10) REVERT: C 456 ARG cc_start: 0.7620 (ttt90) cc_final: 0.7417 (ttt90) REVERT: C 458 ARG cc_start: 0.8224 (ttp-170) cc_final: 0.8005 (ptt180) REVERT: C 466 MET cc_start: 0.7079 (ttm) cc_final: 0.6670 (ttm) REVERT: C 470 LYS cc_start: 0.8546 (mttt) cc_final: 0.8196 (mttt) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.3895 time to fit residues: 329.4079 Evaluate side-chains 551 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 120 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 410 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 472 GLN A 565 HIS A 906 HIS ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN A1102 GLN B 132 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093103 restraints weight = 60709.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098335 restraints weight = 25903.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101795 restraints weight = 14219.147| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16209 Z= 0.224 Angle : 0.585 10.310 22166 Z= 0.312 Chirality : 0.044 0.194 2406 Planarity : 0.005 0.058 2692 Dihedral : 14.755 89.302 2496 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1837 helix: 1.71 (0.18), residues: 785 sheet: 0.20 (0.34), residues: 234 loop : -0.42 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 486 HIS 0.006 0.001 HIS C 258 PHE 0.029 0.002 PHE C 242 TYR 0.033 0.002 TYR B 315 ARG 0.005 0.001 ARG A1208 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 767) hydrogen bonds : angle 5.08710 ( 2137) covalent geometry : bond 0.00454 (16209) covalent geometry : angle 0.58518 (22166) *********************** 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 572 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 571 time to evaluate : 1.800 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: 0.8379 (mm) cc_final: 0.8166 (mm) REVERT: A 79 LEU cc_start: 0.8168 (mt) cc_final: 0.7858 (mp) REVERT: A 110 HIS cc_start: 0.7486 (m90) cc_final: 0.6675 (m90) REVERT: A 145 LYS cc_start: 0.8184 (tptp) cc_final: 0.7750 (tptp) REVERT: A 159 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6692 (pp30) REVERT: A 280 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 293 ASP cc_start: 0.5329 (t0) cc_final: 0.5073 (t0) REVERT: A 295 MET cc_start: 0.7361 (ttt) cc_final: 0.6911 (ttp) REVERT: A 354 ASN cc_start: 0.7606 (m-40) cc_final: 0.7269 (m-40) REVERT: A 355 SER cc_start: 0.7822 (t) cc_final: 0.7561 (t) REVERT: A 375 GLU cc_start: 0.7435 (pt0) cc_final: 0.7026 (pt0) REVERT: A 393 MET cc_start: 0.7193 (ttm) cc_final: 0.6933 (ttm) REVERT: A 441 TRP cc_start: 0.7970 (t-100) cc_final: 0.7556 (t-100) REVERT: A 443 ARG cc_start: 0.7031 (ttt-90) cc_final: 0.6466 (ttt-90) REVERT: A 453 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7604 (mm-30) REVERT: A 457 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7500 (ttp-170) REVERT: A 484 TRP cc_start: 0.8114 (m-90) cc_final: 0.7325 (m-90) REVERT: A 565 HIS cc_start: 0.7501 (t-90) cc_final: 0.7151 (t70) REVERT: A 566 LEU cc_start: 0.8924 (mt) cc_final: 0.8651 (mm) REVERT: A 586 THR cc_start: 0.8267 (t) cc_final: 0.7970 (p) REVERT: A 593 SER cc_start: 0.7968 (m) cc_final: 0.7583 (p) REVERT: A 607 TRP cc_start: 0.8243 (t-100) cc_final: 0.7820 (t60) REVERT: A 617 ARG cc_start: 0.6989 (ttt90) cc_final: 0.6601 (mtp-110) REVERT: A 758 ASN cc_start: 0.7952 (m-40) cc_final: 0.7494 (t0) REVERT: A 797 MET cc_start: 0.7698 (mtt) cc_final: 0.7473 (tpp) REVERT: A 806 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7641 (mmmm) REVERT: A 812 MET cc_start: 0.7447 (mpp) cc_final: 0.7184 (mpp) REVERT: A 816 LEU cc_start: 0.8465 (tp) cc_final: 0.8066 (tp) REVERT: A 823 ARG cc_start: 0.7654 (tmt-80) cc_final: 0.6671 (tmt-80) REVERT: A 826 ILE cc_start: 0.8055 (mt) cc_final: 0.7849 (pt) REVERT: A 853 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7485 (mtp85) REVERT: A 877 MET cc_start: 0.7190 (mmm) cc_final: 0.6885 (mmm) REVERT: A 893 SER cc_start: 0.7303 (t) cc_final: 0.6719 (p) REVERT: A 906 HIS cc_start: 0.8331 (t70) cc_final: 0.8124 (t-90) REVERT: A 916 PHE cc_start: 0.7991 (t80) cc_final: 0.7432 (t80) REVERT: A 919 MET cc_start: 0.7511 (mtt) cc_final: 0.7198 (mpp) REVERT: A 922 GLN cc_start: 0.7503 (tt0) cc_final: 0.7134 (tp40) REVERT: A 934 LYS cc_start: 0.8327 (mmpt) cc_final: 0.8086 (mmtt) REVERT: A 969 PHE cc_start: 0.8041 (m-10) cc_final: 0.7793 (m-10) REVERT: A 981 LYS cc_start: 0.8321 (tttt) cc_final: 0.7747 (tppt) REVERT: A 1057 MET cc_start: 0.7778 (ppp) cc_final: 0.7550 (ppp) REVERT: A 1060 LYS cc_start: 0.8176 (tptp) cc_final: 0.7674 (tptp) REVERT: A 1093 MET cc_start: 0.6996 (pmm) cc_final: 0.6648 (pmm) REVERT: A 1110 HIS cc_start: 0.8684 (m-70) cc_final: 0.8428 (m-70) REVERT: A 1116 MET cc_start: 0.7344 (tpt) cc_final: 0.6493 (tpt) REVERT: A 1126 ASP cc_start: 0.6642 (m-30) cc_final: 0.6347 (m-30) REVERT: A 1148 ARG cc_start: 0.7919 (mtp180) cc_final: 0.6642 (ttm-80) REVERT: A 1163 MET cc_start: 0.7899 (tpp) cc_final: 0.7690 (tpp) REVERT: A 1188 CYS cc_start: 0.8255 (p) cc_final: 0.7931 (p) REVERT: A 1195 MET cc_start: 0.7376 (ttm) cc_final: 0.7045 (ttm) REVERT: A 1222 GLN cc_start: 0.8491 (mp10) cc_final: 0.7869 (mp10) REVERT: B 77 HIS cc_start: 0.6962 (m-70) cc_final: 0.6707 (m170) REVERT: B 88 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7726 (ptp90) REVERT: B 113 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6670 (mm-30) REVERT: B 123 GLU cc_start: 0.7516 (pt0) cc_final: 0.7130 (pt0) REVERT: B 134 LYS cc_start: 0.8423 (mtmt) cc_final: 0.7899 (mtmt) REVERT: B 180 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7631 (ptmt) REVERT: B 183 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 191 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7210 (mt-10) REVERT: B 192 HIS cc_start: 0.8085 (m-70) cc_final: 0.7635 (m-70) REVERT: B 201 ASN cc_start: 0.7910 (m110) cc_final: 0.7509 (m110) REVERT: B 234 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7866 (mtmm) REVERT: B 288 LYS cc_start: 0.7179 (mttt) cc_final: 0.6473 (mtpt) REVERT: B 289 LEU cc_start: 0.7895 (mt) cc_final: 0.7589 (mt) REVERT: B 304 TRP cc_start: 0.7854 (m100) cc_final: 0.7483 (m100) REVERT: B 306 LEU cc_start: 0.8102 (mm) cc_final: 0.7878 (mm) REVERT: B 310 GLU cc_start: 0.7623 (mp0) cc_final: 0.7354 (mp0) REVERT: B 315 TYR cc_start: 0.7929 (m-80) cc_final: 0.7528 (m-80) REVERT: B 339 ASN cc_start: 0.6804 (t0) cc_final: 0.6527 (t0) REVERT: B 352 ASP cc_start: 0.7316 (t0) cc_final: 0.6985 (t0) REVERT: B 378 LEU cc_start: 0.8372 (mp) cc_final: 0.8117 (mt) REVERT: B 396 ARG cc_start: 0.7642 (ttm170) cc_final: 0.7201 (ttm110) REVERT: B 400 GLN cc_start: 0.7797 (tt0) cc_final: 0.7539 (tp40) REVERT: B 412 SER cc_start: 0.8290 (t) cc_final: 0.7793 (p) REVERT: B 431 LYS cc_start: 0.8438 (tttt) cc_final: 0.8006 (tppt) REVERT: B 446 THR cc_start: 0.8311 (m) cc_final: 0.7946 (m) REVERT: B 449 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7302 (mt-10) REVERT: B 457 SER cc_start: 0.7913 (t) cc_final: 0.7562 (p) REVERT: B 460 THR cc_start: 0.8515 (p) cc_final: 0.8103 (p) REVERT: B 461 THR cc_start: 0.8214 (p) cc_final: 0.7933 (t) REVERT: B 462 MET cc_start: 0.8018 (mmt) cc_final: 0.7729 (mmt) REVERT: B 465 MET cc_start: 0.7603 (mtm) cc_final: 0.7200 (mtm) REVERT: B 466 MET cc_start: 0.7417 (mtp) cc_final: 0.7041 (ttp) REVERT: C 67 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 71 GLU cc_start: 0.8390 (tt0) cc_final: 0.8148 (tt0) REVERT: C 75 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7712 (mtp85) REVERT: C 80 SER cc_start: 0.8530 (t) cc_final: 0.8088 (m) REVERT: C 89 ASP cc_start: 0.8102 (m-30) cc_final: 0.7815 (m-30) REVERT: C 107 ARG cc_start: 0.7504 (ttm170) cc_final: 0.7275 (ttp80) REVERT: C 146 ARG cc_start: 0.7428 (mmt-90) cc_final: 0.6953 (mmt180) REVERT: C 183 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6478 (mt-10) REVERT: C 210 GLN cc_start: 0.7710 (tt0) cc_final: 0.7142 (tt0) REVERT: C 233 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6326 (mp0) REVERT: C 256 LEU cc_start: 0.8502 (tp) cc_final: 0.8258 (tp) REVERT: C 259 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7386 (mtp85) REVERT: C 262 TRP cc_start: 0.7921 (t60) cc_final: 0.7319 (t60) REVERT: C 287 ASN cc_start: 0.7181 (t0) cc_final: 0.6945 (t0) REVERT: C 288 LYS cc_start: 0.8248 (mttt) cc_final: 0.7721 (mttt) REVERT: C 299 LEU cc_start: 0.8533 (tp) cc_final: 0.8326 (tt) REVERT: C 301 GLU cc_start: 0.7434 (tt0) cc_final: 0.6704 (tt0) REVERT: C 305 ASN cc_start: 0.7538 (t0) cc_final: 0.7289 (t0) REVERT: C 306 LEU cc_start: 0.8203 (mt) cc_final: 0.7712 (mm) REVERT: C 328 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7588 (mtt180) REVERT: C 336 LEU cc_start: 0.8370 (mt) cc_final: 0.7961 (mt) REVERT: C 346 MET cc_start: 0.7086 (tmm) cc_final: 0.6411 (tmm) REVERT: C 371 VAL cc_start: 0.8383 (p) cc_final: 0.7995 (m) REVERT: C 373 LYS cc_start: 0.8299 (mttt) cc_final: 0.7727 (ptpp) REVERT: C 400 GLN cc_start: 0.7734 (mt0) cc_final: 0.7240 (mt0) REVERT: C 421 MET cc_start: 0.6636 (mtt) cc_final: 0.6313 (mtt) REVERT: C 426 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7649 (mt-10) REVERT: C 427 GLN cc_start: 0.8277 (mt0) cc_final: 0.7774 (mt0) REVERT: C 430 SER cc_start: 0.8460 (t) cc_final: 0.8005 (p) REVERT: C 431 LYS cc_start: 0.8409 (tttt) cc_final: 0.8138 (tttt) REVERT: C 434 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7695 (mt-10) REVERT: C 466 MET cc_start: 0.6915 (ttm) cc_final: 0.6661 (ttm) REVERT: C 470 LYS cc_start: 0.8603 (mttt) cc_final: 0.8222 (mttt) outliers start: 1 outliers final: 1 residues processed: 571 average time/residue: 0.3617 time to fit residues: 293.9780 Evaluate side-chains 540 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 539 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 107 optimal weight: 0.0570 chunk 85 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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 277 HIS A 410 GLN A 420 HIS ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN C 272 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094766 restraints weight = 59883.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100041 restraints weight = 25187.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103577 restraints weight = 13702.221| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16209 Z= 0.141 Angle : 0.549 8.732 22166 Z= 0.288 Chirality : 0.041 0.184 2406 Planarity : 0.004 0.054 2692 Dihedral : 14.610 89.803 2496 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.13 % Allowed : 1.81 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1837 helix: 1.82 (0.19), residues: 781 sheet: 0.26 (0.34), residues: 244 loop : -0.32 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 572 HIS 0.005 0.001 HIS C 258 PHE 0.028 0.002 PHE C 242 TYR 0.028 0.001 TYR B 315 ARG 0.007 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 767) hydrogen bonds : angle 4.77668 ( 2137) covalent geometry : bond 0.00295 (16209) covalent geometry : angle 0.54925 (22166) *********************** 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 576 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8119 (mt) cc_final: 0.7851 (mp) REVERT: A 110 HIS cc_start: 0.7389 (m90) cc_final: 0.6587 (m90) REVERT: A 145 LYS cc_start: 0.8128 (tptp) cc_final: 0.7752 (tptp) REVERT: A 159 GLN cc_start: 0.7178 (tm-30) cc_final: 0.6629 (pp30) REVERT: A 193 ARG cc_start: 0.7837 (ptm160) cc_final: 0.6912 (ttp-110) REVERT: A 205 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7373 (mm-30) REVERT: A 213 VAL cc_start: 0.7381 (t) cc_final: 0.7122 (m) REVERT: A 295 MET cc_start: 0.7502 (ttt) cc_final: 0.7029 (ttp) REVERT: A 355 SER cc_start: 0.7665 (t) cc_final: 0.7450 (t) REVERT: A 375 GLU cc_start: 0.7344 (pt0) cc_final: 0.6958 (pt0) REVERT: A 393 MET cc_start: 0.7246 (ttm) cc_final: 0.7014 (ttm) REVERT: A 410 GLN cc_start: 0.7566 (tt0) cc_final: 0.7217 (tt0) REVERT: A 438 ASN cc_start: 0.7753 (p0) cc_final: 0.7508 (p0) REVERT: A 441 TRP cc_start: 0.7974 (t-100) cc_final: 0.7620 (t-100) REVERT: A 443 ARG cc_start: 0.6899 (ttt-90) cc_final: 0.6323 (ttt-90) REVERT: A 453 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7498 (mm-30) REVERT: A 457 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7505 (ttp-170) REVERT: A 487 ASP cc_start: 0.8283 (m-30) cc_final: 0.8055 (m-30) REVERT: A 565 HIS cc_start: 0.7433 (t-90) cc_final: 0.7147 (t70) REVERT: A 566 LEU cc_start: 0.8919 (mt) cc_final: 0.8687 (mm) REVERT: A 574 ARG cc_start: 0.8424 (ptp90) cc_final: 0.8019 (ptp90) REVERT: A 586 THR cc_start: 0.8118 (t) cc_final: 0.7871 (p) REVERT: A 593 SER cc_start: 0.7960 (m) cc_final: 0.7639 (p) REVERT: A 607 TRP cc_start: 0.8354 (t-100) cc_final: 0.7856 (t60) REVERT: A 758 ASN cc_start: 0.7906 (m-40) cc_final: 0.7489 (t0) REVERT: A 774 MET cc_start: 0.7486 (tpt) cc_final: 0.7250 (tpt) REVERT: A 797 MET cc_start: 0.7688 (mtt) cc_final: 0.7451 (ttm) REVERT: A 806 LYS cc_start: 0.7884 (mmmm) cc_final: 0.7617 (mmmm) REVERT: A 812 MET cc_start: 0.7400 (mpp) cc_final: 0.7092 (mpp) REVERT: A 816 LEU cc_start: 0.8448 (tp) cc_final: 0.8084 (tp) REVERT: A 821 LEU cc_start: 0.8243 (mt) cc_final: 0.7992 (mt) REVERT: A 832 ASP cc_start: 0.8152 (t0) cc_final: 0.7839 (t70) REVERT: A 837 TYR cc_start: 0.6192 (m-80) cc_final: 0.5720 (m-10) REVERT: A 853 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7438 (mtp85) REVERT: A 877 MET cc_start: 0.7087 (mmm) cc_final: 0.6833 (mmm) REVERT: A 892 ASP cc_start: 0.7358 (m-30) cc_final: 0.7152 (m-30) REVERT: A 893 SER cc_start: 0.7300 (t) cc_final: 0.6664 (p) REVERT: A 922 GLN cc_start: 0.7436 (tt0) cc_final: 0.6582 (tp-100) REVERT: A 981 LYS cc_start: 0.8290 (tttt) cc_final: 0.7721 (tppt) REVERT: A 1057 MET cc_start: 0.7784 (ppp) cc_final: 0.7569 (ppp) REVERT: A 1060 LYS cc_start: 0.8188 (tptp) cc_final: 0.7709 (tptp) REVERT: A 1093 MET cc_start: 0.6846 (pmm) cc_final: 0.6555 (pmm) REVERT: A 1116 MET cc_start: 0.7256 (tpt) cc_final: 0.6441 (tpt) REVERT: A 1148 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7546 (ttm-80) REVERT: A 1188 CYS cc_start: 0.8352 (p) cc_final: 0.7864 (p) REVERT: A 1195 MET cc_start: 0.7422 (ttm) cc_final: 0.7003 (ttm) REVERT: A 1206 MET cc_start: 0.6026 (mtm) cc_final: 0.5741 (mtt) REVERT: A 1219 ASP cc_start: 0.7720 (t0) cc_final: 0.7496 (t0) REVERT: A 1222 GLN cc_start: 0.8486 (mp10) cc_final: 0.7813 (mp10) REVERT: B 77 HIS cc_start: 0.6911 (m-70) cc_final: 0.6662 (m170) REVERT: B 85 GLN cc_start: 0.7432 (mt0) cc_final: 0.6830 (mt0) REVERT: B 88 ARG cc_start: 0.7918 (ptp-170) cc_final: 0.7708 (ptp90) REVERT: B 113 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6692 (mm-30) REVERT: B 123 GLU cc_start: 0.7517 (pt0) cc_final: 0.7158 (pt0) REVERT: B 134 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7927 (mtmt) REVERT: B 180 LYS cc_start: 0.8322 (ptmt) cc_final: 0.7618 (ptmt) REVERT: B 183 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6990 (mt-10) REVERT: B 191 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7248 (mt-10) REVERT: B 201 ASN cc_start: 0.7866 (m110) cc_final: 0.7518 (m110) REVERT: B 234 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7949 (mtmm) REVERT: B 235 THR cc_start: 0.8085 (m) cc_final: 0.7881 (m) REVERT: B 288 LYS cc_start: 0.7213 (mttt) cc_final: 0.6503 (mtpt) REVERT: B 289 LEU cc_start: 0.7881 (mt) cc_final: 0.7539 (mt) REVERT: B 304 TRP cc_start: 0.7790 (m100) cc_final: 0.7408 (m100) REVERT: B 310 GLU cc_start: 0.7602 (mp0) cc_final: 0.7322 (mp0) REVERT: B 315 TYR cc_start: 0.7929 (m-80) cc_final: 0.7542 (m-80) REVERT: B 339 ASN cc_start: 0.6677 (t0) cc_final: 0.6414 (t0) REVERT: B 352 ASP cc_start: 0.7211 (t0) cc_final: 0.6883 (t0) REVERT: B 396 ARG cc_start: 0.7567 (ttm170) cc_final: 0.7153 (ttm110) REVERT: B 400 GLN cc_start: 0.7741 (tt0) cc_final: 0.7524 (tp40) REVERT: B 412 SER cc_start: 0.8303 (t) cc_final: 0.7802 (p) REVERT: B 431 LYS cc_start: 0.8412 (tttt) cc_final: 0.8178 (tttt) REVERT: B 446 THR cc_start: 0.8253 (m) cc_final: 0.7952 (m) REVERT: B 449 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7340 (mt-10) REVERT: B 457 SER cc_start: 0.8006 (t) cc_final: 0.7657 (p) REVERT: B 460 THR cc_start: 0.8500 (p) cc_final: 0.8121 (p) REVERT: B 461 THR cc_start: 0.8239 (p) cc_final: 0.7962 (t) REVERT: B 462 MET cc_start: 0.7940 (mmt) cc_final: 0.7686 (mmt) REVERT: B 465 MET cc_start: 0.7540 (mtm) cc_final: 0.7076 (mtm) REVERT: B 466 MET cc_start: 0.7343 (mtp) cc_final: 0.7001 (ttp) REVERT: C 71 GLU cc_start: 0.8371 (tt0) cc_final: 0.8105 (tt0) REVERT: C 75 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7643 (mtp85) REVERT: C 80 SER cc_start: 0.8547 (t) cc_final: 0.8157 (m) REVERT: C 146 ARG cc_start: 0.7397 (mmt-90) cc_final: 0.6960 (mmt180) REVERT: C 183 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6413 (mt-10) REVERT: C 194 VAL cc_start: 0.7863 (m) cc_final: 0.7640 (p) REVERT: C 203 ARG cc_start: 0.7456 (ttt180) cc_final: 0.7250 (ttt180) REVERT: C 233 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6314 (mp0) REVERT: C 256 LEU cc_start: 0.8451 (tp) cc_final: 0.8229 (tp) REVERT: C 259 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7335 (mtp85) REVERT: C 262 TRP cc_start: 0.7828 (t60) cc_final: 0.7186 (t60) REVERT: C 287 ASN cc_start: 0.7122 (t0) cc_final: 0.6862 (t0) REVERT: C 288 LYS cc_start: 0.8245 (mttt) cc_final: 0.7719 (mttt) REVERT: C 291 TYR cc_start: 0.8239 (t80) cc_final: 0.7963 (t80) REVERT: C 301 GLU cc_start: 0.7390 (tt0) cc_final: 0.6653 (tt0) REVERT: C 305 ASN cc_start: 0.7536 (t0) cc_final: 0.7275 (t0) REVERT: C 306 LEU cc_start: 0.8143 (mt) cc_final: 0.7653 (mm) REVERT: C 328 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7577 (mtt180) REVERT: C 336 LEU cc_start: 0.8407 (mt) cc_final: 0.7938 (mt) REVERT: C 343 ASP cc_start: 0.7175 (m-30) cc_final: 0.6974 (m-30) REVERT: C 347 LEU cc_start: 0.8267 (mm) cc_final: 0.7099 (mm) REVERT: C 371 VAL cc_start: 0.8225 (p) cc_final: 0.7949 (m) REVERT: C 396 ARG cc_start: 0.7800 (ttm170) cc_final: 0.6768 (ttm170) REVERT: C 400 GLN cc_start: 0.7848 (mt0) cc_final: 0.6844 (mt0) REVERT: C 404 ASN cc_start: 0.8071 (m-40) cc_final: 0.7470 (m110) REVERT: C 415 PRO cc_start: 0.8696 (Cg_endo) cc_final: 0.8454 (Cg_exo) REVERT: C 421 MET cc_start: 0.6612 (mtt) cc_final: 0.6303 (mtt) REVERT: C 427 GLN cc_start: 0.8264 (mt0) cc_final: 0.7258 (mt0) REVERT: C 430 SER cc_start: 0.8425 (t) cc_final: 0.7938 (p) REVERT: C 431 LYS cc_start: 0.8371 (tttt) cc_final: 0.8152 (tttt) REVERT: C 434 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7612 (mt-10) REVERT: C 466 MET cc_start: 0.6851 (ttm) cc_final: 0.6631 (ttm) REVERT: C 470 LYS cc_start: 0.8530 (mttt) cc_final: 0.8180 (mttt) outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.3235 time to fit residues: 262.6619 Evaluate side-chains 540 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 14 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 277 HIS A 398 GLN A 440 ASN A 468 ASN A 564 GLN A 843 GLN ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 279 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.093615 restraints weight = 63952.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099002 restraints weight = 26543.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102605 restraints weight = 14276.416| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16209 Z= 0.177 Angle : 0.563 8.614 22166 Z= 0.298 Chirality : 0.043 0.210 2406 Planarity : 0.005 0.081 2692 Dihedral : 14.602 89.611 2496 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.25 % Allowed : 1.56 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1837 helix: 1.83 (0.19), residues: 774 sheet: 0.14 (0.34), residues: 242 loop : -0.36 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 312 HIS 0.006 0.001 HIS A 360 PHE 0.029 0.002 PHE C 242 TYR 0.026 0.002 TYR B 315 ARG 0.012 0.001 ARG C 456 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 767) hydrogen bonds : angle 4.84049 ( 2137) covalent geometry : bond 0.00365 (16209) covalent geometry : angle 0.56301 (22166) *********************** 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 588 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 586 time to evaluate : 1.600 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: 0.8492 (mm) cc_final: 0.8225 (mm) REVERT: A 79 LEU cc_start: 0.8091 (mt) cc_final: 0.7858 (mp) REVERT: A 110 HIS cc_start: 0.7385 (m90) cc_final: 0.6637 (m90) REVERT: A 125 LEU cc_start: 0.8566 (tp) cc_final: 0.8364 (tp) REVERT: A 159 GLN cc_start: 0.7178 (tm-30) cc_final: 0.6610 (pp30) REVERT: A 177 ARG cc_start: 0.8227 (ttt90) cc_final: 0.7857 (ttt90) REVERT: A 193 ARG cc_start: 0.7503 (ttm170) cc_final: 0.7263 (ttp-110) REVERT: A 280 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6938 (mm-30) REVERT: A 293 ASP cc_start: 0.5530 (t0) cc_final: 0.5223 (t0) REVERT: A 295 MET cc_start: 0.7559 (ttt) cc_final: 0.7212 (ttp) REVERT: A 299 MET cc_start: 0.7426 (tpt) cc_final: 0.7176 (tpt) REVERT: A 354 ASN cc_start: 0.7511 (m-40) cc_final: 0.7259 (m-40) REVERT: A 355 SER cc_start: 0.7711 (t) cc_final: 0.7468 (t) REVERT: A 393 MET cc_start: 0.7208 (ttm) cc_final: 0.6912 (ttm) REVERT: A 398 GLN cc_start: 0.8027 (pt0) cc_final: 0.7687 (tt0) REVERT: A 410 GLN cc_start: 0.7595 (tt0) cc_final: 0.7059 (tt0) REVERT: A 439 GLN cc_start: 0.8191 (pm20) cc_final: 0.7274 (pm20) REVERT: A 441 TRP cc_start: 0.7975 (t-100) cc_final: 0.7584 (t-100) REVERT: A 443 ARG cc_start: 0.6969 (ttt-90) cc_final: 0.6412 (ttt-90) REVERT: A 453 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7524 (mm-30) REVERT: A 457 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7450 (ttp-170) REVERT: A 458 GLU cc_start: 0.7738 (pp20) cc_final: 0.7535 (tm-30) REVERT: A 565 HIS cc_start: 0.7546 (t-90) cc_final: 0.7102 (t-90) REVERT: A 566 LEU cc_start: 0.8912 (mt) cc_final: 0.8692 (mm) REVERT: A 574 ARG cc_start: 0.8411 (ptp90) cc_final: 0.7969 (ptp90) REVERT: A 579 ARG cc_start: 0.7420 (ttm110) cc_final: 0.7116 (ttm110) REVERT: A 586 THR cc_start: 0.8054 (t) cc_final: 0.7768 (p) REVERT: A 593 SER cc_start: 0.8010 (m) cc_final: 0.7629 (p) REVERT: A 607 TRP cc_start: 0.8348 (t-100) cc_final: 0.7821 (t60) REVERT: A 758 ASN cc_start: 0.7954 (m-40) cc_final: 0.7527 (t0) REVERT: A 806 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7655 (mmmm) REVERT: A 812 MET cc_start: 0.7415 (mpp) cc_final: 0.7174 (mpp) REVERT: A 816 LEU cc_start: 0.8460 (tp) cc_final: 0.8095 (tp) REVERT: A 832 ASP cc_start: 0.8224 (t0) cc_final: 0.7934 (t70) REVERT: A 837 TYR cc_start: 0.6223 (m-80) cc_final: 0.5879 (m-10) REVERT: A 877 MET cc_start: 0.7073 (mmm) cc_final: 0.6839 (mmm) REVERT: A 893 SER cc_start: 0.7349 (t) cc_final: 0.6712 (p) REVERT: A 922 GLN cc_start: 0.7407 (tt0) cc_final: 0.6562 (tp-100) REVERT: A 934 LYS cc_start: 0.8333 (mmpt) cc_final: 0.8110 (mmtt) REVERT: A 981 LYS cc_start: 0.8268 (tttt) cc_final: 0.7711 (tppt) REVERT: A 1060 LYS cc_start: 0.8196 (tptp) cc_final: 0.7706 (tptp) REVERT: A 1093 MET cc_start: 0.6843 (pmm) cc_final: 0.6637 (pmm) REVERT: A 1110 HIS cc_start: 0.8525 (m90) cc_final: 0.8250 (m-70) REVERT: A 1116 MET cc_start: 0.7202 (tpt) cc_final: 0.6485 (tpt) REVERT: A 1136 GLU cc_start: 0.6047 (mt-10) cc_final: 0.5701 (mt-10) REVERT: A 1148 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7563 (ttm-80) REVERT: A 1188 CYS cc_start: 0.8413 (p) cc_final: 0.7856 (p) REVERT: A 1195 MET cc_start: 0.7445 (ttm) cc_final: 0.6998 (ttm) REVERT: A 1206 MET cc_start: 0.6009 (mtm) cc_final: 0.5704 (mtt) REVERT: A 1219 ASP cc_start: 0.7764 (t0) cc_final: 0.7524 (t0) REVERT: A 1222 GLN cc_start: 0.8504 (mp10) cc_final: 0.7801 (mp10) REVERT: B 77 HIS cc_start: 0.6952 (m-70) cc_final: 0.6659 (m170) REVERT: B 85 GLN cc_start: 0.7439 (mt0) cc_final: 0.6866 (mt0) REVERT: B 88 ARG cc_start: 0.7946 (ptp-170) cc_final: 0.7612 (ptp90) REVERT: B 113 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6735 (mm-30) REVERT: B 123 GLU cc_start: 0.7498 (pt0) cc_final: 0.7230 (pt0) REVERT: B 134 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8172 (mtpt) REVERT: B 180 LYS cc_start: 0.8287 (ptmt) cc_final: 0.7876 (ptmt) REVERT: B 183 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6964 (mt-10) REVERT: B 191 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7169 (mt-10) REVERT: B 201 ASN cc_start: 0.7885 (m110) cc_final: 0.7524 (m110) REVERT: B 210 GLN cc_start: 0.7707 (tt0) cc_final: 0.7317 (tt0) REVERT: B 234 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7951 (mtmm) REVERT: B 246 ARG cc_start: 0.8068 (ttp-110) cc_final: 0.7642 (ttp-110) REVERT: B 288 LYS cc_start: 0.7197 (mttt) cc_final: 0.6507 (mtpt) REVERT: B 289 LEU cc_start: 0.7852 (mt) cc_final: 0.7528 (mt) REVERT: B 304 TRP cc_start: 0.7807 (m100) cc_final: 0.7445 (m100) REVERT: B 310 GLU cc_start: 0.7548 (mp0) cc_final: 0.7337 (mp0) REVERT: B 315 TYR cc_start: 0.7852 (m-80) cc_final: 0.7496 (m-80) REVERT: B 339 ASN cc_start: 0.6754 (t0) cc_final: 0.6411 (t0) REVERT: B 352 ASP cc_start: 0.7259 (t0) cc_final: 0.6904 (t0) REVERT: B 396 ARG cc_start: 0.7575 (ttm170) cc_final: 0.7169 (ttm110) REVERT: B 400 GLN cc_start: 0.7710 (tt0) cc_final: 0.7471 (tp40) REVERT: B 412 SER cc_start: 0.8298 (t) cc_final: 0.7828 (p) REVERT: B 427 GLN cc_start: 0.8222 (pt0) cc_final: 0.7614 (pm20) REVERT: B 431 LYS cc_start: 0.8501 (tttt) cc_final: 0.8250 (tttt) REVERT: B 446 THR cc_start: 0.8307 (m) cc_final: 0.7999 (m) REVERT: B 449 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7330 (mt-10) REVERT: B 457 SER cc_start: 0.7800 (t) cc_final: 0.7445 (p) REVERT: B 462 MET cc_start: 0.7829 (mmt) cc_final: 0.7612 (mmt) REVERT: B 465 MET cc_start: 0.7547 (mtm) cc_final: 0.7116 (mtm) REVERT: B 466 MET cc_start: 0.7357 (mtp) cc_final: 0.7050 (ttp) REVERT: C 67 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7811 (mm-30) REVERT: C 71 GLU cc_start: 0.8329 (tt0) cc_final: 0.8106 (tt0) REVERT: C 75 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7664 (mtp85) REVERT: C 80 SER cc_start: 0.8547 (t) cc_final: 0.8174 (m) REVERT: C 89 ASP cc_start: 0.8078 (m-30) cc_final: 0.7764 (m-30) REVERT: C 180 LYS cc_start: 0.7957 (pttt) cc_final: 0.7700 (ptmt) REVERT: C 183 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6387 (mt-10) REVERT: C 185 LEU cc_start: 0.8998 (mt) cc_final: 0.8704 (mt) REVERT: C 194 VAL cc_start: 0.7873 (m) cc_final: 0.7663 (p) REVERT: C 203 ARG cc_start: 0.7472 (ttt180) cc_final: 0.7250 (ttt180) REVERT: C 233 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6264 (mp0) REVERT: C 256 LEU cc_start: 0.8490 (tp) cc_final: 0.8243 (tp) REVERT: C 262 TRP cc_start: 0.7852 (t60) cc_final: 0.7128 (t60) REVERT: C 272 ASN cc_start: 0.7811 (m110) cc_final: 0.7501 (t0) REVERT: C 287 ASN cc_start: 0.7124 (t0) cc_final: 0.6857 (t0) REVERT: C 288 LYS cc_start: 0.8239 (mttt) cc_final: 0.7717 (mttt) REVERT: C 291 TYR cc_start: 0.8281 (t80) cc_final: 0.7486 (t80) REVERT: C 297 LYS cc_start: 0.7878 (mttp) cc_final: 0.7553 (mttp) REVERT: C 301 GLU cc_start: 0.7419 (tt0) cc_final: 0.6887 (tt0) REVERT: C 305 ASN cc_start: 0.7571 (t0) cc_final: 0.7270 (t0) REVERT: C 306 LEU cc_start: 0.8202 (mt) cc_final: 0.7685 (mm) REVERT: C 328 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7600 (mtt180) REVERT: C 336 LEU cc_start: 0.8416 (mt) cc_final: 0.7974 (mt) REVERT: C 346 MET cc_start: 0.6953 (tmm) cc_final: 0.6317 (tmm) REVERT: C 371 VAL cc_start: 0.8220 (p) cc_final: 0.7958 (m) REVERT: C 373 LYS cc_start: 0.8259 (mttt) cc_final: 0.7517 (ptpp) REVERT: C 396 ARG cc_start: 0.7842 (ttm170) cc_final: 0.6828 (ttm170) REVERT: C 400 GLN cc_start: 0.7870 (mt0) cc_final: 0.6864 (mt0) REVERT: C 404 ASN cc_start: 0.8079 (m-40) cc_final: 0.7426 (m110) REVERT: C 415 PRO cc_start: 0.8700 (Cg_endo) cc_final: 0.8469 (Cg_exo) REVERT: C 421 MET cc_start: 0.6598 (mtt) cc_final: 0.6313 (mtt) REVERT: C 426 GLU cc_start: 0.7538 (pp20) cc_final: 0.7329 (pp20) REVERT: C 427 GLN cc_start: 0.8156 (mt0) cc_final: 0.7579 (mt0) REVERT: C 430 SER cc_start: 0.8478 (t) cc_final: 0.7948 (p) REVERT: C 431 LYS cc_start: 0.8390 (tttt) cc_final: 0.8139 (tttt) REVERT: C 434 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7631 (mt-10) REVERT: C 466 MET cc_start: 0.6921 (ttm) cc_final: 0.6721 (ttm) REVERT: C 470 LYS cc_start: 0.8560 (mttt) cc_final: 0.8185 (mttt) outliers start: 2 outliers final: 0 residues processed: 586 average time/residue: 0.3166 time to fit residues: 260.8810 Evaluate side-chains 541 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 116 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 44 optimal weight: 0.0040 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 95 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** 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 277 HIS A 398 GLN A 468 ASN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 409 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094623 restraints weight = 70944.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.100306 restraints weight = 27996.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104053 restraints weight = 14754.342| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16209 Z= 0.118 Angle : 0.550 8.537 22166 Z= 0.287 Chirality : 0.041 0.189 2406 Planarity : 0.004 0.052 2692 Dihedral : 14.459 89.154 2496 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.25 % Allowed : 1.19 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1837 helix: 1.84 (0.19), residues: 787 sheet: 0.26 (0.34), residues: 244 loop : -0.27 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 572 HIS 0.010 0.001 HIS A 138 PHE 0.027 0.001 PHE C 242 TYR 0.024 0.001 TYR B 315 ARG 0.007 0.000 ARG A1208 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 767) hydrogen bonds : angle 4.58225 ( 2137) covalent geometry : bond 0.00251 (16209) covalent geometry : angle 0.55045 (22166) *********************** 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 575 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 573 time to evaluate : 1.852 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: 0.8513 (mm) cc_final: 0.8227 (mm) REVERT: A 79 LEU cc_start: 0.8084 (mt) cc_final: 0.7861 (mp) REVERT: A 110 HIS cc_start: 0.7325 (m90) cc_final: 0.6663 (m90) REVERT: A 159 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6544 (pp30) REVERT: A 177 ARG cc_start: 0.8175 (ttt90) cc_final: 0.7754 (ttt90) REVERT: A 193 ARG cc_start: 0.7475 (ttm170) cc_final: 0.7238 (ttm-80) REVERT: A 262 GLN cc_start: 0.7771 (tp40) cc_final: 0.7556 (tp40) REVERT: A 280 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6922 (mm-30) REVERT: A 295 MET cc_start: 0.7592 (ttt) cc_final: 0.6847 (ttm) REVERT: A 299 MET cc_start: 0.7386 (tpt) cc_final: 0.7021 (tpt) REVERT: A 354 ASN cc_start: 0.7440 (m-40) cc_final: 0.7183 (m-40) REVERT: A 374 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7818 (ttt180) REVERT: A 393 MET cc_start: 0.7215 (ttm) cc_final: 0.6887 (ttm) REVERT: A 439 GLN cc_start: 0.8237 (pm20) cc_final: 0.7362 (pm20) REVERT: A 441 TRP cc_start: 0.7935 (t-100) cc_final: 0.7618 (t-100) REVERT: A 443 ARG cc_start: 0.6808 (ttt-90) cc_final: 0.6315 (ttt-90) REVERT: A 453 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7474 (mm-30) REVERT: A 457 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7496 (ttp-170) REVERT: A 458 GLU cc_start: 0.7855 (pp20) cc_final: 0.7608 (tm-30) REVERT: A 487 ASP cc_start: 0.8333 (m-30) cc_final: 0.8131 (m-30) REVERT: A 565 HIS cc_start: 0.7534 (t-90) cc_final: 0.7286 (t-90) REVERT: A 574 ARG cc_start: 0.8424 (ptp90) cc_final: 0.7976 (ptp90) REVERT: A 579 ARG cc_start: 0.7385 (ttm110) cc_final: 0.7016 (ttm110) REVERT: A 586 THR cc_start: 0.8033 (t) cc_final: 0.7784 (p) REVERT: A 593 SER cc_start: 0.7977 (m) cc_final: 0.7627 (p) REVERT: A 607 TRP cc_start: 0.8336 (t-100) cc_final: 0.7785 (t60) REVERT: A 750 PHE cc_start: 0.7132 (m-80) cc_final: 0.6533 (m-80) REVERT: A 758 ASN cc_start: 0.7894 (m-40) cc_final: 0.7459 (t0) REVERT: A 806 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7525 (mmmm) REVERT: A 812 MET cc_start: 0.7425 (mpp) cc_final: 0.7147 (mpp) REVERT: A 816 LEU cc_start: 0.8462 (tp) cc_final: 0.8082 (tp) REVERT: A 827 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7239 (mpt-90) REVERT: A 832 ASP cc_start: 0.8228 (t0) cc_final: 0.7867 (t70) REVERT: A 837 TYR cc_start: 0.6098 (m-80) cc_final: 0.5796 (m-10) REVERT: A 870 VAL cc_start: 0.8294 (m) cc_final: 0.8060 (p) REVERT: A 877 MET cc_start: 0.7073 (mmm) cc_final: 0.6829 (mmm) REVERT: A 893 SER cc_start: 0.7254 (t) cc_final: 0.6929 (t) REVERT: A 922 GLN cc_start: 0.7385 (tt0) cc_final: 0.6567 (tp-100) REVERT: A 981 LYS cc_start: 0.8236 (tttt) cc_final: 0.7676 (tppt) REVERT: A 1057 MET cc_start: 0.7867 (ppp) cc_final: 0.7629 (ppp) REVERT: A 1060 LYS cc_start: 0.8252 (tptp) cc_final: 0.7765 (tptp) REVERT: A 1102 GLN cc_start: 0.7345 (mp10) cc_final: 0.6492 (mp10) REVERT: A 1110 HIS cc_start: 0.8510 (m90) cc_final: 0.8202 (m-70) REVERT: A 1116 MET cc_start: 0.7237 (tpt) cc_final: 0.6480 (tpt) REVERT: A 1136 GLU cc_start: 0.5881 (mt-10) cc_final: 0.5586 (mt-10) REVERT: A 1195 MET cc_start: 0.7409 (ttm) cc_final: 0.7040 (ttm) REVERT: A 1206 MET cc_start: 0.6054 (mtm) cc_final: 0.5826 (mtt) REVERT: A 1222 GLN cc_start: 0.8470 (mp10) cc_final: 0.7813 (mp10) REVERT: B 71 GLU cc_start: 0.8030 (pp20) cc_final: 0.7767 (tm-30) REVERT: B 85 GLN cc_start: 0.7483 (mt0) cc_final: 0.6965 (mt0) REVERT: B 88 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7700 (ptp90) REVERT: B 113 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6772 (mm-30) REVERT: B 123 GLU cc_start: 0.7551 (pt0) cc_final: 0.7230 (pt0) REVERT: B 134 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8147 (mtpt) REVERT: B 180 LYS cc_start: 0.8289 (ptmt) cc_final: 0.7842 (ptmt) REVERT: B 183 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 191 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 201 ASN cc_start: 0.7789 (m110) cc_final: 0.7504 (m110) REVERT: B 210 GLN cc_start: 0.7599 (tt0) cc_final: 0.7295 (tt0) REVERT: B 234 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7921 (mtmm) REVERT: B 246 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7798 (ttp80) REVERT: B 288 LYS cc_start: 0.7235 (mttt) cc_final: 0.6534 (mtpt) REVERT: B 289 LEU cc_start: 0.7830 (mt) cc_final: 0.7491 (mt) REVERT: B 304 TRP cc_start: 0.7737 (m100) cc_final: 0.7346 (m100) REVERT: B 310 GLU cc_start: 0.7572 (mp0) cc_final: 0.7344 (mp0) REVERT: B 315 TYR cc_start: 0.7889 (m-80) cc_final: 0.7596 (m-80) REVERT: B 339 ASN cc_start: 0.6686 (t0) cc_final: 0.6235 (t0) REVERT: B 352 ASP cc_start: 0.7167 (t0) cc_final: 0.6932 (t0) REVERT: B 396 ARG cc_start: 0.7504 (ttm170) cc_final: 0.7109 (ttm110) REVERT: B 400 GLN cc_start: 0.7715 (tt0) cc_final: 0.7494 (tp40) REVERT: B 412 SER cc_start: 0.8329 (t) cc_final: 0.7809 (p) REVERT: B 427 GLN cc_start: 0.8265 (pt0) cc_final: 0.7624 (pm20) REVERT: B 431 LYS cc_start: 0.8466 (tttt) cc_final: 0.7997 (tppt) REVERT: B 446 THR cc_start: 0.8216 (m) cc_final: 0.7969 (m) REVERT: B 449 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 457 SER cc_start: 0.7873 (t) cc_final: 0.7618 (p) REVERT: B 460 THR cc_start: 0.8495 (p) cc_final: 0.8141 (p) REVERT: B 462 MET cc_start: 0.7793 (mmt) cc_final: 0.7560 (mmt) REVERT: B 465 MET cc_start: 0.7488 (mtm) cc_final: 0.6980 (mtm) REVERT: B 466 MET cc_start: 0.7285 (mtp) cc_final: 0.7030 (ttp) REVERT: B 483 LYS cc_start: 0.6287 (mtpp) cc_final: 0.5953 (mtpp) REVERT: C 75 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7599 (mtp85) REVERT: C 80 SER cc_start: 0.8422 (t) cc_final: 0.8052 (m) REVERT: C 180 LYS cc_start: 0.7808 (pttt) cc_final: 0.7569 (ptmt) REVERT: C 183 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6369 (mt-10) REVERT: C 185 LEU cc_start: 0.8977 (mt) cc_final: 0.8630 (mt) REVERT: C 194 VAL cc_start: 0.7825 (m) cc_final: 0.7554 (p) REVERT: C 203 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7271 (ttt180) REVERT: C 233 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6239 (mp0) REVERT: C 256 LEU cc_start: 0.8493 (tp) cc_final: 0.8220 (tp) REVERT: C 262 TRP cc_start: 0.7744 (t60) cc_final: 0.7094 (t60) REVERT: C 287 ASN cc_start: 0.7074 (t0) cc_final: 0.6812 (t0) REVERT: C 288 LYS cc_start: 0.8249 (mttt) cc_final: 0.7708 (mttt) REVERT: C 297 LYS cc_start: 0.7907 (mttp) cc_final: 0.7601 (mttp) REVERT: C 301 GLU cc_start: 0.7421 (tt0) cc_final: 0.6947 (tt0) REVERT: C 305 ASN cc_start: 0.7569 (t0) cc_final: 0.7281 (t0) REVERT: C 306 LEU cc_start: 0.8138 (mt) cc_final: 0.7664 (mm) REVERT: C 328 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7600 (mtt180) REVERT: C 336 LEU cc_start: 0.8437 (mt) cc_final: 0.7958 (mt) REVERT: C 347 LEU cc_start: 0.8319 (mm) cc_final: 0.8040 (pp) REVERT: C 354 PHE cc_start: 0.7919 (t80) cc_final: 0.7565 (t80) REVERT: C 371 VAL cc_start: 0.8196 (p) cc_final: 0.7988 (m) REVERT: C 372 LEU cc_start: 0.8660 (mt) cc_final: 0.8322 (mt) REVERT: C 373 LYS cc_start: 0.8270 (mttt) cc_final: 0.7541 (ptpp) REVERT: C 396 ARG cc_start: 0.7809 (ttm170) cc_final: 0.6794 (ttm170) REVERT: C 400 GLN cc_start: 0.7824 (mt0) cc_final: 0.6853 (mt0) REVERT: C 404 ASN cc_start: 0.7981 (m-40) cc_final: 0.7405 (m110) REVERT: C 415 PRO cc_start: 0.8687 (Cg_endo) cc_final: 0.8474 (Cg_exo) REVERT: C 421 MET cc_start: 0.6516 (mtt) cc_final: 0.6274 (mtt) REVERT: C 426 GLU cc_start: 0.7531 (pp20) cc_final: 0.7248 (pp20) REVERT: C 427 GLN cc_start: 0.8147 (mt0) cc_final: 0.7547 (mt0) REVERT: C 430 SER cc_start: 0.8395 (t) cc_final: 0.7899 (p) REVERT: C 434 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 470 LYS cc_start: 0.8494 (mttt) cc_final: 0.8150 (mttt) REVERT: C 471 LEU cc_start: 0.8117 (tp) cc_final: 0.7877 (tt) REVERT: C 478 TYR cc_start: 0.8017 (t80) cc_final: 0.7769 (t80) outliers start: 2 outliers final: 0 residues processed: 573 average time/residue: 0.4458 time to fit residues: 364.2889 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 : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 156 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** 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 277 HIS A 398 GLN A 410 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 305 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS C 279 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.121653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094660 restraints weight = 63497.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100129 restraints weight = 26417.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103707 restraints weight = 14237.711| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2825 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= 0.133 Angle : 0.552 8.515 22166 Z= 0.289 Chirality : 0.041 0.185 2406 Planarity : 0.004 0.057 2692 Dihedral : 14.414 88.957 2496 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.25 % Allowed : 1.13 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1837 helix: 1.81 (0.19), residues: 789 sheet: 0.24 (0.33), residues: 249 loop : -0.27 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 572 HIS 0.004 0.001 HIS A 138 PHE 0.036 0.002 PHE C 242 TYR 0.023 0.002 TYR B 315 ARG 0.010 0.000 ARG A1148 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 767) hydrogen bonds : angle 4.57875 ( 2137) covalent geometry : bond 0.00284 (16209) covalent geometry : angle 0.55175 (22166) *********************** 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 573 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 571 time to evaluate : 1.694 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: 0.8473 (mm) cc_final: 0.8136 (mm) REVERT: A 79 LEU cc_start: 0.8099 (mt) cc_final: 0.7881 (mp) REVERT: A 110 HIS cc_start: 0.7328 (m90) cc_final: 0.6660 (m90) REVERT: A 133 ASP cc_start: 0.6707 (p0) cc_final: 0.6053 (m-30) REVERT: A 159 GLN cc_start: 0.7112 (tm-30) cc_final: 0.6544 (pp30) REVERT: A 169 TRP cc_start: 0.7934 (m-90) cc_final: 0.7656 (m-90) REVERT: A 177 ARG cc_start: 0.8183 (ttt90) cc_final: 0.7675 (ttt90) REVERT: A 264 GLN cc_start: 0.7915 (pt0) cc_final: 0.7693 (pt0) REVERT: A 280 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6893 (mm-30) REVERT: A 295 MET cc_start: 0.7525 (ttt) cc_final: 0.6817 (ttm) REVERT: A 308 GLN cc_start: 0.7827 (mt0) cc_final: 0.7471 (tt0) REVERT: A 355 SER cc_start: 0.7564 (t) cc_final: 0.6807 (t) REVERT: A 358 GLU cc_start: 0.7725 (mp0) cc_final: 0.7013 (mp0) REVERT: A 374 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7775 (ttt180) REVERT: A 393 MET cc_start: 0.7143 (ttm) cc_final: 0.6867 (ttm) REVERT: A 439 GLN cc_start: 0.8242 (pm20) cc_final: 0.7367 (pm20) REVERT: A 441 TRP cc_start: 0.7925 (t-100) cc_final: 0.7585 (t-100) REVERT: A 443 ARG cc_start: 0.6836 (ttt-90) cc_final: 0.6361 (ttt-90) REVERT: A 453 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7483 (mm-30) REVERT: A 487 ASP cc_start: 0.8311 (m-30) cc_final: 0.8090 (m-30) REVERT: A 564 GLN cc_start: 0.7510 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 565 HIS cc_start: 0.7649 (t-90) cc_final: 0.7284 (t-90) REVERT: A 574 ARG cc_start: 0.8352 (ptp90) cc_final: 0.7932 (ptp90) REVERT: A 579 ARG cc_start: 0.7441 (ttm110) cc_final: 0.7069 (ttm110) REVERT: A 586 THR cc_start: 0.8028 (t) cc_final: 0.7797 (p) REVERT: A 593 SER cc_start: 0.8010 (m) cc_final: 0.7363 (p) REVERT: A 607 TRP cc_start: 0.8342 (t-100) cc_final: 0.7761 (t60) REVERT: A 758 ASN cc_start: 0.7911 (m-40) cc_final: 0.7442 (t0) REVERT: A 806 LYS cc_start: 0.7879 (mmmm) cc_final: 0.7528 (mmmm) REVERT: A 812 MET cc_start: 0.7405 (mpp) cc_final: 0.7136 (mpp) REVERT: A 816 LEU cc_start: 0.8475 (tp) cc_final: 0.8122 (tp) REVERT: A 832 ASP cc_start: 0.8260 (t0) cc_final: 0.7893 (t0) REVERT: A 837 TYR cc_start: 0.6071 (m-80) cc_final: 0.5772 (m-10) REVERT: A 870 VAL cc_start: 0.8305 (m) cc_final: 0.8068 (p) REVERT: A 893 SER cc_start: 0.7217 (t) cc_final: 0.6863 (t) REVERT: A 922 GLN cc_start: 0.7397 (tt0) cc_final: 0.6589 (tp-100) REVERT: A 981 LYS cc_start: 0.8210 (tttt) cc_final: 0.7691 (tppt) REVERT: A 1057 MET cc_start: 0.7848 (ppp) cc_final: 0.7625 (ppp) REVERT: A 1060 LYS cc_start: 0.8248 (tptp) cc_final: 0.7797 (tptp) REVERT: A 1102 GLN cc_start: 0.7520 (mp10) cc_final: 0.6668 (mp10) REVERT: A 1110 HIS cc_start: 0.8504 (m90) cc_final: 0.8174 (m-70) REVERT: A 1111 LEU cc_start: 0.8381 (mt) cc_final: 0.8140 (mt) REVERT: A 1116 MET cc_start: 0.7223 (tpt) cc_final: 0.6489 (tpt) REVERT: A 1136 GLU cc_start: 0.5860 (mt-10) cc_final: 0.5598 (mt-10) REVERT: A 1145 ASP cc_start: 0.6699 (m-30) cc_final: 0.6395 (m-30) REVERT: A 1188 CYS cc_start: 0.8170 (p) cc_final: 0.7924 (p) REVERT: A 1219 ASP cc_start: 0.8079 (t0) cc_final: 0.7505 (t70) REVERT: A 1222 GLN cc_start: 0.8497 (mp10) cc_final: 0.7750 (mp10) REVERT: B 71 GLU cc_start: 0.8054 (pp20) cc_final: 0.7782 (tm-30) REVERT: B 85 GLN cc_start: 0.7476 (mt0) cc_final: 0.7010 (mt0) REVERT: B 88 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.7711 (ptp90) REVERT: B 113 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6784 (mm-30) REVERT: B 123 GLU cc_start: 0.7518 (pt0) cc_final: 0.7177 (pt0) REVERT: B 180 LYS cc_start: 0.8268 (ptmt) cc_final: 0.7813 (ptmt) REVERT: B 183 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7028 (mt-10) REVERT: B 191 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 201 ASN cc_start: 0.7772 (m110) cc_final: 0.7527 (m110) REVERT: B 246 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7792 (ttp80) REVERT: B 268 MET cc_start: 0.6336 (tmm) cc_final: 0.6057 (tmm) REVERT: B 288 LYS cc_start: 0.7191 (mttt) cc_final: 0.6547 (mtmt) REVERT: B 289 LEU cc_start: 0.7847 (mt) cc_final: 0.7525 (mt) REVERT: B 304 TRP cc_start: 0.7782 (m100) cc_final: 0.7364 (m100) REVERT: B 310 GLU cc_start: 0.7591 (mp0) cc_final: 0.7351 (mp0) REVERT: B 315 TYR cc_start: 0.7883 (m-80) cc_final: 0.7609 (m-80) REVERT: B 339 ASN cc_start: 0.6673 (t0) cc_final: 0.6317 (t0) REVERT: B 352 ASP cc_start: 0.7439 (t0) cc_final: 0.6800 (t0) REVERT: B 396 ARG cc_start: 0.7454 (ttm170) cc_final: 0.7056 (ttm110) REVERT: B 400 GLN cc_start: 0.7705 (tt0) cc_final: 0.7500 (tp40) REVERT: B 412 SER cc_start: 0.8270 (t) cc_final: 0.7829 (p) REVERT: B 427 GLN cc_start: 0.8146 (pt0) cc_final: 0.7625 (pm20) REVERT: B 431 LYS cc_start: 0.8441 (tttt) cc_final: 0.8041 (tppt) REVERT: B 446 THR cc_start: 0.8257 (m) cc_final: 0.8000 (m) REVERT: B 449 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 457 SER cc_start: 0.7904 (t) cc_final: 0.7596 (p) REVERT: B 460 THR cc_start: 0.8497 (p) cc_final: 0.8149 (p) REVERT: B 461 THR cc_start: 0.8236 (p) cc_final: 0.7976 (t) REVERT: B 462 MET cc_start: 0.7716 (mmt) cc_final: 0.7505 (mmt) REVERT: B 465 MET cc_start: 0.7497 (mtm) cc_final: 0.6983 (mtm) REVERT: B 466 MET cc_start: 0.7301 (mtp) cc_final: 0.7004 (ttp) REVERT: B 483 LYS cc_start: 0.6189 (mtpp) cc_final: 0.5859 (mtpp) REVERT: C 71 GLU cc_start: 0.8304 (tt0) cc_final: 0.8098 (tt0) REVERT: C 75 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7464 (mtp85) REVERT: C 80 SER cc_start: 0.8450 (t) cc_final: 0.8060 (m) REVERT: C 180 LYS cc_start: 0.7793 (pttt) cc_final: 0.7553 (ptmt) REVERT: C 183 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6415 (mt-10) REVERT: C 185 LEU cc_start: 0.8985 (mt) cc_final: 0.8622 (mt) REVERT: C 194 VAL cc_start: 0.7840 (m) cc_final: 0.7496 (p) REVERT: C 216 HIS cc_start: 0.7994 (m90) cc_final: 0.7560 (m-70) REVERT: C 233 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6223 (mp0) REVERT: C 234 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7774 (mtmm) REVERT: C 256 LEU cc_start: 0.8493 (tp) cc_final: 0.8206 (tp) REVERT: C 262 TRP cc_start: 0.7694 (t60) cc_final: 0.7151 (t60) REVERT: C 268 MET cc_start: 0.6585 (mpp) cc_final: 0.5802 (mpp) REVERT: C 287 ASN cc_start: 0.7159 (t0) cc_final: 0.6868 (t0) REVERT: C 288 LYS cc_start: 0.8249 (mttt) cc_final: 0.7685 (mttt) REVERT: C 297 LYS cc_start: 0.7838 (mttp) cc_final: 0.7549 (mttp) REVERT: C 301 GLU cc_start: 0.7413 (tt0) cc_final: 0.6711 (tt0) REVERT: C 305 ASN cc_start: 0.7595 (t0) cc_final: 0.7285 (t0) REVERT: C 306 LEU cc_start: 0.8157 (mt) cc_final: 0.7647 (mm) REVERT: C 336 LEU cc_start: 0.8462 (mt) cc_final: 0.7993 (mt) REVERT: C 346 MET cc_start: 0.6867 (tmm) cc_final: 0.6560 (tmm) REVERT: C 352 ASP cc_start: 0.7015 (t70) cc_final: 0.5510 (t70) REVERT: C 354 PHE cc_start: 0.7962 (t80) cc_final: 0.7606 (t80) REVERT: C 371 VAL cc_start: 0.8198 (p) cc_final: 0.7950 (m) REVERT: C 372 LEU cc_start: 0.8615 (mt) cc_final: 0.8382 (tp) REVERT: C 373 LYS cc_start: 0.8095 (mttt) cc_final: 0.7770 (mtmm) REVERT: C 396 ARG cc_start: 0.7812 (ttm170) cc_final: 0.6963 (mmt90) REVERT: C 400 GLN cc_start: 0.7859 (mt0) cc_final: 0.6826 (mt0) REVERT: C 404 ASN cc_start: 0.7984 (m-40) cc_final: 0.7359 (m110) REVERT: C 415 PRO cc_start: 0.8713 (Cg_endo) cc_final: 0.8478 (Cg_exo) REVERT: C 421 MET cc_start: 0.6487 (mtt) cc_final: 0.6244 (mtt) REVERT: C 426 GLU cc_start: 0.7536 (pp20) cc_final: 0.7263 (pp20) REVERT: C 427 GLN cc_start: 0.8147 (mt0) cc_final: 0.7537 (mt0) REVERT: C 430 SER cc_start: 0.8409 (t) cc_final: 0.7915 (p) REVERT: C 434 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7567 (mt-10) REVERT: C 456 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7516 (ttm170) REVERT: C 458 ARG cc_start: 0.8379 (ptt180) cc_final: 0.8076 (ptt180) REVERT: C 466 MET cc_start: 0.6952 (ttm) cc_final: 0.6746 (ttm) REVERT: C 470 LYS cc_start: 0.8495 (mttt) cc_final: 0.8128 (mttt) REVERT: C 478 TYR cc_start: 0.8007 (t80) cc_final: 0.7735 (t80) outliers start: 2 outliers final: 1 residues processed: 571 average time/residue: 0.4630 time to fit residues: 380.3111 Evaluate side-chains 536 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 535 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 126 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** 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 398 GLN A 410 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN C 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095240 restraints weight = 67565.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100831 restraints weight = 27354.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104513 restraints weight = 14556.868| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16209 Z= 0.117 Angle : 0.554 8.559 22166 Z= 0.288 Chirality : 0.041 0.197 2406 Planarity : 0.004 0.054 2692 Dihedral : 14.355 88.827 2496 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.13 % Allowed : 0.75 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1837 helix: 1.92 (0.19), residues: 789 sheet: 0.29 (0.34), residues: 242 loop : -0.30 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 572 HIS 0.007 0.001 HIS A 565 PHE 0.031 0.002 PHE C 242 TYR 0.027 0.001 TYR C 193 ARG 0.007 0.000 ARG A 827 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 767) hydrogen bonds : angle 4.50213 ( 2137) covalent geometry : bond 0.00253 (16209) covalent geometry : angle 0.55441 (22166) *********************** 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 562 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 1.853 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: 0.8517 (mm) cc_final: 0.8239 (mm) REVERT: A 110 HIS cc_start: 0.7273 (m90) cc_final: 0.6637 (m90) REVERT: A 136 ASP cc_start: 0.7946 (t0) cc_final: 0.7731 (t70) REVERT: A 159 GLN cc_start: 0.7092 (tm-30) cc_final: 0.6504 (pp30) REVERT: A 177 ARG cc_start: 0.8161 (ttt90) cc_final: 0.7742 (ttt90) REVERT: A 235 TRP cc_start: 0.7036 (m100) cc_final: 0.6537 (m100) REVERT: A 280 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 295 MET cc_start: 0.7504 (ttt) cc_final: 0.6791 (ttm) REVERT: A 308 GLN cc_start: 0.7849 (mt0) cc_final: 0.7458 (tt0) REVERT: A 355 SER cc_start: 0.7468 (t) cc_final: 0.6755 (t) REVERT: A 358 GLU cc_start: 0.7721 (mp0) cc_final: 0.7000 (mp0) REVERT: A 393 MET cc_start: 0.7204 (ttm) cc_final: 0.6884 (ttm) REVERT: A 439 GLN cc_start: 0.8311 (pm20) cc_final: 0.7336 (pm20) REVERT: A 441 TRP cc_start: 0.7909 (t-100) cc_final: 0.7656 (t-100) REVERT: A 443 ARG cc_start: 0.6803 (ttt-90) cc_final: 0.6298 (ttt-90) REVERT: A 453 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7458 (mm-30) REVERT: A 487 ASP cc_start: 0.8315 (m-30) cc_final: 0.8111 (m-30) REVERT: A 551 LYS cc_start: 0.8447 (tptp) cc_final: 0.8178 (ttmm) REVERT: A 565 HIS cc_start: 0.7627 (t-90) cc_final: 0.7184 (t-90) REVERT: A 574 ARG cc_start: 0.8356 (ptp90) cc_final: 0.7950 (ptp90) REVERT: A 579 ARG cc_start: 0.7442 (ttm110) cc_final: 0.7053 (ttm110) REVERT: A 586 THR cc_start: 0.8058 (t) cc_final: 0.7794 (p) REVERT: A 593 SER cc_start: 0.8021 (m) cc_final: 0.7407 (p) REVERT: A 607 TRP cc_start: 0.8359 (t-100) cc_final: 0.7845 (t60) REVERT: A 758 ASN cc_start: 0.7907 (m-40) cc_final: 0.7446 (t0) REVERT: A 797 MET cc_start: 0.7616 (ttm) cc_final: 0.7334 (ttm) REVERT: A 812 MET cc_start: 0.7390 (mpp) cc_final: 0.7145 (mpp) REVERT: A 816 LEU cc_start: 0.8457 (tp) cc_final: 0.8114 (tp) REVERT: A 832 ASP cc_start: 0.8244 (t0) cc_final: 0.7978 (t0) REVERT: A 837 TYR cc_start: 0.6052 (m-80) cc_final: 0.5746 (m-10) REVERT: A 870 VAL cc_start: 0.8257 (m) cc_final: 0.8031 (p) REVERT: A 893 SER cc_start: 0.7198 (t) cc_final: 0.6850 (t) REVERT: A 919 MET cc_start: 0.7381 (mtt) cc_final: 0.7038 (mpp) REVERT: A 922 GLN cc_start: 0.7370 (tt0) cc_final: 0.6579 (tp-100) REVERT: A 934 LYS cc_start: 0.8227 (mmtt) cc_final: 0.8006 (mmtt) REVERT: A 981 LYS cc_start: 0.8216 (tttt) cc_final: 0.7650 (tppt) REVERT: A 985 MET cc_start: 0.7513 (ttp) cc_final: 0.7306 (ttp) REVERT: A 1057 MET cc_start: 0.7913 (ppp) cc_final: 0.7700 (ppp) REVERT: A 1060 LYS cc_start: 0.8247 (tptp) cc_final: 0.7784 (tptp) REVERT: A 1110 HIS cc_start: 0.8429 (m90) cc_final: 0.8160 (m-70) REVERT: A 1111 LEU cc_start: 0.8307 (mt) cc_final: 0.8019 (mt) REVERT: A 1116 MET cc_start: 0.7180 (tpt) cc_final: 0.6458 (tpt) REVERT: A 1136 GLU cc_start: 0.5872 (mt-10) cc_final: 0.5540 (mt-10) REVERT: A 1156 THR cc_start: 0.7858 (m) cc_final: 0.7133 (m) REVERT: A 1188 CYS cc_start: 0.8177 (p) cc_final: 0.7578 (p) REVERT: A 1192 GLU cc_start: 0.7748 (mp0) cc_final: 0.7489 (mp0) REVERT: A 1206 MET cc_start: 0.6010 (mtm) cc_final: 0.5754 (mtt) REVERT: A 1219 ASP cc_start: 0.8089 (t0) cc_final: 0.7795 (t0) REVERT: A 1222 GLN cc_start: 0.8418 (mp10) cc_final: 0.8216 (mt0) REVERT: B 71 GLU cc_start: 0.8077 (pp20) cc_final: 0.7804 (tm-30) REVERT: B 76 ARG cc_start: 0.8098 (mmp80) cc_final: 0.7791 (mmt-90) REVERT: B 85 GLN cc_start: 0.7531 (mt0) cc_final: 0.7113 (mt0) REVERT: B 88 ARG cc_start: 0.7940 (ptp-170) cc_final: 0.7717 (ptp90) REVERT: B 113 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6758 (mm-30) REVERT: B 123 GLU cc_start: 0.7519 (pt0) cc_final: 0.7165 (pt0) REVERT: B 180 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7748 (pttm) REVERT: B 183 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7042 (mt-10) REVERT: B 191 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7213 (mt-10) REVERT: B 201 ASN cc_start: 0.7736 (m110) cc_final: 0.7526 (m110) REVERT: B 235 THR cc_start: 0.7985 (m) cc_final: 0.7774 (m) REVERT: B 246 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7803 (ttp80) REVERT: B 247 THR cc_start: 0.7893 (p) cc_final: 0.7685 (p) REVERT: B 268 MET cc_start: 0.6279 (tmm) cc_final: 0.6036 (tmm) REVERT: B 288 LYS cc_start: 0.7184 (mttt) cc_final: 0.6539 (mtmt) REVERT: B 289 LEU cc_start: 0.7821 (mt) cc_final: 0.7489 (mt) REVERT: B 304 TRP cc_start: 0.7719 (m100) cc_final: 0.7307 (m100) REVERT: B 310 GLU cc_start: 0.7579 (mp0) cc_final: 0.7343 (mp0) REVERT: B 352 ASP cc_start: 0.7397 (t0) cc_final: 0.6757 (t0) REVERT: B 396 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7025 (ttm110) REVERT: B 400 GLN cc_start: 0.7686 (tt0) cc_final: 0.7484 (tp40) REVERT: B 412 SER cc_start: 0.8316 (t) cc_final: 0.7808 (p) REVERT: B 427 GLN cc_start: 0.8172 (pt0) cc_final: 0.7625 (pm20) REVERT: B 431 LYS cc_start: 0.8413 (tttt) cc_final: 0.8119 (tttt) REVERT: B 449 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 457 SER cc_start: 0.7911 (t) cc_final: 0.7615 (p) REVERT: B 460 THR cc_start: 0.8475 (p) cc_final: 0.8169 (p) REVERT: B 461 THR cc_start: 0.8204 (p) cc_final: 0.7964 (t) REVERT: B 462 MET cc_start: 0.7674 (mmt) cc_final: 0.7446 (mmt) REVERT: B 465 MET cc_start: 0.7451 (mtm) cc_final: 0.7052 (mpp) REVERT: B 466 MET cc_start: 0.7281 (mtp) cc_final: 0.7011 (ttp) REVERT: B 483 LYS cc_start: 0.6160 (mtpp) cc_final: 0.5834 (mtpp) REVERT: C 71 GLU cc_start: 0.8336 (tt0) cc_final: 0.8089 (tt0) REVERT: C 75 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7500 (mtp85) REVERT: C 80 SER cc_start: 0.8431 (t) cc_final: 0.8012 (m) REVERT: C 146 ARG cc_start: 0.7420 (mmt90) cc_final: 0.7033 (mpt180) REVERT: C 183 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6360 (mt-10) REVERT: C 185 LEU cc_start: 0.8955 (mt) cc_final: 0.8616 (mt) REVERT: C 194 VAL cc_start: 0.7813 (m) cc_final: 0.7486 (p) REVERT: C 216 HIS cc_start: 0.8024 (m90) cc_final: 0.7637 (m-70) REVERT: C 234 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7642 (mtmm) REVERT: C 235 THR cc_start: 0.7851 (t) cc_final: 0.7043 (p) REVERT: C 256 LEU cc_start: 0.8515 (tp) cc_final: 0.8218 (tp) REVERT: C 262 TRP cc_start: 0.7560 (t60) cc_final: 0.6924 (t60) REVERT: C 265 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7822 (tmtt) REVERT: C 266 PHE cc_start: 0.8364 (m-80) cc_final: 0.8065 (m-10) REVERT: C 287 ASN cc_start: 0.7155 (t0) cc_final: 0.6818 (t0) REVERT: C 288 LYS cc_start: 0.8271 (mttt) cc_final: 0.7692 (mttt) REVERT: C 291 TYR cc_start: 0.7905 (t80) cc_final: 0.7673 (t80) REVERT: C 301 GLU cc_start: 0.7324 (tt0) cc_final: 0.6910 (tt0) REVERT: C 305 ASN cc_start: 0.7595 (t0) cc_final: 0.7300 (t0) REVERT: C 306 LEU cc_start: 0.8109 (mt) cc_final: 0.7627 (mm) REVERT: C 336 LEU cc_start: 0.8467 (mt) cc_final: 0.7986 (mt) REVERT: C 346 MET cc_start: 0.6949 (tmm) cc_final: 0.6667 (tmm) REVERT: C 371 VAL cc_start: 0.8205 (p) cc_final: 0.7924 (m) REVERT: C 372 LEU cc_start: 0.8570 (mt) cc_final: 0.8360 (tp) REVERT: C 373 LYS cc_start: 0.8102 (mttt) cc_final: 0.7826 (mtmm) REVERT: C 396 ARG cc_start: 0.7804 (ttm170) cc_final: 0.6825 (ttm170) REVERT: C 400 GLN cc_start: 0.7846 (mt0) cc_final: 0.7231 (mt0) REVERT: C 415 PRO cc_start: 0.8704 (Cg_endo) cc_final: 0.8462 (Cg_exo) REVERT: C 430 SER cc_start: 0.8409 (t) cc_final: 0.7896 (p) REVERT: C 434 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7504 (mt-10) REVERT: C 466 MET cc_start: 0.6954 (ttm) cc_final: 0.6715 (ttm) REVERT: C 470 LYS cc_start: 0.8486 (mttt) cc_final: 0.8099 (mttt) REVERT: C 471 LEU cc_start: 0.8163 (tp) cc_final: 0.7930 (tt) REVERT: C 478 TYR cc_start: 0.8007 (t80) cc_final: 0.7753 (t80) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.3602 time to fit residues: 287.1130 Evaluate side-chains 524 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 0.0170 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 398 GLN A 410 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A 803 ASN A 906 HIS ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 305 ASN B 404 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 261 GLN C 279 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.094459 restraints weight = 69826.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100074 restraints weight = 27990.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103785 restraints weight = 14887.433| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16209 Z= 0.133 Angle : 0.574 12.742 22166 Z= 0.296 Chirality : 0.042 0.211 2406 Planarity : 0.004 0.052 2692 Dihedral : 14.330 88.853 2496 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1837 helix: 1.90 (0.19), residues: 790 sheet: 0.23 (0.33), residues: 250 loop : -0.30 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 572 HIS 0.007 0.001 HIS B 216 PHE 0.027 0.002 PHE C 242 TYR 0.022 0.001 TYR B 315 ARG 0.010 0.001 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 767) hydrogen bonds : angle 4.52122 ( 2137) covalent geometry : bond 0.00285 (16209) covalent geometry : angle 0.57433 (22166) *********************** 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 555 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 554 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8558 (mm) cc_final: 0.8273 (mm) REVERT: A 110 HIS cc_start: 0.7248 (m90) cc_final: 0.6594 (m90) REVERT: A 125 LEU cc_start: 0.8554 (tp) cc_final: 0.8347 (tp) REVERT: A 159 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6492 (pp30) REVERT: A 169 TRP cc_start: 0.7971 (m-90) cc_final: 0.7677 (m-90) REVERT: A 213 VAL cc_start: 0.7394 (m) cc_final: 0.6974 (p) REVERT: A 270 ASN cc_start: 0.7616 (m-40) cc_final: 0.7244 (m-40) REVERT: A 280 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6957 (mm-30) REVERT: A 295 MET cc_start: 0.7567 (ttt) cc_final: 0.6768 (ttm) REVERT: A 297 MET cc_start: 0.7554 (mtt) cc_final: 0.7328 (mtp) REVERT: A 308 GLN cc_start: 0.7874 (mt0) cc_final: 0.7451 (tt0) REVERT: A 393 MET cc_start: 0.7177 (ttm) cc_final: 0.6865 (ttm) REVERT: A 410 GLN cc_start: 0.7733 (tt0) cc_final: 0.7066 (tt0) REVERT: A 439 GLN cc_start: 0.8281 (pm20) cc_final: 0.7778 (pm20) REVERT: A 443 ARG cc_start: 0.6787 (ttt-90) cc_final: 0.6303 (ttt-90) REVERT: A 453 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7369 (mm-30) REVERT: A 551 LYS cc_start: 0.8447 (tptp) cc_final: 0.8164 (ttmm) REVERT: A 552 LEU cc_start: 0.8982 (mm) cc_final: 0.8768 (mt) REVERT: A 565 HIS cc_start: 0.7603 (t-90) cc_final: 0.7343 (t-90) REVERT: A 574 ARG cc_start: 0.8375 (ptp90) cc_final: 0.7959 (ptp90) REVERT: A 579 ARG cc_start: 0.7454 (ttm110) cc_final: 0.7032 (ttm110) REVERT: A 586 THR cc_start: 0.8115 (t) cc_final: 0.7875 (p) REVERT: A 593 SER cc_start: 0.8031 (m) cc_final: 0.7537 (p) REVERT: A 607 TRP cc_start: 0.8400 (t-100) cc_final: 0.8002 (t60) REVERT: A 758 ASN cc_start: 0.7931 (m-40) cc_final: 0.7466 (t0) REVERT: A 806 LYS cc_start: 0.7994 (tptm) cc_final: 0.7757 (tptm) REVERT: A 812 MET cc_start: 0.7341 (mpp) cc_final: 0.7138 (mpp) REVERT: A 816 LEU cc_start: 0.8492 (tp) cc_final: 0.8154 (tp) REVERT: A 832 ASP cc_start: 0.8228 (t0) cc_final: 0.7973 (t0) REVERT: A 893 SER cc_start: 0.7212 (t) cc_final: 0.6858 (t) REVERT: A 919 MET cc_start: 0.7436 (mtt) cc_final: 0.7056 (mpp) REVERT: A 922 GLN cc_start: 0.7388 (tt0) cc_final: 0.6587 (tp-100) REVERT: A 934 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7988 (mmtt) REVERT: A 981 LYS cc_start: 0.8228 (tttt) cc_final: 0.7705 (tppt) REVERT: A 1060 LYS cc_start: 0.8251 (tptp) cc_final: 0.7792 (tptp) REVERT: A 1110 HIS cc_start: 0.8485 (m90) cc_final: 0.8215 (m-70) REVERT: A 1116 MET cc_start: 0.7173 (tpt) cc_final: 0.6449 (tpt) REVERT: A 1136 GLU cc_start: 0.5874 (mt-10) cc_final: 0.5593 (mt-10) REVERT: A 1148 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7478 (ttt180) REVERT: A 1188 CYS cc_start: 0.8287 (p) cc_final: 0.7921 (p) REVERT: A 1206 MET cc_start: 0.6065 (mtm) cc_final: 0.5725 (mtt) REVERT: A 1219 ASP cc_start: 0.8128 (t0) cc_final: 0.7536 (t0) REVERT: A 1222 GLN cc_start: 0.8428 (mp10) cc_final: 0.7736 (mp10) REVERT: B 71 GLU cc_start: 0.8088 (pp20) cc_final: 0.7835 (tm-30) REVERT: B 76 ARG cc_start: 0.8158 (mmp80) cc_final: 0.7872 (mmp80) REVERT: B 85 GLN cc_start: 0.7552 (mt0) cc_final: 0.7095 (mt0) REVERT: B 88 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7684 (ptp90) REVERT: B 113 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6802 (mm-30) REVERT: B 123 GLU cc_start: 0.7506 (pt0) cc_final: 0.7054 (pt0) REVERT: B 134 LYS cc_start: 0.8302 (mtpt) cc_final: 0.8003 (mtmt) REVERT: B 180 LYS cc_start: 0.8191 (ptmt) cc_final: 0.7455 (ptmt) REVERT: B 183 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6982 (mt-10) REVERT: B 191 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7197 (mt-10) REVERT: B 246 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7810 (ttp80) REVERT: B 247 THR cc_start: 0.7892 (p) cc_final: 0.7684 (p) REVERT: B 268 MET cc_start: 0.6361 (tmm) cc_final: 0.6086 (tmm) REVERT: B 288 LYS cc_start: 0.7180 (mttt) cc_final: 0.6521 (mtmt) REVERT: B 289 LEU cc_start: 0.7811 (mt) cc_final: 0.7509 (mt) REVERT: B 304 TRP cc_start: 0.7733 (m100) cc_final: 0.7331 (m100) REVERT: B 310 GLU cc_start: 0.7589 (mp0) cc_final: 0.7363 (mp0) REVERT: B 315 TYR cc_start: 0.7895 (m-80) cc_final: 0.7625 (m-80) REVERT: B 339 ASN cc_start: 0.6697 (t0) cc_final: 0.6292 (t0) REVERT: B 352 ASP cc_start: 0.7399 (t0) cc_final: 0.6746 (t0) REVERT: B 353 SER cc_start: 0.8195 (p) cc_final: 0.7982 (p) REVERT: B 396 ARG cc_start: 0.7481 (ttm170) cc_final: 0.7038 (ttm110) REVERT: B 412 SER cc_start: 0.8284 (t) cc_final: 0.7793 (p) REVERT: B 427 GLN cc_start: 0.8153 (pt0) cc_final: 0.7628 (pm20) REVERT: B 431 LYS cc_start: 0.8443 (tttt) cc_final: 0.7923 (tppt) REVERT: B 449 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7228 (mt-10) REVERT: B 457 SER cc_start: 0.7915 (t) cc_final: 0.7614 (p) REVERT: B 460 THR cc_start: 0.8515 (p) cc_final: 0.8166 (p) REVERT: B 461 THR cc_start: 0.8212 (p) cc_final: 0.7959 (t) REVERT: B 462 MET cc_start: 0.7665 (mmt) cc_final: 0.7413 (mmt) REVERT: B 465 MET cc_start: 0.7412 (mtm) cc_final: 0.6983 (mpp) REVERT: B 466 MET cc_start: 0.7243 (mtp) cc_final: 0.6977 (ttp) REVERT: B 483 LYS cc_start: 0.6178 (mtpp) cc_final: 0.5857 (mtpp) REVERT: C 80 SER cc_start: 0.8456 (t) cc_final: 0.8019 (m) REVERT: C 183 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6367 (mt-10) REVERT: C 185 LEU cc_start: 0.8974 (mt) cc_final: 0.8603 (mt) REVERT: C 194 VAL cc_start: 0.7887 (m) cc_final: 0.7509 (p) REVERT: C 203 ARG cc_start: 0.7576 (ttt180) cc_final: 0.7166 (ttt180) REVERT: C 216 HIS cc_start: 0.8044 (m90) cc_final: 0.7622 (m-70) REVERT: C 234 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7648 (mtmm) REVERT: C 235 THR cc_start: 0.7848 (t) cc_final: 0.7071 (p) REVERT: C 256 LEU cc_start: 0.8519 (tp) cc_final: 0.8247 (tp) REVERT: C 262 TRP cc_start: 0.7546 (t60) cc_final: 0.6939 (t60) REVERT: C 265 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7838 (tmtt) REVERT: C 266 PHE cc_start: 0.8383 (m-80) cc_final: 0.8114 (m-10) REVERT: C 287 ASN cc_start: 0.7110 (t0) cc_final: 0.6797 (t0) REVERT: C 288 LYS cc_start: 0.8266 (mttt) cc_final: 0.7683 (mttt) REVERT: C 291 TYR cc_start: 0.7889 (t80) cc_final: 0.7507 (t80) REVERT: C 301 GLU cc_start: 0.7330 (tt0) cc_final: 0.6878 (tt0) REVERT: C 305 ASN cc_start: 0.7640 (t0) cc_final: 0.7344 (t0) REVERT: C 306 LEU cc_start: 0.8111 (mt) cc_final: 0.7584 (mm) REVERT: C 323 HIS cc_start: 0.6344 (m90) cc_final: 0.6032 (m90) REVERT: C 336 LEU cc_start: 0.8449 (mt) cc_final: 0.7981 (mt) REVERT: C 354 PHE cc_start: 0.7965 (t80) cc_final: 0.7563 (t80) REVERT: C 371 VAL cc_start: 0.8206 (p) cc_final: 0.7965 (m) REVERT: C 396 ARG cc_start: 0.7840 (ttm170) cc_final: 0.6873 (ttm170) REVERT: C 400 GLN cc_start: 0.7660 (mt0) cc_final: 0.7303 (mt0) REVERT: C 415 PRO cc_start: 0.8738 (Cg_endo) cc_final: 0.8465 (Cg_exo) REVERT: C 421 MET cc_start: 0.6373 (mtm) cc_final: 0.5854 (mtm) REVERT: C 427 GLN cc_start: 0.8472 (tt0) cc_final: 0.8152 (tt0) REVERT: C 430 SER cc_start: 0.8489 (t) cc_final: 0.7937 (p) REVERT: C 434 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7493 (mt-10) REVERT: C 466 MET cc_start: 0.6969 (ttm) cc_final: 0.6753 (ttm) REVERT: C 470 LYS cc_start: 0.8514 (mttt) cc_final: 0.8102 (mttt) REVERT: C 471 LEU cc_start: 0.8176 (tp) cc_final: 0.7975 (tt) REVERT: C 478 TYR cc_start: 0.8019 (t80) cc_final: 0.7744 (t80) outliers start: 1 outliers final: 0 residues processed: 554 average time/residue: 0.3134 time to fit residues: 245.0370 Evaluate side-chains 523 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 154 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 398 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 906 HIS A1098 ASN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094885 restraints weight = 65170.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100323 restraints weight = 26919.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103926 restraints weight = 14476.530| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16209 Z= 0.136 Angle : 0.579 11.157 22166 Z= 0.300 Chirality : 0.042 0.220 2406 Planarity : 0.004 0.052 2692 Dihedral : 14.304 88.951 2496 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.13 % Allowed : 0.75 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1837 helix: 1.89 (0.19), residues: 790 sheet: 0.20 (0.33), residues: 255 loop : -0.31 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 490 HIS 0.006 0.001 HIS B 216 PHE 0.033 0.002 PHE A 139 TYR 0.022 0.001 TYR B 315 ARG 0.008 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 767) hydrogen bonds : angle 4.52075 ( 2137) covalent geometry : bond 0.00290 (16209) covalent geometry : angle 0.57852 (22166) ********************** 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 548 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8564 (mm) cc_final: 0.8240 (mm) REVERT: A 125 LEU cc_start: 0.8550 (tp) cc_final: 0.8349 (tp) REVERT: A 159 GLN cc_start: 0.7087 (tm-30) cc_final: 0.6512 (pp30) REVERT: A 169 TRP cc_start: 0.7951 (m-90) cc_final: 0.7687 (m-90) REVERT: A 213 VAL cc_start: 0.7427 (m) cc_final: 0.7047 (p) REVERT: A 235 TRP cc_start: 0.6958 (m100) cc_final: 0.6651 (m100) REVERT: A 270 ASN cc_start: 0.7630 (m-40) cc_final: 0.7285 (m-40) REVERT: A 280 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6889 (mm-30) REVERT: A 295 MET cc_start: 0.7568 (ttt) cc_final: 0.6754 (ttm) REVERT: A 297 MET cc_start: 0.7535 (mtt) cc_final: 0.7334 (mtp) REVERT: A 299 MET cc_start: 0.7410 (tpt) cc_final: 0.7019 (tpt) REVERT: A 308 GLN cc_start: 0.7902 (mt0) cc_final: 0.7483 (tt0) REVERT: A 393 MET cc_start: 0.7162 (ttm) cc_final: 0.6831 (ttm) REVERT: A 410 GLN cc_start: 0.7610 (tt0) cc_final: 0.6978 (tt0) REVERT: A 439 GLN cc_start: 0.8259 (pm20) cc_final: 0.7916 (pm20) REVERT: A 443 ARG cc_start: 0.6787 (ttt-90) cc_final: 0.6302 (ttt-90) REVERT: A 453 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7353 (mm-30) REVERT: A 454 GLU cc_start: 0.7553 (pp20) cc_final: 0.7321 (pp20) REVERT: A 464 MET cc_start: 0.7404 (mtp) cc_final: 0.7176 (mtt) REVERT: A 487 ASP cc_start: 0.8366 (m-30) cc_final: 0.8089 (m-30) REVERT: A 551 LYS cc_start: 0.8441 (tptp) cc_final: 0.8169 (ttmm) REVERT: A 565 HIS cc_start: 0.7606 (t-90) cc_final: 0.7191 (t-90) REVERT: A 574 ARG cc_start: 0.8333 (ptp90) cc_final: 0.7904 (ptp90) REVERT: A 579 ARG cc_start: 0.7476 (ttm110) cc_final: 0.6979 (ttm110) REVERT: A 586 THR cc_start: 0.8042 (t) cc_final: 0.7797 (p) REVERT: A 593 SER cc_start: 0.8013 (m) cc_final: 0.7563 (p) REVERT: A 607 TRP cc_start: 0.8415 (t-100) cc_final: 0.7918 (t60) REVERT: A 758 ASN cc_start: 0.7928 (m-40) cc_final: 0.7518 (t0) REVERT: A 806 LYS cc_start: 0.7981 (tptm) cc_final: 0.7753 (tptm) REVERT: A 812 MET cc_start: 0.7362 (mpp) cc_final: 0.7133 (mpp) REVERT: A 816 LEU cc_start: 0.8508 (tp) cc_final: 0.8172 (tp) REVERT: A 832 ASP cc_start: 0.8155 (t0) cc_final: 0.7910 (t70) REVERT: A 890 ASP cc_start: 0.6994 (t0) cc_final: 0.6783 (t0) REVERT: A 893 SER cc_start: 0.7205 (t) cc_final: 0.6861 (t) REVERT: A 919 MET cc_start: 0.7383 (mtt) cc_final: 0.7051 (mmp) REVERT: A 922 GLN cc_start: 0.7384 (tt0) cc_final: 0.6916 (tp40) REVERT: A 934 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7987 (mmtt) REVERT: A 981 LYS cc_start: 0.8171 (tttt) cc_final: 0.7689 (tppt) REVERT: A 1057 MET cc_start: 0.7834 (ppp) cc_final: 0.7627 (ppp) REVERT: A 1060 LYS cc_start: 0.8247 (tptp) cc_final: 0.7805 (tptp) REVERT: A 1116 MET cc_start: 0.7202 (tpt) cc_final: 0.6437 (tpt) REVERT: A 1136 GLU cc_start: 0.5808 (mt-10) cc_final: 0.5540 (mt-10) REVERT: A 1140 LEU cc_start: 0.8268 (mt) cc_final: 0.7793 (mt) REVERT: A 1156 THR cc_start: 0.7874 (m) cc_final: 0.7155 (m) REVERT: A 1188 CYS cc_start: 0.8248 (p) cc_final: 0.7863 (p) REVERT: A 1206 MET cc_start: 0.6095 (mtm) cc_final: 0.5853 (mtt) REVERT: A 1219 ASP cc_start: 0.8153 (t0) cc_final: 0.7591 (t0) REVERT: A 1222 GLN cc_start: 0.8422 (mp10) cc_final: 0.7743 (mp10) REVERT: B 85 GLN cc_start: 0.7565 (mt0) cc_final: 0.7088 (mt0) REVERT: B 88 ARG cc_start: 0.7950 (ptp-170) cc_final: 0.7699 (ptp90) REVERT: B 113 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6825 (mm-30) REVERT: B 123 GLU cc_start: 0.7508 (pt0) cc_final: 0.7128 (pt0) REVERT: B 134 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7927 (mtmt) REVERT: B 180 LYS cc_start: 0.8211 (ptmt) cc_final: 0.7340 (ptmt) REVERT: B 183 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 191 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 246 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7817 (ttp80) REVERT: B 247 THR cc_start: 0.7905 (p) cc_final: 0.7686 (p) REVERT: B 268 MET cc_start: 0.6358 (tmm) cc_final: 0.6082 (tmm) REVERT: B 288 LYS cc_start: 0.7223 (mttt) cc_final: 0.6567 (mtmt) REVERT: B 289 LEU cc_start: 0.7822 (mt) cc_final: 0.7514 (mt) REVERT: B 304 TRP cc_start: 0.7719 (m100) cc_final: 0.7341 (m100) REVERT: B 315 TYR cc_start: 0.7895 (m-80) cc_final: 0.7624 (m-80) REVERT: B 352 ASP cc_start: 0.7419 (t0) cc_final: 0.6790 (t0) REVERT: B 378 LEU cc_start: 0.8356 (mp) cc_final: 0.7853 (pp) REVERT: B 396 ARG cc_start: 0.7368 (ttm170) cc_final: 0.6987 (ttm110) REVERT: B 412 SER cc_start: 0.8282 (t) cc_final: 0.7800 (p) REVERT: B 427 GLN cc_start: 0.8144 (pt0) cc_final: 0.7795 (pm20) REVERT: B 431 LYS cc_start: 0.8430 (tttt) cc_final: 0.7928 (tppt) REVERT: B 457 SER cc_start: 0.7848 (t) cc_final: 0.7565 (p) REVERT: B 460 THR cc_start: 0.8462 (p) cc_final: 0.8140 (p) REVERT: B 461 THR cc_start: 0.8189 (p) cc_final: 0.7947 (t) REVERT: B 462 MET cc_start: 0.7698 (mmt) cc_final: 0.7463 (mmt) REVERT: B 463 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8222 (mtmt) REVERT: B 465 MET cc_start: 0.7420 (mtm) cc_final: 0.6935 (mpp) REVERT: B 466 MET cc_start: 0.7295 (mtp) cc_final: 0.6989 (ttp) REVERT: B 483 LYS cc_start: 0.6230 (mtpp) cc_final: 0.5885 (mtpp) REVERT: C 80 SER cc_start: 0.8462 (t) cc_final: 0.8007 (m) REVERT: C 110 LEU cc_start: 0.7984 (tt) cc_final: 0.7768 (tp) REVERT: C 185 LEU cc_start: 0.8946 (mt) cc_final: 0.8602 (mt) REVERT: C 194 VAL cc_start: 0.7844 (m) cc_final: 0.7451 (p) REVERT: C 203 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7182 (ttt180) REVERT: C 216 HIS cc_start: 0.8065 (m90) cc_final: 0.7610 (m-70) REVERT: C 231 ILE cc_start: 0.7678 (mm) cc_final: 0.7445 (mm) REVERT: C 234 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7687 (mtmm) REVERT: C 235 THR cc_start: 0.7855 (t) cc_final: 0.7058 (p) REVERT: C 256 LEU cc_start: 0.8545 (tp) cc_final: 0.8245 (tp) REVERT: C 262 TRP cc_start: 0.7511 (t60) cc_final: 0.6850 (t60) REVERT: C 265 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7832 (tmtt) REVERT: C 266 PHE cc_start: 0.8394 (m-80) cc_final: 0.8128 (m-10) REVERT: C 287 ASN cc_start: 0.7103 (t0) cc_final: 0.6781 (t0) REVERT: C 288 LYS cc_start: 0.8218 (mttt) cc_final: 0.7651 (mttt) REVERT: C 291 TYR cc_start: 0.7830 (t80) cc_final: 0.7400 (t80) REVERT: C 301 GLU cc_start: 0.7298 (tt0) cc_final: 0.6845 (tt0) REVERT: C 305 ASN cc_start: 0.7621 (t0) cc_final: 0.7332 (t0) REVERT: C 336 LEU cc_start: 0.8425 (mt) cc_final: 0.7968 (mt) REVERT: C 354 PHE cc_start: 0.8016 (t80) cc_final: 0.7606 (t80) REVERT: C 371 VAL cc_start: 0.8210 (p) cc_final: 0.7939 (m) REVERT: C 373 LYS cc_start: 0.8093 (mttt) cc_final: 0.7810 (mtmm) REVERT: C 396 ARG cc_start: 0.7821 (ttm170) cc_final: 0.6829 (ttm170) REVERT: C 400 GLN cc_start: 0.7866 (mt0) cc_final: 0.6747 (mt0) REVERT: C 404 ASN cc_start: 0.8054 (m-40) cc_final: 0.7166 (m110) REVERT: C 415 PRO cc_start: 0.8719 (Cg_endo) cc_final: 0.8475 (Cg_exo) REVERT: C 421 MET cc_start: 0.6379 (mtm) cc_final: 0.5913 (mtm) REVERT: C 427 GLN cc_start: 0.8453 (tt0) cc_final: 0.8155 (tt0) REVERT: C 430 SER cc_start: 0.8487 (t) cc_final: 0.8246 (p) REVERT: C 466 MET cc_start: 0.6963 (ttm) cc_final: 0.6715 (ttm) REVERT: C 470 LYS cc_start: 0.8526 (mttt) cc_final: 0.8116 (mttt) REVERT: C 475 LEU cc_start: 0.8212 (mt) cc_final: 0.7954 (mm) REVERT: C 478 TYR cc_start: 0.8018 (t80) cc_final: 0.7783 (t80) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.3258 time to fit residues: 252.8134 Evaluate side-chains 521 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 170 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 106 HIS A 110 HIS ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 360 HIS A 398 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 906 HIS ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 404 ASN B 409 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN C 279 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094139 restraints weight = 76557.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099889 restraints weight = 29638.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103694 restraints weight = 15492.023| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3239 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= 0.124 Angle : 0.570 8.211 22166 Z= 0.294 Chirality : 0.042 0.214 2406 Planarity : 0.004 0.054 2692 Dihedral : 14.265 88.888 2496 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1837 helix: 1.90 (0.19), residues: 790 sheet: 0.25 (0.33), residues: 249 loop : -0.27 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 572 HIS 0.007 0.001 HIS B 216 PHE 0.030 0.002 PHE A 139 TYR 0.019 0.001 TYR B 315 ARG 0.008 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 767) hydrogen bonds : angle 4.47376 ( 2137) covalent geometry : bond 0.00267 (16209) covalent geometry : angle 0.57022 (22166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7734.75 seconds wall clock time: 138 minutes 59.37 seconds (8339.37 seconds total)