Starting phenix.real_space_refine on Mon Jan 20 20:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v54_42979/01_2025/8v54_42979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v54_42979/01_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_42979/01_2025/8v54_42979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v54_42979/01_2025/8v54_42979.map" model { file = "/net/cci-nas-00/data/ceres_data/8v54_42979/01_2025/8v54_42979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v54_42979/01_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-5571/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: 11.89, per 1000 atoms: 0.76 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: 4.03 Conformation dependent library (CDL) restraints added in 2.6 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: 4.94 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: 6.16 Time building geometry restraints manager: 4.62 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 43.090 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- 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= 0.213 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 *********************** 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 : 1.582 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: 0.3399 time to fit residues: 296.5215 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 : 1.525 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.094039 restraints weight = 75080.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099814 restraints weight = 29556.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103700 restraints weight = 15584.327| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 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 = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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= 0.201 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 *********************** 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 : 1.611 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: 0.8508 (mm) cc_final: 0.8192 (mm) REVERT: A 79 LEU cc_start: 0.8132 (mt) cc_final: 0.7869 (mp) REVERT: A 133 ASP cc_start: 0.6656 (p0) cc_final: 0.6394 (m-30) REVERT: A 136 ASP cc_start: 0.7727 (t70) cc_final: 0.7208 (t0) REVERT: A 145 LYS cc_start: 0.8127 (tptp) cc_final: 0.7685 (tptp) REVERT: A 159 GLN cc_start: 0.7133 (tm-30) cc_final: 0.6609 (pp30) REVERT: A 205 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 280 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 289 MET cc_start: 0.7352 (ttm) cc_final: 0.6697 (ttm) REVERT: A 290 ARG cc_start: 0.7532 (mmt-90) cc_final: 0.7315 (mmp80) REVERT: A 295 MET cc_start: 0.7367 (ttt) cc_final: 0.6758 (ttp) REVERT: A 299 MET cc_start: 0.7391 (tpt) cc_final: 0.6927 (tmm) REVERT: A 308 GLN cc_start: 0.7983 (mt0) cc_final: 0.7238 (mt0) REVERT: A 354 ASN cc_start: 0.7493 (m-40) cc_final: 0.7149 (m-40) REVERT: A 355 SER cc_start: 0.7723 (t) cc_final: 0.7513 (t) REVERT: A 375 GLU cc_start: 0.7384 (pt0) cc_final: 0.7014 (pt0) REVERT: A 393 MET cc_start: 0.7249 (ttm) cc_final: 0.6842 (ttm) REVERT: A 439 GLN cc_start: 0.7765 (pt0) cc_final: 0.7455 (pt0) REVERT: A 443 ARG cc_start: 0.7006 (ttt-90) cc_final: 0.6316 (ttt-90) REVERT: A 453 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7529 (mm-30) REVERT: A 457 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7491 (ttp-170) REVERT: A 484 TRP cc_start: 0.8115 (m-90) cc_final: 0.7433 (m-90) REVERT: A 565 HIS cc_start: 0.7857 (t70) cc_final: 0.7229 (t-170) REVERT: A 566 LEU cc_start: 0.8937 (mt) cc_final: 0.8605 (mm) REVERT: A 572 TRP cc_start: 0.8545 (p-90) cc_final: 0.8241 (p-90) REVERT: A 593 SER cc_start: 0.7917 (m) cc_final: 0.7628 (p) REVERT: A 598 VAL cc_start: 0.7929 (m) cc_final: 0.7695 (p) REVERT: A 607 TRP cc_start: 0.8239 (t-100) cc_final: 0.7702 (t60) REVERT: A 758 ASN cc_start: 0.7854 (m-40) cc_final: 0.7408 (t0) REVERT: A 769 ASP cc_start: 0.7504 (p0) cc_final: 0.6949 (p0) REVERT: A 806 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7655 (mmmm) REVERT: A 812 MET cc_start: 0.7472 (mpp) cc_final: 0.7186 (mpp) REVERT: A 816 LEU cc_start: 0.8455 (tp) cc_final: 0.8063 (tp) REVERT: A 823 ARG cc_start: 0.7522 (tmt-80) cc_final: 0.7297 (tmt-80) REVERT: A 826 ILE cc_start: 0.8038 (mt) cc_final: 0.7807 (pt) REVERT: A 877 MET cc_start: 0.7200 (mmm) cc_final: 0.6966 (mmm) REVERT: A 893 SER cc_start: 0.7224 (t) cc_final: 0.6630 (p) REVERT: A 916 PHE cc_start: 0.7993 (t80) cc_final: 0.7362 (t80) REVERT: A 922 GLN cc_start: 0.7548 (tt0) cc_final: 0.7041 (tp40) REVERT: A 981 LYS cc_start: 0.8293 (tttt) cc_final: 0.7779 (tptt) REVERT: A 1057 MET cc_start: 0.7762 (ppp) cc_final: 0.7515 (ppp) REVERT: A 1060 LYS cc_start: 0.8178 (tptp) cc_final: 0.7614 (tptp) REVERT: A 1093 MET cc_start: 0.6993 (pmm) cc_final: 0.6627 (pmm) REVERT: A 1111 LEU cc_start: 0.8612 (mt) cc_final: 0.8374 (mt) REVERT: A 1112 MET cc_start: 0.8402 (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: 0.7415 (tpt) cc_final: 0.6603 (tpt) REVERT: A 1126 ASP cc_start: 0.6620 (m-30) cc_final: 0.6289 (m-30) REVERT: A 1188 CYS cc_start: 0.8055 (p) cc_final: 0.7805 (p) REVERT: A 1195 MET cc_start: 0.7335 (ttm) cc_final: 0.7121 (ttm) REVERT: A 1222 GLN cc_start: 0.8443 (mp10) cc_final: 0.7886 (mp10) REVERT: B 72 ILE cc_start: 0.8388 (mm) cc_final: 0.8118 (mm) REVERT: B 77 HIS cc_start: 0.6762 (m-70) cc_final: 0.6448 (m170) REVERT: B 88 ARG cc_start: 0.7902 (ptp-170) cc_final: 0.7673 (ptp90) REVERT: B 113 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6602 (mm-30) REVERT: B 123 GLU cc_start: 0.7564 (pt0) cc_final: 0.7177 (pt0) REVERT: B 134 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8050 (mtmt) REVERT: B 180 LYS cc_start: 0.8300 (ptmt) cc_final: 0.7614 (ptmt) REVERT: B 183 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6858 (mt-10) REVERT: B 191 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 201 ASN cc_start: 0.7832 (m110) cc_final: 0.7406 (m110) REVERT: B 234 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7898 (mtmm) REVERT: B 235 THR cc_start: 0.8178 (m) cc_final: 0.7868 (m) REVERT: B 251 TRP cc_start: 0.7320 (m100) cc_final: 0.6871 (m100) REVERT: B 257 ARG cc_start: 0.7604 (ttm110) cc_final: 0.7323 (mtp85) REVERT: B 288 LYS cc_start: 0.7156 (mttt) cc_final: 0.6468 (mtpt) REVERT: B 289 LEU cc_start: 0.7785 (mt) cc_final: 0.7556 (mt) REVERT: B 304 TRP cc_start: 0.7811 (m100) cc_final: 0.7583 (m100) REVERT: B 310 GLU cc_start: 0.7555 (mp0) cc_final: 0.7214 (mp0) REVERT: B 315 TYR cc_start: 0.7887 (m-80) cc_final: 0.7508 (m-80) REVERT: B 339 ASN cc_start: 0.6938 (t0) cc_final: 0.6283 (t0) REVERT: B 352 ASP cc_start: 0.7204 (t0) cc_final: 0.6884 (t0) REVERT: B 353 SER cc_start: 0.7940 (p) cc_final: 0.7726 (p) REVERT: B 378 LEU cc_start: 0.8363 (mp) cc_final: 0.8023 (mt) REVERT: B 396 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7130 (ttm110) REVERT: B 412 SER cc_start: 0.8324 (t) cc_final: 0.7848 (p) REVERT: B 426 GLU cc_start: 0.7724 (pp20) cc_final: 0.7317 (pp20) REVERT: B 427 GLN cc_start: 0.8218 (pt0) cc_final: 0.8005 (pt0) REVERT: B 431 LYS cc_start: 0.8350 (tttt) cc_final: 0.7960 (tppt) REVERT: B 446 THR cc_start: 0.8198 (m) cc_final: 0.7876 (m) REVERT: B 449 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7255 (mt-10) REVERT: B 457 SER cc_start: 0.7912 (t) cc_final: 0.7587 (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: 0.7932 (t) REVERT: B 462 MET cc_start: 0.8023 (mmt) cc_final: 0.7726 (mmt) REVERT: B 465 MET cc_start: 0.7550 (mtm) cc_final: 0.7122 (mtm) REVERT: B 466 MET cc_start: 0.7266 (mtp) cc_final: 0.7014 (ttp) REVERT: B 483 LYS cc_start: 0.6555 (tttt) cc_final: 0.6325 (ttmm) REVERT: C 75 ARG cc_start: 0.7875 (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: 0.8622 (mt) cc_final: 0.8336 (mm) REVERT: C 146 ARG cc_start: 0.7431 (mmt-90) cc_final: 0.6990 (mmt180) REVERT: C 183 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6484 (mt-10) REVERT: C 210 GLN cc_start: 0.7624 (tt0) cc_final: 0.7147 (tt0) REVERT: C 211 ILE cc_start: 0.7985 (mt) cc_final: 0.7775 (mt) REVERT: C 215 PHE cc_start: 0.8115 (m-80) cc_final: 0.7860 (m-80) REVERT: C 233 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6266 (mp0) REVERT: C 256 LEU cc_start: 0.8482 (tp) cc_final: 0.8206 (tp) REVERT: C 259 ARG cc_start: 0.7731 (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: 0.7122 (t0) cc_final: 0.6873 (t0) REVERT: C 288 LYS cc_start: 0.8205 (mttt) cc_final: 0.7692 (mttt) REVERT: C 291 TYR cc_start: 0.8048 (t80) cc_final: 0.7736 (t80) REVERT: C 299 LEU cc_start: 0.8473 (tp) cc_final: 0.8251 (tt) REVERT: C 301 GLU cc_start: 0.7443 (tt0) cc_final: 0.6666 (tt0) REVERT: C 306 LEU cc_start: 0.8395 (mt) cc_final: 0.7903 (mm) REVERT: C 310 GLU cc_start: 0.8398 (mp0) cc_final: 0.8197 (mp0) REVERT: C 328 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7531 (mtt180) REVERT: C 336 LEU cc_start: 0.8341 (mt) cc_final: 0.8026 (mt) REVERT: C 347 LEU cc_start: 0.8259 (mm) cc_final: 0.7245 (mm) REVERT: C 371 VAL cc_start: 0.8410 (p) cc_final: 0.8047 (m) REVERT: C 400 GLN cc_start: 0.7714 (mt0) cc_final: 0.6858 (mt0) REVERT: C 404 ASN cc_start: 0.7977 (m110) cc_final: 0.7604 (m110) REVERT: C 421 MET cc_start: 0.6523 (mtt) cc_final: 0.6151 (mtt) REVERT: C 427 GLN cc_start: 0.8312 (mt0) cc_final: 0.7796 (mt0) REVERT: C 430 SER cc_start: 0.8443 (t) cc_final: 0.7935 (p) REVERT: C 431 LYS cc_start: 0.8420 (tttt) cc_final: 0.8129 (tttt) REVERT: C 434 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 456 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7416 (ttt90) REVERT: C 458 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.8006 (ptt180) REVERT: C 466 MET cc_start: 0.7079 (ttm) cc_final: 0.6668 (ttm) REVERT: C 470 LYS cc_start: 0.8547 (mttt) cc_final: 0.8196 (mttt) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.3507 time to fit residues: 296.5803 Evaluate side-chains 552 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 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: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093596 restraints weight = 60782.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098852 restraints weight = 25836.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102309 restraints weight = 14181.783| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16209 Z= 0.251 Angle : 0.569 9.986 22166 Z= 0.302 Chirality : 0.043 0.191 2406 Planarity : 0.004 0.058 2692 Dihedral : 14.707 89.513 2496 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.19 % Allowed : 2.00 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.18), residues: 786 sheet: 0.27 (0.34), residues: 234 loop : -0.38 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 486 HIS 0.006 0.001 HIS C 258 PHE 0.028 0.002 PHE C 242 TYR 0.033 0.002 TYR B 315 ARG 0.006 0.001 ARG A1208 *********************** 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 581 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 580 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8169 (mt) cc_final: 0.7855 (mp) REVERT: A 110 HIS cc_start: 0.7455 (m90) cc_final: 0.6660 (m90) REVERT: A 145 LYS cc_start: 0.8172 (tptp) cc_final: 0.7715 (tptp) REVERT: A 159 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6678 (pp30) REVERT: A 280 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7061 (mm-30) REVERT: A 293 ASP cc_start: 0.5346 (t0) cc_final: 0.5105 (t0) REVERT: A 295 MET cc_start: 0.7351 (ttt) cc_final: 0.6914 (ttp) REVERT: A 354 ASN cc_start: 0.7579 (m-40) cc_final: 0.7234 (m-40) REVERT: A 355 SER cc_start: 0.7786 (t) cc_final: 0.7534 (t) REVERT: A 375 GLU cc_start: 0.7417 (pt0) cc_final: 0.7008 (pt0) REVERT: A 393 MET cc_start: 0.7189 (ttm) cc_final: 0.6911 (ttm) REVERT: A 439 GLN cc_start: 0.7818 (pt0) cc_final: 0.7589 (pt0) REVERT: A 441 TRP cc_start: 0.7976 (t-100) cc_final: 0.7551 (t-100) REVERT: A 443 ARG cc_start: 0.7004 (ttt-90) cc_final: 0.6421 (ttt-90) REVERT: A 453 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7571 (mm-30) REVERT: A 457 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7444 (ttp-170) REVERT: A 484 TRP cc_start: 0.8115 (m-90) cc_final: 0.7361 (m-90) REVERT: A 487 ASP cc_start: 0.8281 (m-30) cc_final: 0.8016 (m-30) REVERT: A 565 HIS cc_start: 0.7510 (t-90) cc_final: 0.7188 (t-90) REVERT: A 566 LEU cc_start: 0.8916 (mt) cc_final: 0.8639 (mm) REVERT: A 586 THR cc_start: 0.8264 (t) cc_final: 0.7976 (p) REVERT: A 593 SER cc_start: 0.7962 (m) cc_final: 0.7584 (p) REVERT: A 607 TRP cc_start: 0.8244 (t-100) cc_final: 0.7848 (t60) REVERT: A 758 ASN cc_start: 0.7932 (m-40) cc_final: 0.7435 (t0) REVERT: A 797 MET cc_start: 0.7734 (mtt) cc_final: 0.7467 (tpp) REVERT: A 806 LYS cc_start: 0.7881 (mmmm) cc_final: 0.7640 (mmmm) REVERT: A 812 MET cc_start: 0.7440 (mpp) cc_final: 0.7142 (mpp) REVERT: A 816 LEU cc_start: 0.8457 (tp) cc_final: 0.8049 (tp) REVERT: A 823 ARG cc_start: 0.7604 (tmt-80) cc_final: 0.6635 (tmt-80) REVERT: A 826 ILE cc_start: 0.8061 (mt) cc_final: 0.7854 (pt) REVERT: A 832 ASP cc_start: 0.8162 (t0) cc_final: 0.7527 (t0) REVERT: A 853 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7459 (mtp85) REVERT: A 877 MET cc_start: 0.7173 (mmm) cc_final: 0.6901 (mmm) REVERT: A 893 SER cc_start: 0.7296 (t) cc_final: 0.6693 (p) REVERT: A 916 PHE cc_start: 0.7985 (t80) cc_final: 0.7408 (t80) REVERT: A 919 MET cc_start: 0.7443 (mtt) cc_final: 0.7192 (mpp) REVERT: A 922 GLN cc_start: 0.7485 (tt0) cc_final: 0.7115 (tp40) REVERT: A 934 LYS cc_start: 0.8304 (mmpt) cc_final: 0.8056 (mmtt) REVERT: A 969 PHE cc_start: 0.7987 (m-10) cc_final: 0.7731 (m-10) REVERT: A 981 LYS cc_start: 0.8309 (tttt) cc_final: 0.7737 (tppt) REVERT: A 1057 MET cc_start: 0.7766 (ppp) cc_final: 0.7541 (ppp) REVERT: A 1060 LYS cc_start: 0.8177 (tptp) cc_final: 0.7694 (tptp) REVERT: A 1093 MET cc_start: 0.6942 (pmm) cc_final: 0.6598 (pmm) REVERT: A 1110 HIS cc_start: 0.8661 (m-70) cc_final: 0.8402 (m-70) REVERT: A 1116 MET cc_start: 0.7328 (tpt) cc_final: 0.6477 (tpt) REVERT: A 1126 ASP cc_start: 0.6637 (m-30) cc_final: 0.6353 (m-30) REVERT: A 1148 ARG cc_start: 0.7904 (mtp180) cc_final: 0.6597 (ttm-80) REVERT: A 1195 MET cc_start: 0.7372 (ttm) cc_final: 0.7017 (ttm) REVERT: A 1219 ASP cc_start: 0.7769 (t0) cc_final: 0.7528 (t70) REVERT: A 1222 GLN cc_start: 0.8484 (mp10) cc_final: 0.7847 (mp10) REVERT: B 77 HIS cc_start: 0.6920 (m-70) cc_final: 0.6708 (m170) REVERT: B 88 ARG cc_start: 0.7974 (ptp-170) cc_final: 0.7711 (ptp90) REVERT: B 113 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6657 (mm-30) REVERT: B 123 GLU cc_start: 0.7514 (pt0) cc_final: 0.7150 (pt0) REVERT: B 134 LYS cc_start: 0.8411 (mtmt) cc_final: 0.8145 (mtpt) REVERT: B 180 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7916 (ptmt) REVERT: B 183 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 191 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7093 (mt-10) REVERT: B 192 HIS cc_start: 0.8069 (m-70) cc_final: 0.7574 (m-70) REVERT: B 201 ASN cc_start: 0.7886 (m110) cc_final: 0.7493 (m110) REVERT: B 234 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7857 (mtmm) REVERT: B 288 LYS cc_start: 0.7186 (mttt) cc_final: 0.6483 (mtpt) REVERT: B 289 LEU cc_start: 0.7867 (mt) cc_final: 0.7583 (mt) REVERT: B 304 TRP cc_start: 0.7834 (m100) cc_final: 0.7496 (m100) REVERT: B 306 LEU cc_start: 0.8072 (mm) cc_final: 0.7856 (mm) REVERT: B 310 GLU cc_start: 0.7614 (mp0) cc_final: 0.7342 (mp0) REVERT: B 315 TYR cc_start: 0.7930 (m-80) cc_final: 0.7532 (m-80) REVERT: B 339 ASN cc_start: 0.6792 (t0) cc_final: 0.6509 (t0) REVERT: B 352 ASP cc_start: 0.7288 (t0) cc_final: 0.6976 (t0) REVERT: B 378 LEU cc_start: 0.8405 (mp) cc_final: 0.8153 (mt) REVERT: B 396 ARG cc_start: 0.7630 (ttm170) cc_final: 0.7201 (ttm110) REVERT: B 400 GLN cc_start: 0.7808 (tt0) cc_final: 0.7559 (tp40) REVERT: B 412 SER cc_start: 0.8294 (t) cc_final: 0.7813 (p) REVERT: B 446 THR cc_start: 0.8304 (m) cc_final: 0.7944 (m) REVERT: B 449 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 457 SER cc_start: 0.7920 (t) cc_final: 0.7565 (p) REVERT: B 460 THR cc_start: 0.8472 (p) cc_final: 0.8094 (p) REVERT: B 461 THR cc_start: 0.8205 (p) cc_final: 0.7903 (t) REVERT: B 462 MET cc_start: 0.8008 (mmt) cc_final: 0.7754 (mmt) REVERT: B 465 MET cc_start: 0.7604 (mtm) cc_final: 0.7180 (mtm) REVERT: B 466 MET cc_start: 0.7405 (mtp) cc_final: 0.7056 (ttp) REVERT: C 71 GLU cc_start: 0.8374 (tt0) cc_final: 0.8135 (tt0) REVERT: C 75 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7687 (mtp85) REVERT: C 80 SER cc_start: 0.8528 (t) cc_final: 0.8092 (m) REVERT: C 89 ASP cc_start: 0.8056 (m-30) cc_final: 0.7790 (m-30) REVERT: C 107 ARG cc_start: 0.7481 (ttm170) cc_final: 0.7251 (ttp80) REVERT: C 146 ARG cc_start: 0.7388 (mmt-90) cc_final: 0.6949 (mmt180) REVERT: C 183 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6469 (mt-10) REVERT: C 210 GLN cc_start: 0.7707 (tt0) cc_final: 0.7117 (tt0) REVERT: C 233 GLU cc_start: 0.6616 (mt-10) cc_final: 0.6322 (mp0) REVERT: C 256 LEU cc_start: 0.8479 (tp) cc_final: 0.8235 (tp) REVERT: C 259 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7365 (mtp85) REVERT: C 262 TRP cc_start: 0.7910 (t60) cc_final: 0.7255 (t60) REVERT: C 287 ASN cc_start: 0.7159 (t0) cc_final: 0.6920 (t0) REVERT: C 288 LYS cc_start: 0.8248 (mttt) cc_final: 0.7735 (mttt) REVERT: C 291 TYR cc_start: 0.8071 (t80) cc_final: 0.7862 (t80) REVERT: C 299 LEU cc_start: 0.8527 (tp) cc_final: 0.8320 (tt) REVERT: C 301 GLU cc_start: 0.7424 (tt0) cc_final: 0.6695 (tt0) REVERT: C 305 ASN cc_start: 0.7537 (t0) cc_final: 0.7266 (t0) REVERT: C 306 LEU cc_start: 0.8319 (mt) cc_final: 0.7949 (mm) REVERT: C 328 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7581 (mtt180) REVERT: C 336 LEU cc_start: 0.8352 (mt) cc_final: 0.7973 (mt) REVERT: C 346 MET cc_start: 0.7052 (tmm) cc_final: 0.6375 (tmm) REVERT: C 371 VAL cc_start: 0.8386 (p) cc_final: 0.8002 (m) REVERT: C 373 LYS cc_start: 0.8285 (mttt) cc_final: 0.7711 (ptpp) REVERT: C 396 ARG cc_start: 0.7858 (ttm170) cc_final: 0.6816 (ttm170) REVERT: C 400 GLN cc_start: 0.7732 (mt0) cc_final: 0.7259 (mt0) REVERT: C 421 MET cc_start: 0.6563 (mtt) cc_final: 0.6263 (mtt) REVERT: C 426 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 427 GLN cc_start: 0.8271 (mt0) cc_final: 0.7771 (mt0) REVERT: C 430 SER cc_start: 0.8465 (t) cc_final: 0.8008 (p) REVERT: C 431 LYS cc_start: 0.8404 (tttt) cc_final: 0.8134 (tttt) REVERT: C 434 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 458 ARG cc_start: 0.8256 (ttp-170) cc_final: 0.8049 (ptt180) REVERT: C 466 MET cc_start: 0.6909 (ttm) cc_final: 0.6639 (ttm) REVERT: C 470 LYS cc_start: 0.8587 (mttt) cc_final: 0.8214 (mttt) outliers start: 1 outliers final: 0 residues processed: 580 average time/residue: 0.3579 time to fit residues: 296.0816 Evaluate side-chains 533 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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: 9.9990 chunk 131 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 410 GLN A 420 HIS A 468 ASN A 906 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 409 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094492 restraints weight = 60051.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099767 restraints weight = 25502.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103271 restraints weight = 13885.816| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 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 = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2277 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= 0.189 Angle : 0.552 9.494 22166 Z= 0.288 Chirality : 0.041 0.183 2406 Planarity : 0.004 0.056 2692 Dihedral : 14.609 89.819 2496 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.19 % Allowed : 1.50 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.19), residues: 781 sheet: 0.31 (0.34), residues: 241 loop : -0.30 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 241 HIS 0.006 0.001 HIS C 258 PHE 0.033 0.002 PHE C 242 TYR 0.029 0.001 TYR B 315 ARG 0.007 0.000 ARG A 232 *********************** 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: 1 poor density : 575 time to evaluate : 1.466 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: 0.8488 (mm) cc_final: 0.8236 (mm) REVERT: A 79 LEU cc_start: 0.8126 (mt) cc_final: 0.7858 (mp) REVERT: A 110 HIS cc_start: 0.7408 (m90) cc_final: 0.6582 (m90) REVERT: A 145 LYS cc_start: 0.8139 (tptp) cc_final: 0.7756 (tptp) REVERT: A 159 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6637 (pp30) REVERT: A 213 VAL cc_start: 0.7388 (t) cc_final: 0.7128 (m) REVERT: A 295 MET cc_start: 0.7524 (ttt) cc_final: 0.7046 (ttp) REVERT: A 354 ASN cc_start: 0.7461 (m-40) cc_final: 0.7133 (m-40) REVERT: A 355 SER cc_start: 0.7648 (t) cc_final: 0.7416 (t) REVERT: A 375 GLU cc_start: 0.7381 (pt0) cc_final: 0.6969 (pt0) REVERT: A 393 MET cc_start: 0.7243 (ttm) cc_final: 0.7013 (ttm) REVERT: A 405 GLU cc_start: 0.7608 (pp20) cc_final: 0.7407 (pp20) REVERT: A 439 GLN cc_start: 0.7801 (pt0) cc_final: 0.7530 (pt0) REVERT: A 441 TRP cc_start: 0.7966 (t-100) cc_final: 0.7137 (t-100) REVERT: A 443 ARG cc_start: 0.6872 (ttt-90) cc_final: 0.6252 (ttt-90) REVERT: A 453 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7494 (mm-30) REVERT: A 457 ARG cc_start: 0.7725 (ttp-170) cc_final: 0.7495 (ttp-170) REVERT: A 487 ASP cc_start: 0.8284 (m-30) cc_final: 0.8036 (m-30) REVERT: A 566 LEU cc_start: 0.8924 (mt) cc_final: 0.8682 (mm) REVERT: A 574 ARG cc_start: 0.8436 (ptp90) cc_final: 0.8023 (ptp90) REVERT: A 586 THR cc_start: 0.8145 (t) cc_final: 0.7904 (p) REVERT: A 593 SER cc_start: 0.7946 (m) cc_final: 0.7597 (p) REVERT: A 607 TRP cc_start: 0.8348 (t-100) cc_final: 0.7810 (t60) REVERT: A 758 ASN cc_start: 0.7885 (m-40) cc_final: 0.7438 (t0) REVERT: A 774 MET cc_start: 0.7393 (tpt) cc_final: 0.7093 (tpt) REVERT: A 797 MET cc_start: 0.7666 (mtt) cc_final: 0.7454 (ttm) REVERT: A 806 LYS cc_start: 0.7874 (mmmm) cc_final: 0.7611 (mmmm) REVERT: A 812 MET cc_start: 0.7395 (mpp) cc_final: 0.7102 (mpp) REVERT: A 816 LEU cc_start: 0.8450 (tp) cc_final: 0.8069 (tp) REVERT: A 832 ASP cc_start: 0.8125 (t0) cc_final: 0.7470 (t0) REVERT: A 877 MET cc_start: 0.7075 (mmm) cc_final: 0.6824 (mmm) REVERT: A 893 SER cc_start: 0.7278 (t) cc_final: 0.6641 (p) REVERT: A 922 GLN cc_start: 0.7385 (tt0) cc_final: 0.6521 (tp-100) REVERT: A 981 LYS cc_start: 0.8297 (tttt) cc_final: 0.7724 (tppt) REVERT: A 1057 MET cc_start: 0.7792 (ppp) cc_final: 0.7560 (ppp) REVERT: A 1060 LYS cc_start: 0.8186 (tptp) cc_final: 0.7723 (tptp) REVERT: A 1093 MET cc_start: 0.6830 (pmm) cc_final: 0.6547 (pmm) REVERT: A 1110 HIS cc_start: 0.8602 (m-70) cc_final: 0.8349 (m-70) REVERT: A 1116 MET cc_start: 0.7249 (tpt) cc_final: 0.6450 (tpt) REVERT: A 1148 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7449 (ttm-80) REVERT: A 1195 MET cc_start: 0.7436 (ttm) cc_final: 0.6981 (ttm) REVERT: A 1206 MET cc_start: 0.6081 (mtm) cc_final: 0.5792 (mtt) REVERT: A 1219 ASP cc_start: 0.7716 (t0) cc_final: 0.7511 (t70) REVERT: A 1222 GLN cc_start: 0.8485 (mp10) cc_final: 0.7851 (mp10) REVERT: B 77 HIS cc_start: 0.6943 (m-70) cc_final: 0.6595 (m170) REVERT: B 88 ARG cc_start: 0.7918 (ptp-170) cc_final: 0.7704 (ptp90) REVERT: B 113 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6706 (mm-30) REVERT: B 123 GLU cc_start: 0.7518 (pt0) cc_final: 0.7152 (pt0) REVERT: B 134 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8120 (mtpt) REVERT: B 180 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7849 (ptmt) REVERT: B 183 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6979 (mt-10) REVERT: B 191 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7237 (mt-10) REVERT: B 201 ASN cc_start: 0.7854 (m110) cc_final: 0.7497 (m110) REVERT: B 234 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7953 (mtmm) REVERT: B 288 LYS cc_start: 0.7214 (mttt) cc_final: 0.6499 (mtpt) REVERT: B 289 LEU cc_start: 0.7881 (mt) cc_final: 0.7543 (mt) REVERT: B 304 TRP cc_start: 0.7819 (m100) cc_final: 0.7462 (m100) REVERT: B 310 GLU cc_start: 0.7586 (mp0) cc_final: 0.7332 (mp0) REVERT: B 315 TYR cc_start: 0.7929 (m-80) cc_final: 0.7549 (m-80) REVERT: B 339 ASN cc_start: 0.6703 (t0) cc_final: 0.6431 (t0) REVERT: B 352 ASP cc_start: 0.7226 (t0) cc_final: 0.6893 (t0) REVERT: B 396 ARG cc_start: 0.7567 (ttm170) cc_final: 0.7167 (ttm110) REVERT: B 412 SER cc_start: 0.8302 (t) cc_final: 0.7808 (p) REVERT: B 431 LYS cc_start: 0.8318 (tttm) cc_final: 0.8058 (tttm) REVERT: B 446 THR cc_start: 0.8261 (m) cc_final: 0.7961 (m) REVERT: B 449 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7341 (mt-10) REVERT: B 457 SER cc_start: 0.7984 (t) cc_final: 0.7641 (p) REVERT: B 460 THR cc_start: 0.8529 (p) cc_final: 0.8143 (p) REVERT: B 462 MET cc_start: 0.7979 (mmt) cc_final: 0.7719 (mmt) REVERT: B 465 MET cc_start: 0.7557 (mtm) cc_final: 0.7106 (mtm) REVERT: B 466 MET cc_start: 0.7329 (mtp) cc_final: 0.7017 (ttp) REVERT: C 71 GLU cc_start: 0.8338 (tt0) cc_final: 0.8099 (tt0) REVERT: C 75 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7640 (mtp85) REVERT: C 80 SER cc_start: 0.8557 (t) cc_final: 0.8191 (m) REVERT: C 89 ASP cc_start: 0.8058 (m-30) cc_final: 0.7737 (m-30) REVERT: C 146 ARG cc_start: 0.7387 (mmt-90) cc_final: 0.6961 (mmt180) REVERT: C 183 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6395 (mt-10) REVERT: C 194 VAL cc_start: 0.7885 (m) cc_final: 0.7681 (p) REVERT: C 210 GLN cc_start: 0.7676 (tt0) cc_final: 0.7122 (tt0) REVERT: C 231 ILE cc_start: 0.7972 (mt) cc_final: 0.7772 (mm) REVERT: C 235 THR cc_start: 0.7750 (t) cc_final: 0.7006 (p) REVERT: C 256 LEU cc_start: 0.8462 (tp) cc_final: 0.8204 (tp) REVERT: C 262 TRP cc_start: 0.7839 (t60) cc_final: 0.7184 (t60) REVERT: C 287 ASN cc_start: 0.7119 (t0) cc_final: 0.6833 (t0) REVERT: C 288 LYS cc_start: 0.8255 (mttt) cc_final: 0.7737 (mttt) REVERT: C 301 GLU cc_start: 0.7404 (tt0) cc_final: 0.6917 (tt0) REVERT: C 305 ASN cc_start: 0.7536 (t0) cc_final: 0.7272 (t0) REVERT: C 306 LEU cc_start: 0.8373 (mt) cc_final: 0.7996 (mm) REVERT: C 328 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7557 (mtt180) REVERT: C 336 LEU cc_start: 0.8388 (mt) cc_final: 0.7985 (mt) REVERT: C 343 ASP cc_start: 0.7165 (m-30) cc_final: 0.6845 (m-30) REVERT: C 347 LEU cc_start: 0.8259 (mm) cc_final: 0.7100 (mm) REVERT: C 371 VAL cc_start: 0.8359 (p) cc_final: 0.7976 (m) REVERT: C 396 ARG cc_start: 0.7800 (ttm170) cc_final: 0.6766 (ttm170) REVERT: C 400 GLN cc_start: 0.7817 (mt0) cc_final: 0.6809 (mt0) REVERT: C 404 ASN cc_start: 0.8075 (m-40) cc_final: 0.7485 (m110) REVERT: C 415 PRO cc_start: 0.8696 (Cg_endo) cc_final: 0.8452 (Cg_exo) REVERT: C 421 MET cc_start: 0.6594 (mtt) cc_final: 0.6263 (mtt) REVERT: C 427 GLN cc_start: 0.8269 (mt0) cc_final: 0.7279 (mt0) REVERT: C 430 SER cc_start: 0.8423 (t) cc_final: 0.7936 (p) REVERT: C 431 LYS cc_start: 0.8376 (tttt) cc_final: 0.8154 (tttt) REVERT: C 434 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7626 (mt-10) REVERT: C 458 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.8009 (ptt180) REVERT: C 466 MET cc_start: 0.6854 (ttm) cc_final: 0.6619 (ttm) REVERT: C 470 LYS cc_start: 0.8529 (mttt) cc_final: 0.8196 (mttt) REVERT: C 478 TYR cc_start: 0.8090 (t80) cc_final: 0.7800 (t80) outliers start: 1 outliers final: 0 residues processed: 575 average time/residue: 0.3449 time to fit residues: 280.5724 Evaluate side-chains 534 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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: 0.0270 chunk 142 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- 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 410 GLN A 468 ASN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 305 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093664 restraints weight = 63397.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099011 restraints weight = 26418.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102588 restraints weight = 14284.990| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2426 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= 0.218 Angle : 0.551 8.184 22166 Z= 0.292 Chirality : 0.042 0.181 2406 Planarity : 0.005 0.073 2692 Dihedral : 14.575 89.500 2496 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.25 % Allowed : 1.81 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.89 (0.19), residues: 778 sheet: 0.13 (0.34), residues: 244 loop : -0.36 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 572 HIS 0.007 0.001 HIS A 360 PHE 0.027 0.002 PHE C 242 TYR 0.025 0.002 TYR B 315 ARG 0.014 0.001 ARG C 456 *********************** 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 578 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 576 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8489 (mm) cc_final: 0.8209 (mm) REVERT: A 79 LEU cc_start: 0.8105 (mt) cc_final: 0.7856 (mp) REVERT: A 110 HIS cc_start: 0.7375 (m90) cc_final: 0.6628 (m90) REVERT: A 133 ASP cc_start: 0.6716 (p0) cc_final: 0.6208 (m-30) REVERT: A 159 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6616 (pp30) REVERT: A 193 ARG cc_start: 0.7544 (ttm170) cc_final: 0.7299 (ttm-80) REVERT: A 280 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 293 ASP cc_start: 0.5487 (t0) cc_final: 0.5171 (t0) REVERT: A 295 MET cc_start: 0.7509 (ttt) cc_final: 0.7095 (ttp) REVERT: A 354 ASN cc_start: 0.7493 (m-40) cc_final: 0.7148 (m-40) REVERT: A 355 SER cc_start: 0.7699 (t) cc_final: 0.7436 (t) REVERT: A 375 GLU cc_start: 0.7373 (pt0) cc_final: 0.6948 (pt0) REVERT: A 393 MET cc_start: 0.7230 (ttm) cc_final: 0.6782 (ttm) REVERT: A 439 GLN cc_start: 0.7812 (pt0) cc_final: 0.7604 (pt0) REVERT: A 441 TRP cc_start: 0.7891 (t-100) cc_final: 0.7073 (t-100) REVERT: A 443 ARG cc_start: 0.6919 (ttt-90) cc_final: 0.6295 (ttt-90) REVERT: A 453 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7529 (mm-30) REVERT: A 457 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7476 (ttp-170) REVERT: A 484 TRP cc_start: 0.8132 (m-90) cc_final: 0.7457 (m-90) REVERT: A 487 ASP cc_start: 0.8296 (m-30) cc_final: 0.8036 (m-30) REVERT: A 564 GLN cc_start: 0.7014 (tm-30) cc_final: 0.6550 (tm-30) REVERT: A 574 ARG cc_start: 0.8322 (ptp90) cc_final: 0.8091 (ptp90) REVERT: A 586 THR cc_start: 0.8110 (t) cc_final: 0.7825 (p) REVERT: A 593 SER cc_start: 0.7991 (m) cc_final: 0.7628 (p) REVERT: A 607 TRP cc_start: 0.8349 (t-100) cc_final: 0.7817 (t60) REVERT: A 758 ASN cc_start: 0.7937 (m-40) cc_final: 0.7557 (t0) REVERT: A 774 MET cc_start: 0.7438 (tpt) cc_final: 0.7110 (tpt) REVERT: A 806 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7630 (mmmm) REVERT: A 812 MET cc_start: 0.7402 (mpp) cc_final: 0.7146 (mpp) REVERT: A 816 LEU cc_start: 0.8468 (tp) cc_final: 0.8088 (tp) REVERT: A 832 ASP cc_start: 0.8105 (t0) cc_final: 0.7340 (t0) REVERT: A 877 MET cc_start: 0.7157 (mmm) cc_final: 0.6899 (mmm) REVERT: A 893 SER cc_start: 0.7294 (t) cc_final: 0.6608 (p) REVERT: A 910 MET cc_start: 0.7220 (tpt) cc_final: 0.6879 (tpt) REVERT: A 922 GLN cc_start: 0.7407 (tt0) cc_final: 0.6591 (tp-100) REVERT: A 981 LYS cc_start: 0.8296 (tttt) cc_final: 0.7733 (tppt) REVERT: A 1060 LYS cc_start: 0.8213 (tptp) cc_final: 0.7735 (tptp) REVERT: A 1110 HIS cc_start: 0.8595 (m-70) cc_final: 0.8302 (m-70) REVERT: A 1111 LEU cc_start: 0.8505 (mt) cc_final: 0.8277 (mt) REVERT: A 1116 MET cc_start: 0.7246 (tpt) cc_final: 0.6472 (tpt) REVERT: A 1136 GLU cc_start: 0.5875 (mt-10) cc_final: 0.5567 (mt-10) REVERT: A 1148 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7598 (ttm-80) REVERT: A 1195 MET cc_start: 0.7458 (ttm) cc_final: 0.6988 (ttm) REVERT: A 1206 MET cc_start: 0.6102 (mtm) cc_final: 0.5733 (mtt) REVERT: A 1219 ASP cc_start: 0.7772 (t0) cc_final: 0.7545 (t0) REVERT: A 1222 GLN cc_start: 0.8504 (mp10) cc_final: 0.7849 (mp10) REVERT: B 77 HIS cc_start: 0.6912 (m-70) cc_final: 0.6657 (m170) REVERT: B 85 GLN cc_start: 0.7451 (mt0) cc_final: 0.6889 (mt0) REVERT: B 88 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7619 (ptp90) REVERT: B 113 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6749 (mm-30) REVERT: B 123 GLU cc_start: 0.7491 (pt0) cc_final: 0.7218 (pt0) REVERT: B 124 GLN cc_start: 0.8646 (pm20) cc_final: 0.8338 (pm20) REVERT: B 134 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7868 (mtmt) REVERT: B 180 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7495 (ptmt) REVERT: B 183 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 191 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 201 ASN cc_start: 0.7888 (m110) cc_final: 0.7534 (m110) REVERT: B 234 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7930 (mtmm) REVERT: B 246 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7663 (ttp-110) REVERT: B 288 LYS cc_start: 0.7189 (mttt) cc_final: 0.6487 (mtpt) REVERT: B 289 LEU cc_start: 0.7837 (mt) cc_final: 0.7500 (mt) REVERT: B 304 TRP cc_start: 0.7791 (m100) cc_final: 0.7438 (m100) REVERT: B 315 TYR cc_start: 0.7900 (m-80) cc_final: 0.7536 (m-80) REVERT: B 339 ASN cc_start: 0.6790 (t0) cc_final: 0.6433 (t0) REVERT: B 352 ASP cc_start: 0.7251 (t0) cc_final: 0.6908 (t0) REVERT: B 378 LEU cc_start: 0.8391 (mp) cc_final: 0.8059 (mt) REVERT: B 396 ARG cc_start: 0.7543 (ttm170) cc_final: 0.7151 (ttm110) REVERT: B 412 SER cc_start: 0.8279 (t) cc_final: 0.7811 (p) REVERT: B 427 GLN cc_start: 0.8193 (pt0) cc_final: 0.7783 (pm20) REVERT: B 431 LYS cc_start: 0.8214 (tttm) cc_final: 0.7913 (tppt) REVERT: B 446 THR cc_start: 0.8304 (m) cc_final: 0.8011 (m) REVERT: B 449 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7329 (mt-10) REVERT: B 457 SER cc_start: 0.7801 (t) cc_final: 0.7436 (p) REVERT: B 461 THR cc_start: 0.8234 (p) cc_final: 0.7982 (t) REVERT: B 462 MET cc_start: 0.7965 (mmt) cc_final: 0.7713 (mmt) REVERT: B 465 MET cc_start: 0.7523 (mtm) cc_final: 0.7076 (mtm) REVERT: B 466 MET cc_start: 0.7361 (mtp) cc_final: 0.7046 (ttp) REVERT: C 71 GLU cc_start: 0.8339 (tt0) cc_final: 0.8105 (tt0) REVERT: C 75 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7670 (mtp85) REVERT: C 80 SER cc_start: 0.8533 (t) cc_final: 0.8158 (m) REVERT: C 89 ASP cc_start: 0.8079 (m-30) cc_final: 0.7750 (m-30) REVERT: C 180 LYS cc_start: 0.7912 (pttt) cc_final: 0.7679 (ptmt) REVERT: C 183 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6439 (mt-10) REVERT: C 190 LEU cc_start: 0.8658 (mt) cc_final: 0.8456 (mm) REVERT: C 203 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7263 (ttt180) REVERT: C 210 GLN cc_start: 0.7708 (tt0) cc_final: 0.7064 (tt0) REVERT: C 235 THR cc_start: 0.7882 (t) cc_final: 0.6987 (p) REVERT: C 256 LEU cc_start: 0.8480 (tp) cc_final: 0.8261 (tp) REVERT: C 262 TRP cc_start: 0.7843 (t60) cc_final: 0.7118 (t60) REVERT: C 287 ASN cc_start: 0.7143 (t0) cc_final: 0.6904 (t0) REVERT: C 288 LYS cc_start: 0.8242 (mttt) cc_final: 0.7710 (mttt) REVERT: C 301 GLU cc_start: 0.7415 (tt0) cc_final: 0.6892 (tt0) REVERT: C 305 ASN cc_start: 0.7551 (t0) cc_final: 0.7253 (t0) REVERT: C 306 LEU cc_start: 0.8377 (mt) cc_final: 0.7837 (mm) REVERT: C 328 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7608 (mtt180) REVERT: C 336 LEU cc_start: 0.8393 (mt) cc_final: 0.7961 (mt) REVERT: C 346 MET cc_start: 0.6990 (tmm) cc_final: 0.6390 (tmm) REVERT: C 371 VAL cc_start: 0.8365 (p) cc_final: 0.7966 (m) REVERT: C 373 LYS cc_start: 0.8239 (mttt) cc_final: 0.7696 (ptpp) REVERT: C 396 ARG cc_start: 0.7848 (ttm170) cc_final: 0.6828 (ttm170) REVERT: C 400 GLN cc_start: 0.7856 (mt0) cc_final: 0.6869 (mt0) REVERT: C 404 ASN cc_start: 0.8069 (m-40) cc_final: 0.7407 (m110) REVERT: C 415 PRO cc_start: 0.8701 (Cg_endo) cc_final: 0.8485 (Cg_exo) REVERT: C 421 MET cc_start: 0.6610 (mtt) cc_final: 0.6321 (mtt) REVERT: C 426 GLU cc_start: 0.7585 (pp20) cc_final: 0.7326 (pp20) REVERT: C 427 GLN cc_start: 0.8188 (mt0) cc_final: 0.7595 (mt0) REVERT: C 430 SER cc_start: 0.8479 (t) cc_final: 0.7953 (p) REVERT: C 431 LYS cc_start: 0.8392 (tttt) cc_final: 0.8129 (tttt) REVERT: C 434 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7666 (mt-10) REVERT: C 466 MET cc_start: 0.6973 (ttm) cc_final: 0.6748 (ttm) REVERT: C 470 LYS cc_start: 0.8564 (mttt) cc_final: 0.8181 (mttt) REVERT: C 478 TYR cc_start: 0.8022 (t80) cc_final: 0.7759 (t80) outliers start: 2 outliers final: 0 residues processed: 576 average time/residue: 0.3437 time to fit residues: 278.0684 Evaluate side-chains 533 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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: 0.9990 chunk 44 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS A 906 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 305 ASN B 400 GLN ** B 409 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093667 restraints weight = 70934.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099265 restraints weight = 28135.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102975 restraints weight = 15040.615| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16209 Z= 0.169 Angle : 0.543 8.469 22166 Z= 0.284 Chirality : 0.041 0.181 2406 Planarity : 0.004 0.055 2692 Dihedral : 14.464 89.173 2496 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.25 % Allowed : 1.06 % Favored : 98.69 % 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: 1.91 (0.19), residues: 787 sheet: 0.22 (0.34), residues: 244 loop : -0.30 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 572 HIS 0.005 0.001 HIS C 258 PHE 0.028 0.001 PHE C 242 TYR 0.025 0.001 TYR A 837 ARG 0.007 0.000 ARG A 827 *********************** 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 583 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 581 time to evaluate : 1.472 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: 0.8480 (mm) cc_final: 0.8237 (mm) REVERT: A 79 LEU cc_start: 0.8081 (mt) cc_final: 0.7856 (mp) REVERT: A 110 HIS cc_start: 0.7354 (m90) cc_final: 0.6652 (m90) REVERT: A 159 GLN cc_start: 0.7145 (tm-30) cc_final: 0.6571 (pp30) REVERT: A 193 ARG cc_start: 0.7524 (ttm170) cc_final: 0.7299 (ttm-80) REVERT: A 264 GLN cc_start: 0.8044 (pt0) cc_final: 0.7586 (pt0) REVERT: A 280 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6964 (mm-30) REVERT: A 293 ASP cc_start: 0.5535 (t0) cc_final: 0.5171 (t0) REVERT: A 295 MET cc_start: 0.7564 (ttt) cc_final: 0.7243 (ttm) REVERT: A 299 MET cc_start: 0.7375 (tpt) cc_final: 0.7061 (tpt) REVERT: A 316 LYS cc_start: 0.8575 (tttp) cc_final: 0.8296 (ttmm) REVERT: A 354 ASN cc_start: 0.7560 (m-40) cc_final: 0.7115 (m-40) REVERT: A 358 GLU cc_start: 0.7658 (mp0) cc_final: 0.7113 (mp0) REVERT: A 393 MET cc_start: 0.7239 (ttm) cc_final: 0.6809 (ttm) REVERT: A 427 MET cc_start: 0.7580 (ttm) cc_final: 0.7255 (ttm) REVERT: A 441 TRP cc_start: 0.7877 (t-100) cc_final: 0.7554 (t-100) REVERT: A 443 ARG cc_start: 0.6776 (ttt-90) cc_final: 0.6259 (ttt-90) REVERT: A 453 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7521 (mm-30) REVERT: A 457 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7511 (ttp-170) REVERT: A 487 ASP cc_start: 0.8313 (m-30) cc_final: 0.8065 (m-30) REVERT: A 574 ARG cc_start: 0.8290 (ptp90) cc_final: 0.7935 (ptp90) REVERT: A 579 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7021 (mtp85) REVERT: A 586 THR cc_start: 0.8077 (t) cc_final: 0.7832 (p) REVERT: A 593 SER cc_start: 0.8020 (m) cc_final: 0.7627 (p) REVERT: A 601 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7561 (mtmm) REVERT: A 607 TRP cc_start: 0.8313 (t-100) cc_final: 0.7813 (t60) REVERT: A 758 ASN cc_start: 0.7897 (m-40) cc_final: 0.7463 (t0) REVERT: A 806 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7644 (mmmm) REVERT: A 812 MET cc_start: 0.7415 (mpp) cc_final: 0.7140 (mpp) REVERT: A 816 LEU cc_start: 0.8488 (tp) cc_final: 0.8110 (tp) REVERT: A 832 ASP cc_start: 0.8073 (t0) cc_final: 0.7456 (t0) REVERT: A 836 LEU cc_start: 0.7198 (mm) cc_final: 0.6817 (mm) REVERT: A 875 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8226 (mtpp) REVERT: A 893 SER cc_start: 0.7239 (t) cc_final: 0.6903 (t) REVERT: A 922 GLN cc_start: 0.7394 (tt0) cc_final: 0.6888 (tp40) REVERT: A 981 LYS cc_start: 0.8257 (tttt) cc_final: 0.7699 (tppt) REVERT: A 1057 MET cc_start: 0.7881 (ppp) cc_final: 0.7641 (ppp) REVERT: A 1060 LYS cc_start: 0.8238 (tptp) cc_final: 0.7790 (tptp) REVERT: A 1110 HIS cc_start: 0.8600 (m-70) cc_final: 0.8273 (m-70) REVERT: A 1116 MET cc_start: 0.7258 (tpt) cc_final: 0.6481 (tpt) REVERT: A 1136 GLU cc_start: 0.5917 (mt-10) cc_final: 0.5625 (mt-10) REVERT: A 1195 MET cc_start: 0.7429 (ttm) cc_final: 0.7174 (ttp) REVERT: A 1219 ASP cc_start: 0.7746 (t0) cc_final: 0.7530 (t70) REVERT: A 1222 GLN cc_start: 0.8473 (mp10) cc_final: 0.7818 (mp10) REVERT: B 85 GLN cc_start: 0.7490 (mt0) cc_final: 0.6955 (mt0) REVERT: B 88 ARG cc_start: 0.7949 (ptp-170) cc_final: 0.7742 (ptp90) REVERT: B 113 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6780 (mm-30) REVERT: B 123 GLU cc_start: 0.7472 (pt0) cc_final: 0.7221 (pt0) REVERT: B 124 GLN cc_start: 0.8655 (pm20) cc_final: 0.8406 (pm20) REVERT: B 134 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7864 (mtmt) REVERT: B 180 LYS cc_start: 0.8274 (ptmt) cc_final: 0.7478 (ptmt) REVERT: B 183 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6977 (mt-10) REVERT: B 191 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 201 ASN cc_start: 0.7807 (m110) cc_final: 0.7538 (m110) REVERT: B 234 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7910 (mtmm) REVERT: B 246 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7498 (ptp90) REVERT: B 288 LYS cc_start: 0.7229 (mttt) cc_final: 0.6535 (mtpt) REVERT: B 289 LEU cc_start: 0.7834 (mt) cc_final: 0.7511 (mt) REVERT: B 304 TRP cc_start: 0.7688 (m100) cc_final: 0.7393 (m100) REVERT: B 315 TYR cc_start: 0.7874 (m-80) cc_final: 0.7546 (m-80) REVERT: B 339 ASN cc_start: 0.6717 (t0) cc_final: 0.6183 (t0) REVERT: B 352 ASP cc_start: 0.7193 (t0) cc_final: 0.6880 (t0) REVERT: B 353 SER cc_start: 0.8039 (p) cc_final: 0.7832 (p) REVERT: B 396 ARG cc_start: 0.7465 (ttm170) cc_final: 0.7101 (ttm110) REVERT: B 412 SER cc_start: 0.8297 (t) cc_final: 0.7809 (p) REVERT: B 427 GLN cc_start: 0.8218 (pt0) cc_final: 0.7744 (pm20) REVERT: B 431 LYS cc_start: 0.8288 (tttm) cc_final: 0.7960 (tppt) REVERT: B 446 THR cc_start: 0.8268 (m) cc_final: 0.8019 (m) REVERT: B 449 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7312 (mt-10) REVERT: B 457 SER cc_start: 0.7973 (t) cc_final: 0.7690 (p) REVERT: B 460 THR cc_start: 0.8484 (p) cc_final: 0.8104 (p) REVERT: B 462 MET cc_start: 0.7790 (mmt) cc_final: 0.7550 (mmt) REVERT: B 465 MET cc_start: 0.7513 (mtm) cc_final: 0.6990 (mtm) REVERT: B 466 MET cc_start: 0.7348 (mtp) cc_final: 0.7035 (ttp) REVERT: B 483 LYS cc_start: 0.6160 (mtpp) cc_final: 0.5884 (mtpp) REVERT: C 75 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7593 (mtp85) REVERT: C 80 SER cc_start: 0.8458 (t) cc_final: 0.8037 (m) REVERT: C 180 LYS cc_start: 0.7879 (pttt) cc_final: 0.7635 (ptmt) REVERT: C 183 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6458 (mt-10) REVERT: C 185 LEU cc_start: 0.9010 (mt) cc_final: 0.8717 (mt) REVERT: C 190 LEU cc_start: 0.8644 (mt) cc_final: 0.8409 (mm) REVERT: C 234 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7606 (mtmm) REVERT: C 235 THR cc_start: 0.7844 (t) cc_final: 0.7067 (p) REVERT: C 242 PHE cc_start: 0.6830 (m-10) cc_final: 0.6458 (m-10) REVERT: C 256 LEU cc_start: 0.8479 (tp) cc_final: 0.8234 (tp) REVERT: C 259 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7466 (mtp85) REVERT: C 262 TRP cc_start: 0.7790 (t60) cc_final: 0.7119 (t60) REVERT: C 279 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: C 287 ASN cc_start: 0.7173 (t0) cc_final: 0.6881 (t0) REVERT: C 288 LYS cc_start: 0.8234 (mttt) cc_final: 0.7690 (mttt) REVERT: C 301 GLU cc_start: 0.7415 (tt0) cc_final: 0.6706 (tt0) REVERT: C 305 ASN cc_start: 0.7555 (t0) cc_final: 0.7273 (t0) REVERT: C 306 LEU cc_start: 0.8236 (mt) cc_final: 0.7959 (mm) REVERT: C 328 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7612 (mtt180) REVERT: C 336 LEU cc_start: 0.8399 (mt) cc_final: 0.7964 (mt) REVERT: C 343 ASP cc_start: 0.7337 (m-30) cc_final: 0.6967 (m-30) REVERT: C 347 LEU cc_start: 0.8289 (mm) cc_final: 0.7296 (mm) REVERT: C 354 PHE cc_start: 0.7971 (t80) cc_final: 0.7580 (t80) REVERT: C 371 VAL cc_start: 0.8231 (p) cc_final: 0.7982 (m) REVERT: C 372 LEU cc_start: 0.8621 (mt) cc_final: 0.8343 (mt) REVERT: C 373 LYS cc_start: 0.8311 (mttt) cc_final: 0.7582 (ptpp) REVERT: C 396 ARG cc_start: 0.7807 (ttm170) cc_final: 0.6819 (ttm170) REVERT: C 400 GLN cc_start: 0.7839 (mt0) cc_final: 0.6852 (mt0) REVERT: C 404 ASN cc_start: 0.8042 (m-40) cc_final: 0.7425 (m110) REVERT: C 415 PRO cc_start: 0.8696 (Cg_endo) cc_final: 0.8473 (Cg_exo) REVERT: C 421 MET cc_start: 0.6541 (mtt) cc_final: 0.6283 (mtt) REVERT: C 426 GLU cc_start: 0.7566 (pp20) cc_final: 0.7273 (pp20) REVERT: C 427 GLN cc_start: 0.8136 (mt0) cc_final: 0.7553 (mt0) REVERT: C 430 SER cc_start: 0.8406 (t) cc_final: 0.7911 (p) REVERT: C 434 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7557 (mt-10) REVERT: C 466 MET cc_start: 0.6955 (ttm) cc_final: 0.6740 (ttm) REVERT: C 470 LYS cc_start: 0.8523 (mttt) cc_final: 0.8165 (mttt) REVERT: C 471 LEU cc_start: 0.8142 (tp) cc_final: 0.7933 (tt) REVERT: C 478 TYR cc_start: 0.8013 (t80) cc_final: 0.7748 (t80) outliers start: 2 outliers final: 0 residues processed: 581 average time/residue: 0.3390 time to fit residues: 276.5929 Evaluate side-chains 533 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 532 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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: 0.6980 chunk 15 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 811 GLN A 906 HIS B 77 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 400 GLN B 409 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094073 restraints weight = 64443.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099412 restraints weight = 26768.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103022 restraints weight = 14448.383| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 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 = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2725 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= 0.199 Angle : 0.559 8.488 22166 Z= 0.292 Chirality : 0.042 0.197 2406 Planarity : 0.004 0.057 2692 Dihedral : 14.439 89.131 2496 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.19 % Allowed : 1.06 % Favored : 98.75 % 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: 1.06 (0.20), residues: 1837 helix: 1.92 (0.19), residues: 786 sheet: 0.20 (0.33), residues: 250 loop : -0.32 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 490 HIS 0.005 0.001 HIS C 258 PHE 0.038 0.002 PHE C 242 TYR 0.030 0.002 TYR C 193 ARG 0.008 0.000 ARG A1071 *********************** 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 568 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 567 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.7692 (p0) cc_final: 0.7157 (p0) REVERT: A 76 ILE cc_start: 0.8422 (mm) cc_final: 0.8171 (mm) REVERT: A 79 LEU cc_start: 0.8132 (mt) cc_final: 0.7869 (mp) REVERT: A 110 HIS cc_start: 0.7362 (m90) cc_final: 0.6694 (m90) REVERT: A 159 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6551 (pp30) REVERT: A 213 VAL cc_start: 0.7569 (m) cc_final: 0.7161 (p) REVERT: A 280 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6963 (mm-30) REVERT: A 295 MET cc_start: 0.7551 (ttt) cc_final: 0.6585 (ttm) REVERT: A 297 MET cc_start: 0.7549 (mtt) cc_final: 0.7333 (mtp) REVERT: A 354 ASN cc_start: 0.7589 (m-40) cc_final: 0.7339 (m-40) REVERT: A 358 GLU cc_start: 0.7687 (mp0) cc_final: 0.7211 (mp0) REVERT: A 393 MET cc_start: 0.7194 (ttm) cc_final: 0.6850 (ttm) REVERT: A 410 GLN cc_start: 0.7908 (tt0) cc_final: 0.7677 (tt0) REVERT: A 427 MET cc_start: 0.7537 (ttm) cc_final: 0.7193 (ttm) REVERT: A 441 TRP cc_start: 0.7871 (t-100) cc_final: 0.7561 (t-100) REVERT: A 443 ARG cc_start: 0.6793 (ttt-90) cc_final: 0.6298 (ttt-90) REVERT: A 453 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7526 (mm-30) REVERT: A 457 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7499 (ttp-170) REVERT: A 484 TRP cc_start: 0.8128 (m-90) cc_final: 0.7520 (m-90) REVERT: A 487 ASP cc_start: 0.8336 (m-30) cc_final: 0.8058 (m-30) REVERT: A 574 ARG cc_start: 0.8359 (ptp90) cc_final: 0.7865 (ptp90) REVERT: A 579 ARG cc_start: 0.7514 (ttm110) cc_final: 0.6815 (mtp85) REVERT: A 586 THR cc_start: 0.8012 (t) cc_final: 0.7763 (p) REVERT: A 593 SER cc_start: 0.7935 (m) cc_final: 0.7613 (p) REVERT: A 607 TRP cc_start: 0.8325 (t-100) cc_final: 0.7826 (t60) REVERT: A 758 ASN cc_start: 0.7893 (m-40) cc_final: 0.7493 (t0) REVERT: A 806 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7518 (mmmm) REVERT: A 812 MET cc_start: 0.7369 (mpp) cc_final: 0.7129 (mpp) REVERT: A 816 LEU cc_start: 0.8509 (tp) cc_final: 0.8146 (tp) REVERT: A 836 LEU cc_start: 0.7197 (mm) cc_final: 0.6777 (mm) REVERT: A 893 SER cc_start: 0.7199 (t) cc_final: 0.6854 (t) REVERT: A 919 MET cc_start: 0.7464 (mtt) cc_final: 0.7071 (mpp) REVERT: A 922 GLN cc_start: 0.7385 (tt0) cc_final: 0.6893 (tp40) REVERT: A 934 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8076 (mmtt) REVERT: A 981 LYS cc_start: 0.8231 (tttt) cc_final: 0.7715 (tppt) REVERT: A 1060 LYS cc_start: 0.8252 (tptp) cc_final: 0.7835 (tptp) REVERT: A 1110 HIS cc_start: 0.8590 (m-70) cc_final: 0.8251 (m-70) REVERT: A 1116 MET cc_start: 0.7218 (tpt) cc_final: 0.6492 (tpt) REVERT: A 1136 GLU cc_start: 0.5894 (mt-10) cc_final: 0.5612 (mt-10) REVERT: A 1156 THR cc_start: 0.7897 (m) cc_final: 0.7351 (m) REVERT: A 1219 ASP cc_start: 0.7748 (t0) cc_final: 0.7528 (t0) REVERT: A 1222 GLN cc_start: 0.8502 (mp10) cc_final: 0.7821 (mp10) REVERT: B 71 GLU cc_start: 0.8038 (pp20) cc_final: 0.7424 (tm-30) REVERT: B 85 GLN cc_start: 0.7460 (mt0) cc_final: 0.6990 (mt0) REVERT: B 88 ARG cc_start: 0.7977 (ptp-170) cc_final: 0.7695 (ptp90) REVERT: B 113 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 123 GLU cc_start: 0.7433 (pt0) cc_final: 0.7224 (pt0) REVERT: B 124 GLN cc_start: 0.8614 (pm20) cc_final: 0.8398 (pm20) REVERT: B 134 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7870 (mtmt) REVERT: B 180 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7486 (ptmt) REVERT: B 183 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 191 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7325 (mt-10) REVERT: B 201 ASN cc_start: 0.7788 (m110) cc_final: 0.7541 (m110) REVERT: B 234 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7886 (mtmm) REVERT: B 246 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7823 (ttp80) REVERT: B 288 LYS cc_start: 0.7252 (mttt) cc_final: 0.6586 (mtmt) REVERT: B 289 LEU cc_start: 0.7836 (mt) cc_final: 0.7542 (mt) REVERT: B 304 TRP cc_start: 0.7736 (m100) cc_final: 0.7445 (m100) REVERT: B 315 TYR cc_start: 0.7879 (m-80) cc_final: 0.7579 (m-80) REVERT: B 339 ASN cc_start: 0.6696 (t0) cc_final: 0.6276 (t0) REVERT: B 352 ASP cc_start: 0.7208 (t0) cc_final: 0.6892 (t0) REVERT: B 353 SER cc_start: 0.8109 (p) cc_final: 0.7880 (p) REVERT: B 396 ARG cc_start: 0.7451 (ttm170) cc_final: 0.7112 (ttm110) REVERT: B 412 SER cc_start: 0.8268 (t) cc_final: 0.7829 (p) REVERT: B 427 GLN cc_start: 0.8174 (pt0) cc_final: 0.7767 (pm20) REVERT: B 431 LYS cc_start: 0.8273 (tttm) cc_final: 0.7963 (tppt) REVERT: B 446 THR cc_start: 0.8259 (m) cc_final: 0.8013 (m) REVERT: B 449 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7296 (mt-10) REVERT: B 457 SER cc_start: 0.7897 (t) cc_final: 0.7576 (p) REVERT: B 460 THR cc_start: 0.8533 (p) cc_final: 0.8146 (p) REVERT: B 461 THR cc_start: 0.8178 (p) cc_final: 0.7941 (t) REVERT: B 462 MET cc_start: 0.7733 (mmt) cc_final: 0.7491 (mmt) REVERT: B 465 MET cc_start: 0.7475 (mtm) cc_final: 0.6987 (mtm) REVERT: B 466 MET cc_start: 0.7335 (mtp) cc_final: 0.7026 (ttp) REVERT: B 483 LYS cc_start: 0.6241 (mtpp) cc_final: 0.5955 (mtpp) REVERT: C 75 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7457 (mtp85) REVERT: C 80 SER cc_start: 0.8447 (t) cc_final: 0.8024 (m) REVERT: C 180 LYS cc_start: 0.7821 (pttt) cc_final: 0.7605 (ptmt) REVERT: C 183 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6390 (mt-10) REVERT: C 185 LEU cc_start: 0.9003 (mt) cc_final: 0.8687 (mt) REVERT: C 190 LEU cc_start: 0.8619 (mt) cc_final: 0.8410 (mm) REVERT: C 194 VAL cc_start: 0.7831 (m) cc_final: 0.7432 (p) REVERT: C 234 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7600 (mtmm) REVERT: C 235 THR cc_start: 0.7833 (t) cc_final: 0.7032 (p) REVERT: C 242 PHE cc_start: 0.6934 (m-10) cc_final: 0.6657 (m-10) REVERT: C 243 THR cc_start: 0.7859 (t) cc_final: 0.7526 (p) REVERT: C 256 LEU cc_start: 0.8482 (tp) cc_final: 0.8241 (tp) REVERT: C 259 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7480 (mtp85) REVERT: C 262 TRP cc_start: 0.7722 (t60) cc_final: 0.6987 (t60) REVERT: C 280 ASP cc_start: 0.6216 (p0) cc_final: 0.5980 (p0) REVERT: C 287 ASN cc_start: 0.7172 (t0) cc_final: 0.6846 (t0) REVERT: C 288 LYS cc_start: 0.8229 (mttt) cc_final: 0.7671 (mttt) REVERT: C 301 GLU cc_start: 0.7405 (tt0) cc_final: 0.6688 (tt0) REVERT: C 305 ASN cc_start: 0.7576 (t0) cc_final: 0.7300 (t0) REVERT: C 306 LEU cc_start: 0.8352 (mt) cc_final: 0.7937 (mm) REVERT: C 328 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7601 (mtt180) REVERT: C 336 LEU cc_start: 0.8457 (mt) cc_final: 0.8028 (mt) REVERT: C 343 ASP cc_start: 0.7292 (m-30) cc_final: 0.6999 (m-30) REVERT: C 347 LEU cc_start: 0.8301 (mm) cc_final: 0.7408 (mm) REVERT: C 354 PHE cc_start: 0.7975 (t80) cc_final: 0.7559 (t80) REVERT: C 371 VAL cc_start: 0.8245 (p) cc_final: 0.8024 (m) REVERT: C 372 LEU cc_start: 0.8567 (mt) cc_final: 0.8329 (mt) REVERT: C 396 ARG cc_start: 0.7801 (ttm170) cc_final: 0.6988 (mmt90) REVERT: C 400 GLN cc_start: 0.7851 (mt0) cc_final: 0.6836 (mt0) REVERT: C 404 ASN cc_start: 0.8021 (m-40) cc_final: 0.7366 (m110) REVERT: C 415 PRO cc_start: 0.8707 (Cg_endo) cc_final: 0.8465 (Cg_exo) REVERT: C 421 MET cc_start: 0.6540 (mtt) cc_final: 0.6277 (mtt) REVERT: C 426 GLU cc_start: 0.7565 (pp20) cc_final: 0.7283 (pp20) REVERT: C 427 GLN cc_start: 0.8170 (mt0) cc_final: 0.7569 (mt0) REVERT: C 430 SER cc_start: 0.8444 (t) cc_final: 0.7902 (p) REVERT: C 434 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7558 (mt-10) REVERT: C 456 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7521 (ttm170) REVERT: C 466 MET cc_start: 0.6980 (ttm) cc_final: 0.6751 (ttm) REVERT: C 470 LYS cc_start: 0.8523 (mttt) cc_final: 0.8167 (mttt) REVERT: C 478 TYR cc_start: 0.8019 (t80) cc_final: 0.7730 (t80) outliers start: 1 outliers final: 0 residues processed: 567 average time/residue: 0.3501 time to fit residues: 278.9832 Evaluate side-chains 526 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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: 7.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 126 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 410 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 400 GLN B 404 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094102 restraints weight = 68297.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099643 restraints weight = 27551.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103298 restraints weight = 14637.796| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2848 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= 0.185 Angle : 0.552 8.531 22166 Z= 0.287 Chirality : 0.041 0.194 2406 Planarity : 0.004 0.055 2692 Dihedral : 14.399 89.176 2496 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.19 % Allowed : 0.81 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.20), residues: 1837 helix: 1.95 (0.19), residues: 787 sheet: 0.34 (0.33), residues: 241 loop : -0.28 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 572 HIS 0.009 0.001 HIS A 360 PHE 0.026 0.002 PHE C 242 TYR 0.037 0.002 TYR C 291 ARG 0.010 0.000 ARG A 232 *********************** 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: 1 poor density : 561 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8428 (mm) cc_final: 0.8198 (mm) REVERT: A 79 LEU cc_start: 0.8102 (mt) cc_final: 0.7875 (mp) REVERT: A 110 HIS cc_start: 0.7374 (m90) cc_final: 0.6715 (m90) REVERT: A 159 GLN cc_start: 0.7096 (tm-30) cc_final: 0.6535 (pp30) REVERT: A 169 TRP cc_start: 0.7979 (m-90) cc_final: 0.7667 (m-90) REVERT: A 177 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7598 (ttt90) REVERT: A 213 VAL cc_start: 0.7515 (m) cc_final: 0.7126 (p) REVERT: A 232 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7666 (mtp-110) REVERT: A 275 ARG cc_start: 0.8029 (ttt180) cc_final: 0.7743 (ttt-90) REVERT: A 280 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6915 (mm-30) REVERT: A 289 MET cc_start: 0.7124 (ttm) cc_final: 0.6716 (ttm) REVERT: A 358 GLU cc_start: 0.7742 (mp0) cc_final: 0.7238 (mp0) REVERT: A 393 MET cc_start: 0.7210 (ttm) cc_final: 0.6878 (ttm) REVERT: A 405 GLU cc_start: 0.7635 (pp20) cc_final: 0.7225 (tm-30) REVERT: A 410 GLN cc_start: 0.7763 (tt0) cc_final: 0.7293 (tt0) REVERT: A 427 MET cc_start: 0.7549 (ttm) cc_final: 0.7191 (ttm) REVERT: A 439 GLN cc_start: 0.7768 (pt0) cc_final: 0.7502 (pt0) REVERT: A 443 ARG cc_start: 0.6793 (ttt-90) cc_final: 0.6283 (ttt-90) REVERT: A 453 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7485 (mm-30) REVERT: A 457 ARG cc_start: 0.7761 (ttp-170) cc_final: 0.7549 (ttp-170) REVERT: A 487 ASP cc_start: 0.8324 (m-30) cc_final: 0.8083 (m-30) REVERT: A 565 HIS cc_start: 0.7432 (t-90) cc_final: 0.7177 (t-90) REVERT: A 574 ARG cc_start: 0.8370 (ptp90) cc_final: 0.7894 (ptp90) REVERT: A 579 ARG cc_start: 0.7492 (ttm110) cc_final: 0.6939 (ttm110) REVERT: A 586 THR cc_start: 0.8032 (t) cc_final: 0.7791 (p) REVERT: A 593 SER cc_start: 0.7972 (m) cc_final: 0.7582 (p) REVERT: A 607 TRP cc_start: 0.8314 (t-100) cc_final: 0.7796 (t60) REVERT: A 758 ASN cc_start: 0.7888 (m-40) cc_final: 0.7468 (t0) REVERT: A 774 MET cc_start: 0.7287 (tpt) cc_final: 0.7022 (mmm) REVERT: A 806 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7527 (mmmm) REVERT: A 812 MET cc_start: 0.7356 (mpp) cc_final: 0.7129 (mpp) REVERT: A 816 LEU cc_start: 0.8532 (tp) cc_final: 0.8164 (tp) REVERT: A 832 ASP cc_start: 0.7898 (t70) cc_final: 0.7542 (t0) REVERT: A 836 LEU cc_start: 0.7163 (mm) cc_final: 0.6742 (mm) REVERT: A 893 SER cc_start: 0.7186 (t) cc_final: 0.6838 (t) REVERT: A 919 MET cc_start: 0.7461 (mtt) cc_final: 0.7032 (mpp) REVERT: A 922 GLN cc_start: 0.7357 (tt0) cc_final: 0.6840 (tp40) REVERT: A 934 LYS cc_start: 0.8260 (mmtt) cc_final: 0.8038 (mmtt) REVERT: A 969 PHE cc_start: 0.7895 (m-10) cc_final: 0.7623 (m-10) REVERT: A 981 LYS cc_start: 0.8243 (tttt) cc_final: 0.7694 (tppt) REVERT: A 985 MET cc_start: 0.7533 (ttp) cc_final: 0.7313 (ttp) REVERT: A 1057 MET cc_start: 0.7867 (ppp) cc_final: 0.7653 (ppp) REVERT: A 1060 LYS cc_start: 0.8253 (tptp) cc_final: 0.7810 (tptp) REVERT: A 1110 HIS cc_start: 0.8566 (m-70) cc_final: 0.8232 (m-70) REVERT: A 1113 LEU cc_start: 0.8276 (mp) cc_final: 0.8058 (mp) REVERT: A 1116 MET cc_start: 0.7226 (tpt) cc_final: 0.6430 (tpt) REVERT: A 1136 GLU cc_start: 0.5904 (mt-10) cc_final: 0.5540 (mt-10) REVERT: A 1206 MET cc_start: 0.6104 (mtt) cc_final: 0.5675 (mmt) REVERT: A 1219 ASP cc_start: 0.7745 (t0) cc_final: 0.7530 (t0) REVERT: A 1222 GLN cc_start: 0.8535 (mp10) cc_final: 0.7832 (mp10) REVERT: B 71 GLU cc_start: 0.8040 (pp20) cc_final: 0.7763 (tm-30) REVERT: B 85 GLN cc_start: 0.7500 (mt0) cc_final: 0.7003 (mt0) REVERT: B 88 ARG cc_start: 0.7942 (ptp-170) cc_final: 0.7715 (ptp90) REVERT: B 113 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6763 (mm-30) REVERT: B 124 GLN cc_start: 0.8564 (pm20) cc_final: 0.8325 (pm20) REVERT: B 134 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7860 (mtmt) REVERT: B 180 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7488 (ptmt) REVERT: B 183 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6977 (mt-10) REVERT: B 191 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 201 ASN cc_start: 0.7800 (m110) cc_final: 0.7569 (m110) REVERT: B 234 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7837 (mtmm) REVERT: B 246 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.7808 (ttp80) REVERT: B 288 LYS cc_start: 0.7251 (mttt) cc_final: 0.6581 (mtmt) REVERT: B 289 LEU cc_start: 0.7833 (mt) cc_final: 0.7531 (mt) REVERT: B 304 TRP cc_start: 0.7738 (m100) cc_final: 0.7441 (m100) REVERT: B 310 GLU cc_start: 0.7610 (mp0) cc_final: 0.7398 (mp0) REVERT: B 315 TYR cc_start: 0.7876 (m-80) cc_final: 0.7587 (m-80) REVERT: B 339 ASN cc_start: 0.6691 (t0) cc_final: 0.6293 (t0) REVERT: B 352 ASP cc_start: 0.7227 (t0) cc_final: 0.6909 (t0) REVERT: B 353 SER cc_start: 0.8098 (p) cc_final: 0.7880 (p) REVERT: B 396 ARG cc_start: 0.7443 (ttm170) cc_final: 0.7109 (ttm110) REVERT: B 412 SER cc_start: 0.8304 (t) cc_final: 0.7844 (p) REVERT: B 427 GLN cc_start: 0.8122 (pt0) cc_final: 0.7763 (pm20) REVERT: B 431 LYS cc_start: 0.8313 (tttm) cc_final: 0.7850 (tppt) REVERT: B 446 THR cc_start: 0.8239 (m) cc_final: 0.7990 (m) REVERT: B 449 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 457 SER cc_start: 0.7976 (t) cc_final: 0.7678 (p) REVERT: B 460 THR cc_start: 0.8533 (p) cc_final: 0.8124 (p) REVERT: B 461 THR cc_start: 0.8179 (p) cc_final: 0.7928 (t) REVERT: B 462 MET cc_start: 0.7713 (mmt) cc_final: 0.7448 (mmt) REVERT: B 463 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8240 (mtmt) REVERT: B 465 MET cc_start: 0.7440 (mtm) cc_final: 0.6950 (mtm) REVERT: B 466 MET cc_start: 0.7282 (mtp) cc_final: 0.7047 (ttp) REVERT: B 483 LYS cc_start: 0.6210 (mtpp) cc_final: 0.5906 (mtpp) REVERT: C 80 SER cc_start: 0.8460 (t) cc_final: 0.8075 (m) REVERT: C 122 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7478 (mmt90) REVERT: C 180 LYS cc_start: 0.7787 (pttt) cc_final: 0.7573 (ptmt) REVERT: C 183 GLU cc_start: 0.6567 (mt-10) cc_final: 0.6292 (mt-10) REVERT: C 185 LEU cc_start: 0.8967 (mt) cc_final: 0.8630 (mt) REVERT: C 194 VAL cc_start: 0.7833 (m) cc_final: 0.7420 (p) REVERT: C 235 THR cc_start: 0.7807 (t) cc_final: 0.6941 (p) REVERT: C 242 PHE cc_start: 0.6816 (m-10) cc_final: 0.6561 (m-10) REVERT: C 243 THR cc_start: 0.7796 (t) cc_final: 0.7490 (p) REVERT: C 256 LEU cc_start: 0.8501 (tp) cc_final: 0.8228 (tp) REVERT: C 262 TRP cc_start: 0.7626 (t60) cc_final: 0.7099 (t60) REVERT: C 287 ASN cc_start: 0.7156 (t0) cc_final: 0.6875 (t0) REVERT: C 288 LYS cc_start: 0.8234 (mttt) cc_final: 0.7686 (mttt) REVERT: C 301 GLU cc_start: 0.7322 (tt0) cc_final: 0.6537 (tt0) REVERT: C 305 ASN cc_start: 0.7592 (t0) cc_final: 0.7307 (t0) REVERT: C 306 LEU cc_start: 0.8269 (mt) cc_final: 0.7972 (mm) REVERT: C 328 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7600 (mtt180) REVERT: C 336 LEU cc_start: 0.8429 (mt) cc_final: 0.8000 (mt) REVERT: C 346 MET cc_start: 0.6940 (tmm) cc_final: 0.6627 (tmm) REVERT: C 354 PHE cc_start: 0.7988 (t80) cc_final: 0.7573 (t80) REVERT: C 371 VAL cc_start: 0.8422 (p) cc_final: 0.7973 (m) REVERT: C 373 LYS cc_start: 0.8156 (mttt) cc_final: 0.7702 (mtmm) REVERT: C 396 ARG cc_start: 0.7775 (ttm170) cc_final: 0.6834 (ttm170) REVERT: C 400 GLN cc_start: 0.7858 (mt0) cc_final: 0.6877 (mt0) REVERT: C 404 ASN cc_start: 0.8003 (m-40) cc_final: 0.7360 (m110) REVERT: C 415 PRO cc_start: 0.8695 (Cg_endo) cc_final: 0.8462 (Cg_exo) REVERT: C 421 MET cc_start: 0.6470 (mtt) cc_final: 0.6225 (mtt) REVERT: C 426 GLU cc_start: 0.7565 (pp20) cc_final: 0.7270 (pp20) REVERT: C 427 GLN cc_start: 0.8167 (mt0) cc_final: 0.7532 (mt0) REVERT: C 430 SER cc_start: 0.8444 (t) cc_final: 0.7896 (p) REVERT: C 434 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7515 (mt-10) REVERT: C 466 MET cc_start: 0.6986 (ttm) cc_final: 0.6717 (ttm) REVERT: C 470 LYS cc_start: 0.8512 (mttt) cc_final: 0.8120 (mttt) REVERT: C 471 LEU cc_start: 0.8185 (tp) cc_final: 0.7926 (tt) REVERT: C 478 TYR cc_start: 0.8007 (t80) cc_final: 0.7757 (t80) outliers start: 1 outliers final: 0 residues processed: 561 average time/residue: 0.3377 time to fit residues: 267.3663 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 : 1.601 ------------------------------------------------------------------------------- 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: 0.7980 chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 152 optimal weight: 0.0070 chunk 143 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 60 optimal weight: 0.0980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 398 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS B 210 GLN B 305 ASN B 400 GLN B 404 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095466 restraints weight = 69141.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.101008 restraints weight = 27735.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104703 restraints weight = 14769.096| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 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 = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16209 Z= 0.151 Angle : 0.550 8.175 22166 Z= 0.283 Chirality : 0.041 0.185 2406 Planarity : 0.004 0.053 2692 Dihedral : 14.280 88.801 2496 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.19 % Allowed : 0.63 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.20), residues: 1837 helix: 2.01 (0.19), residues: 781 sheet: 0.35 (0.33), residues: 244 loop : -0.16 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 572 HIS 0.007 0.001 HIS A 360 PHE 0.022 0.001 PHE B 254 TYR 0.024 0.001 TYR C 291 ARG 0.009 0.001 ARG A 193 *********************** 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 559 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 558 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8431 (mm) cc_final: 0.8190 (mm) REVERT: A 159 GLN cc_start: 0.7061 (tm-30) cc_final: 0.6473 (pp30) REVERT: A 169 TRP cc_start: 0.7944 (m-90) cc_final: 0.7648 (m-90) REVERT: A 171 TRP cc_start: 0.8153 (t-100) cc_final: 0.7905 (t-100) REVERT: A 177 ARG cc_start: 0.8148 (ttt90) cc_final: 0.7691 (ttt90) REVERT: A 280 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6967 (mm-30) REVERT: A 297 MET cc_start: 0.7598 (mtt) cc_final: 0.7356 (mtp) REVERT: A 299 MET cc_start: 0.7331 (tpt) cc_final: 0.6884 (tpt) REVERT: A 358 GLU cc_start: 0.7707 (mp0) cc_final: 0.7227 (mp0) REVERT: A 393 MET cc_start: 0.7137 (ttm) cc_final: 0.6850 (ttm) REVERT: A 410 GLN cc_start: 0.7635 (tt0) cc_final: 0.7037 (tt0) REVERT: A 427 MET cc_start: 0.7555 (ttm) cc_final: 0.7253 (ttm) REVERT: A 441 TRP cc_start: 0.7922 (t-100) cc_final: 0.7564 (t-100) REVERT: A 443 ARG cc_start: 0.6766 (ttt-90) cc_final: 0.6261 (ttt-90) REVERT: A 453 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7359 (mm-30) REVERT: A 457 ARG cc_start: 0.7746 (ttp-170) cc_final: 0.7523 (ttp-170) REVERT: A 487 ASP cc_start: 0.8351 (m-30) cc_final: 0.8092 (m-30) REVERT: A 565 HIS cc_start: 0.7374 (t-90) cc_final: 0.7159 (t-90) REVERT: A 574 ARG cc_start: 0.8309 (ptp90) cc_final: 0.7846 (ptp90) REVERT: A 579 ARG cc_start: 0.7431 (ttm110) cc_final: 0.6941 (ttm110) REVERT: A 586 THR cc_start: 0.8062 (t) cc_final: 0.7847 (p) REVERT: A 592 LEU cc_start: 0.8577 (mm) cc_final: 0.8219 (mt) REVERT: A 593 SER cc_start: 0.7823 (m) cc_final: 0.7231 (p) REVERT: A 601 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7692 (mtmm) REVERT: A 607 TRP cc_start: 0.8309 (t-100) cc_final: 0.7807 (t60) REVERT: A 617 ARG cc_start: 0.6887 (ttt90) cc_final: 0.6666 (mtp85) REVERT: A 750 PHE cc_start: 0.7154 (m-80) cc_final: 0.6638 (m-80) REVERT: A 758 ASN cc_start: 0.7877 (m-40) cc_final: 0.7587 (t0) REVERT: A 812 MET cc_start: 0.7344 (mpp) cc_final: 0.7121 (mpp) REVERT: A 816 LEU cc_start: 0.8503 (tp) cc_final: 0.8138 (tp) REVERT: A 832 ASP cc_start: 0.7948 (t70) cc_final: 0.7599 (t0) REVERT: A 836 LEU cc_start: 0.7114 (mm) cc_final: 0.6776 (mm) REVERT: A 875 LYS cc_start: 0.8522 (mtpp) cc_final: 0.7675 (ttmm) REVERT: A 877 MET cc_start: 0.7039 (mmp) cc_final: 0.6818 (tpp) REVERT: A 893 SER cc_start: 0.7099 (t) cc_final: 0.6734 (t) REVERT: A 919 MET cc_start: 0.7494 (mtt) cc_final: 0.7128 (mpp) REVERT: A 922 GLN cc_start: 0.7354 (tt0) cc_final: 0.6800 (tp40) REVERT: A 934 LYS cc_start: 0.8188 (mmpt) cc_final: 0.7963 (mmtt) REVERT: A 969 PHE cc_start: 0.7801 (m-10) cc_final: 0.7535 (m-10) REVERT: A 981 LYS cc_start: 0.8229 (tttt) cc_final: 0.7676 (tppt) REVERT: A 1057 MET cc_start: 0.7896 (ppp) cc_final: 0.7675 (ppp) REVERT: A 1060 LYS cc_start: 0.8265 (tptp) cc_final: 0.7827 (tptp) REVERT: A 1102 GLN cc_start: 0.7521 (mp10) cc_final: 0.6561 (mp10) REVERT: A 1110 HIS cc_start: 0.8556 (m-70) cc_final: 0.8281 (m-70) REVERT: A 1116 MET cc_start: 0.7190 (tpt) cc_final: 0.6455 (tpt) REVERT: A 1120 PHE cc_start: 0.7997 (m-80) cc_final: 0.7037 (m-80) REVERT: A 1136 GLU cc_start: 0.5865 (mt-10) cc_final: 0.5553 (mt-10) REVERT: A 1156 THR cc_start: 0.7877 (m) cc_final: 0.7290 (m) REVERT: A 1206 MET cc_start: 0.6089 (mtt) cc_final: 0.5727 (mmt) REVERT: A 1219 ASP cc_start: 0.7749 (t0) cc_final: 0.7517 (t0) REVERT: A 1222 GLN cc_start: 0.8499 (mp10) cc_final: 0.7810 (mp10) REVERT: B 76 ARG cc_start: 0.8229 (mmp80) cc_final: 0.7901 (mmm-85) REVERT: B 85 GLN cc_start: 0.7545 (mt0) cc_final: 0.7123 (mt0) REVERT: B 88 ARG cc_start: 0.7916 (ptp-170) cc_final: 0.7693 (ptp90) REVERT: B 113 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6875 (mm-30) REVERT: B 124 GLN cc_start: 0.8628 (pm20) cc_final: 0.8240 (pm20) REVERT: B 134 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7895 (mtmt) REVERT: B 180 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7433 (ptmt) REVERT: B 183 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6958 (mt-10) REVERT: B 191 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 201 ASN cc_start: 0.7737 (m110) cc_final: 0.7497 (m110) REVERT: B 247 THR cc_start: 0.7846 (p) cc_final: 0.7587 (p) REVERT: B 288 LYS cc_start: 0.7282 (mttt) cc_final: 0.6597 (mtmt) REVERT: B 289 LEU cc_start: 0.7790 (mt) cc_final: 0.7486 (mt) REVERT: B 304 TRP cc_start: 0.7726 (m100) cc_final: 0.7370 (m100) REVERT: B 310 GLU cc_start: 0.7618 (mp0) cc_final: 0.7335 (mp0) REVERT: B 339 ASN cc_start: 0.6653 (t0) cc_final: 0.6330 (t0) REVERT: B 352 ASP cc_start: 0.7093 (t0) cc_final: 0.6808 (t0) REVERT: B 353 SER cc_start: 0.8020 (p) cc_final: 0.7781 (p) REVERT: B 396 ARG cc_start: 0.7386 (ttm170) cc_final: 0.7019 (ttm110) REVERT: B 412 SER cc_start: 0.8294 (t) cc_final: 0.7849 (p) REVERT: B 426 GLU cc_start: 0.7770 (pm20) cc_final: 0.7407 (pp20) REVERT: B 427 GLN cc_start: 0.8070 (pt0) cc_final: 0.7724 (pm20) REVERT: B 457 SER cc_start: 0.7895 (t) cc_final: 0.7608 (p) REVERT: B 460 THR cc_start: 0.8494 (p) cc_final: 0.8211 (p) REVERT: B 461 THR cc_start: 0.8175 (p) cc_final: 0.7951 (t) REVERT: B 462 MET cc_start: 0.7680 (mmt) cc_final: 0.7435 (mmt) REVERT: B 465 MET cc_start: 0.7390 (mtm) cc_final: 0.6950 (mpp) REVERT: B 483 LYS cc_start: 0.6162 (mtpp) cc_final: 0.5825 (mtpp) REVERT: C 75 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7634 (mtm110) REVERT: C 80 SER cc_start: 0.8435 (t) cc_final: 0.7993 (m) REVERT: C 180 LYS cc_start: 0.7746 (pttt) cc_final: 0.7512 (ptmt) REVERT: C 183 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6276 (mt-10) REVERT: C 185 LEU cc_start: 0.8981 (mt) cc_final: 0.8652 (mt) REVERT: C 194 VAL cc_start: 0.7810 (m) cc_final: 0.7422 (p) REVERT: C 216 HIS cc_start: 0.8046 (m90) cc_final: 0.7619 (m-70) REVERT: C 234 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7655 (mtmm) REVERT: C 235 THR cc_start: 0.7787 (t) cc_final: 0.6979 (p) REVERT: C 243 THR cc_start: 0.7754 (t) cc_final: 0.7472 (p) REVERT: C 252 LEU cc_start: 0.7938 (tp) cc_final: 0.7700 (tt) REVERT: C 256 LEU cc_start: 0.8478 (tp) cc_final: 0.8168 (tp) REVERT: C 259 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7347 (mtp85) REVERT: C 262 TRP cc_start: 0.7586 (t60) cc_final: 0.7077 (t60) REVERT: C 279 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6928 (tm-30) REVERT: C 287 ASN cc_start: 0.7098 (t0) cc_final: 0.6744 (t0) REVERT: C 288 LYS cc_start: 0.8263 (mttt) cc_final: 0.7677 (mttt) REVERT: C 301 GLU cc_start: 0.7349 (tt0) cc_final: 0.6804 (tt0) REVERT: C 305 ASN cc_start: 0.7597 (t0) cc_final: 0.7332 (t0) REVERT: C 306 LEU cc_start: 0.8277 (mt) cc_final: 0.7791 (mm) REVERT: C 328 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7594 (mtt180) REVERT: C 336 LEU cc_start: 0.8484 (mt) cc_final: 0.8012 (mt) REVERT: C 339 ASN cc_start: 0.7440 (t0) cc_final: 0.7085 (t0) REVERT: C 343 ASP cc_start: 0.7300 (m-30) cc_final: 0.7093 (m-30) REVERT: C 346 MET cc_start: 0.6905 (tmm) cc_final: 0.6568 (tmm) REVERT: C 354 PHE cc_start: 0.7959 (t80) cc_final: 0.7542 (t80) REVERT: C 371 VAL cc_start: 0.8156 (p) cc_final: 0.7930 (m) REVERT: C 372 LEU cc_start: 0.8627 (mt) cc_final: 0.8296 (mt) REVERT: C 392 THR cc_start: 0.8681 (t) cc_final: 0.8429 (p) REVERT: C 396 ARG cc_start: 0.7796 (ttm170) cc_final: 0.6792 (ttm170) REVERT: C 400 GLN cc_start: 0.7807 (mt0) cc_final: 0.6795 (mt0) REVERT: C 404 ASN cc_start: 0.8004 (m-40) cc_final: 0.7415 (m110) REVERT: C 415 PRO cc_start: 0.8697 (Cg_endo) cc_final: 0.8463 (Cg_exo) REVERT: C 430 SER cc_start: 0.8453 (t) cc_final: 0.7921 (p) REVERT: C 434 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 466 MET cc_start: 0.6984 (ttm) cc_final: 0.6744 (ttm) REVERT: C 470 LYS cc_start: 0.8503 (mttt) cc_final: 0.8109 (mttt) REVERT: C 471 LEU cc_start: 0.8185 (tp) cc_final: 0.7969 (tt) REVERT: C 478 TYR cc_start: 0.7993 (t80) cc_final: 0.7752 (t80) outliers start: 1 outliers final: 0 residues processed: 558 average time/residue: 0.3492 time to fit residues: 272.0280 Evaluate side-chains 522 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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: 0.0070 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 89 optimal weight: 0.0770 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 110 HIS 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 906 HIS B 305 ASN B 400 GLN B 404 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096040 restraints weight = 64590.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101505 restraints weight = 26429.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105160 restraints weight = 14159.791| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 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 = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16209 Z= 0.154 Angle : 0.559 8.370 22166 Z= 0.287 Chirality : 0.041 0.179 2406 Planarity : 0.004 0.052 2692 Dihedral : 14.225 88.585 2496 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.20), residues: 1837 helix: 2.03 (0.19), residues: 786 sheet: 0.37 (0.33), residues: 244 loop : -0.18 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 490 HIS 0.007 0.001 HIS B 216 PHE 0.023 0.001 PHE B 254 TYR 0.022 0.001 TYR B 315 ARG 0.009 0.001 ARG A 232 ********************** 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 554 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 553 time to evaluate : 1.605 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 72 ASN cc_start: 0.7718 (p0) cc_final: 0.6576 (p0) REVERT: A 76 ILE cc_start: 0.8374 (mm) cc_final: 0.8042 (mm) REVERT: A 125 LEU cc_start: 0.8590 (tp) cc_final: 0.8389 (tp) REVERT: A 159 GLN cc_start: 0.7021 (tm-30) cc_final: 0.6431 (pp30) REVERT: A 169 TRP cc_start: 0.7932 (m-90) cc_final: 0.7578 (m-90) REVERT: A 171 TRP cc_start: 0.8146 (t-100) cc_final: 0.7870 (t-100) REVERT: A 177 ARG cc_start: 0.8240 (ttt90) cc_final: 0.7729 (ttt90) REVERT: A 213 VAL cc_start: 0.7275 (m) cc_final: 0.6878 (p) REVERT: A 275 ARG cc_start: 0.7940 (ttt180) cc_final: 0.7653 (ttt-90) REVERT: A 280 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6930 (mm-30) REVERT: A 299 MET cc_start: 0.7330 (tpt) cc_final: 0.6871 (tpt) REVERT: A 308 GLN cc_start: 0.7860 (mt0) cc_final: 0.7585 (mt0) REVERT: A 358 GLU cc_start: 0.7728 (mp0) cc_final: 0.7311 (mp0) REVERT: A 375 GLU cc_start: 0.7303 (pt0) cc_final: 0.6985 (pm20) REVERT: A 393 MET cc_start: 0.7117 (ttm) cc_final: 0.6767 (ttm) REVERT: A 410 GLN cc_start: 0.7603 (tt0) cc_final: 0.7043 (tt0) REVERT: A 427 MET cc_start: 0.7550 (ttm) cc_final: 0.7239 (ttm) REVERT: A 439 GLN cc_start: 0.7899 (pt0) cc_final: 0.7617 (pt0) REVERT: A 441 TRP cc_start: 0.7939 (t-100) cc_final: 0.7599 (t-100) REVERT: A 443 ARG cc_start: 0.6771 (ttt-90) cc_final: 0.6261 (ttt-90) REVERT: A 453 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7343 (mm-30) REVERT: A 487 ASP cc_start: 0.8400 (m-30) cc_final: 0.8133 (m-30) REVERT: A 537 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7836 (mp0) REVERT: A 565 HIS cc_start: 0.7407 (t-90) cc_final: 0.7102 (t-90) REVERT: A 566 LEU cc_start: 0.8799 (mp) cc_final: 0.8353 (mm) REVERT: A 572 TRP cc_start: 0.8455 (p-90) cc_final: 0.8144 (p-90) REVERT: A 574 ARG cc_start: 0.8259 (ptp90) cc_final: 0.7375 (mtm-85) REVERT: A 579 ARG cc_start: 0.7406 (ttm110) cc_final: 0.6929 (ttm110) REVERT: A 586 THR cc_start: 0.8082 (t) cc_final: 0.7849 (p) REVERT: A 603 MET cc_start: 0.7961 (mtt) cc_final: 0.7474 (mmm) REVERT: A 607 TRP cc_start: 0.8299 (t-100) cc_final: 0.7795 (t60) REVERT: A 617 ARG cc_start: 0.6899 (ttt90) cc_final: 0.6667 (mtp85) REVERT: A 750 PHE cc_start: 0.7135 (m-80) cc_final: 0.6619 (m-80) REVERT: A 758 ASN cc_start: 0.7932 (m-40) cc_final: 0.7551 (t0) REVERT: A 796 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7711 (ttmm) REVERT: A 806 LYS cc_start: 0.7982 (tptm) cc_final: 0.7742 (tptm) REVERT: A 812 MET cc_start: 0.7323 (mpp) cc_final: 0.7121 (mpp) REVERT: A 816 LEU cc_start: 0.8494 (tp) cc_final: 0.8160 (tp) REVERT: A 832 ASP cc_start: 0.7939 (t70) cc_final: 0.7610 (t0) REVERT: A 836 LEU cc_start: 0.7020 (mm) cc_final: 0.6714 (mm) REVERT: A 893 SER cc_start: 0.7080 (t) cc_final: 0.6726 (t) REVERT: A 906 HIS cc_start: 0.8262 (t70) cc_final: 0.8057 (t-90) REVERT: A 907 PHE cc_start: 0.7991 (t80) cc_final: 0.7598 (t80) REVERT: A 919 MET cc_start: 0.7426 (mtt) cc_final: 0.7034 (mpp) REVERT: A 922 GLN cc_start: 0.7340 (tt0) cc_final: 0.6805 (tp40) REVERT: A 934 LYS cc_start: 0.8203 (mmpt) cc_final: 0.7973 (mmtt) REVERT: A 969 PHE cc_start: 0.7776 (m-10) cc_final: 0.7515 (m-10) REVERT: A 981 LYS cc_start: 0.8213 (tttt) cc_final: 0.7678 (tppt) REVERT: A 1057 MET cc_start: 0.7898 (ppp) cc_final: 0.7670 (ppp) REVERT: A 1060 LYS cc_start: 0.8280 (tptp) cc_final: 0.7846 (tptp) REVERT: A 1102 GLN cc_start: 0.7480 (mp10) cc_final: 0.6861 (mp10) REVERT: A 1110 HIS cc_start: 0.8553 (m-70) cc_final: 0.8340 (m-70) REVERT: A 1113 LEU cc_start: 0.8302 (mp) cc_final: 0.7995 (tt) REVERT: A 1116 MET cc_start: 0.7147 (tpt) cc_final: 0.6447 (tpt) REVERT: A 1120 PHE cc_start: 0.7971 (m-80) cc_final: 0.7034 (m-80) REVERT: A 1136 GLU cc_start: 0.5834 (mt-10) cc_final: 0.5546 (mt-10) REVERT: A 1145 ASP cc_start: 0.6736 (m-30) cc_final: 0.6428 (m-30) REVERT: A 1156 THR cc_start: 0.7858 (m) cc_final: 0.7257 (m) REVERT: A 1219 ASP cc_start: 0.7753 (t0) cc_final: 0.7524 (t0) REVERT: A 1222 GLN cc_start: 0.8482 (mp10) cc_final: 0.7813 (mp10) REVERT: B 71 GLU cc_start: 0.8044 (pp20) cc_final: 0.7759 (tm-30) REVERT: B 76 ARG cc_start: 0.8216 (mmp80) cc_final: 0.7869 (mmm-85) REVERT: B 85 GLN cc_start: 0.7555 (mt0) cc_final: 0.7127 (mt0) REVERT: B 88 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.7668 (ptp90) REVERT: B 113 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6831 (mm-30) REVERT: B 124 GLN cc_start: 0.8461 (pm20) cc_final: 0.8173 (pm20) REVERT: B 134 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7907 (mtmt) REVERT: B 180 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7384 (ptmt) REVERT: B 183 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7025 (mt-10) REVERT: B 191 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7217 (mt-10) REVERT: B 247 THR cc_start: 0.7866 (p) cc_final: 0.7550 (p) REVERT: B 288 LYS cc_start: 0.7270 (mttt) cc_final: 0.6574 (mtmt) REVERT: B 289 LEU cc_start: 0.7784 (mt) cc_final: 0.7522 (mt) REVERT: B 304 TRP cc_start: 0.7708 (m100) cc_final: 0.7458 (m100) REVERT: B 310 GLU cc_start: 0.7630 (mp0) cc_final: 0.7364 (mp0) REVERT: B 339 ASN cc_start: 0.6709 (t0) cc_final: 0.6230 (t0) REVERT: B 352 ASP cc_start: 0.7104 (t0) cc_final: 0.6820 (t0) REVERT: B 353 SER cc_start: 0.8056 (p) cc_final: 0.7832 (p) REVERT: B 396 ARG cc_start: 0.7343 (ttm170) cc_final: 0.6959 (ttm110) REVERT: B 407 LEU cc_start: 0.8052 (mt) cc_final: 0.7843 (mm) REVERT: B 412 SER cc_start: 0.8315 (t) cc_final: 0.7881 (p) REVERT: B 427 GLN cc_start: 0.8082 (pt0) cc_final: 0.7756 (pm20) REVERT: B 457 SER cc_start: 0.7881 (t) cc_final: 0.7603 (p) REVERT: B 460 THR cc_start: 0.8469 (p) cc_final: 0.8205 (p) REVERT: B 461 THR cc_start: 0.8144 (p) cc_final: 0.7940 (t) REVERT: B 462 MET cc_start: 0.7679 (mmt) cc_final: 0.7438 (mmt) REVERT: B 465 MET cc_start: 0.7284 (mtm) cc_final: 0.6979 (mpp) REVERT: B 466 MET cc_start: 0.7395 (ttm) cc_final: 0.7021 (ttp) REVERT: B 483 LYS cc_start: 0.6132 (mtpp) cc_final: 0.5833 (mtpp) REVERT: C 75 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7643 (mtm110) REVERT: C 80 SER cc_start: 0.8449 (t) cc_final: 0.7991 (m) REVERT: C 180 LYS cc_start: 0.7677 (pttt) cc_final: 0.7468 (ptmt) REVERT: C 183 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6285 (mt-10) REVERT: C 185 LEU cc_start: 0.8950 (mt) cc_final: 0.8631 (mt) REVERT: C 194 VAL cc_start: 0.7816 (m) cc_final: 0.7416 (p) REVERT: C 216 HIS cc_start: 0.8084 (m90) cc_final: 0.7654 (m-70) REVERT: C 234 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7674 (mtmm) REVERT: C 235 THR cc_start: 0.7798 (t) cc_final: 0.6971 (p) REVERT: C 243 THR cc_start: 0.7762 (t) cc_final: 0.7484 (p) REVERT: C 252 LEU cc_start: 0.7951 (tp) cc_final: 0.7720 (tt) REVERT: C 256 LEU cc_start: 0.8501 (tp) cc_final: 0.8210 (tp) REVERT: C 259 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7336 (mtp85) REVERT: C 262 TRP cc_start: 0.7550 (t60) cc_final: 0.7008 (t60) REVERT: C 265 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7879 (tmtt) REVERT: C 266 PHE cc_start: 0.8352 (m-80) cc_final: 0.8101 (m-10) REVERT: C 279 GLN cc_start: 0.7150 (tm-30) cc_final: 0.6900 (tm-30) REVERT: C 287 ASN cc_start: 0.7108 (t0) cc_final: 0.6764 (t0) REVERT: C 288 LYS cc_start: 0.8229 (mttt) cc_final: 0.7631 (mttt) REVERT: C 301 GLU cc_start: 0.7300 (tt0) cc_final: 0.6757 (tt0) REVERT: C 305 ASN cc_start: 0.7583 (t0) cc_final: 0.7366 (t0) REVERT: C 306 LEU cc_start: 0.8116 (mt) cc_final: 0.7900 (mm) REVERT: C 323 HIS cc_start: 0.6340 (m90) cc_final: 0.6050 (m90) REVERT: C 336 LEU cc_start: 0.8441 (mt) cc_final: 0.7950 (mt) REVERT: C 339 ASN cc_start: 0.7430 (t0) cc_final: 0.7066 (t0) REVERT: C 354 PHE cc_start: 0.7924 (t80) cc_final: 0.7528 (t80) REVERT: C 371 VAL cc_start: 0.8128 (p) cc_final: 0.7872 (m) REVERT: C 372 LEU cc_start: 0.8565 (mt) cc_final: 0.8353 (mt) REVERT: C 396 ARG cc_start: 0.7801 (ttm170) cc_final: 0.6715 (ttm170) REVERT: C 400 GLN cc_start: 0.7811 (mt0) cc_final: 0.6762 (mt0) REVERT: C 404 ASN cc_start: 0.8016 (m-40) cc_final: 0.7380 (m110) REVERT: C 415 PRO cc_start: 0.8700 (Cg_endo) cc_final: 0.8468 (Cg_exo) REVERT: C 421 MET cc_start: 0.6354 (mtm) cc_final: 0.5934 (mtm) REVERT: C 427 GLN cc_start: 0.8453 (tt0) cc_final: 0.8127 (tt0) REVERT: C 430 SER cc_start: 0.8442 (t) cc_final: 0.7913 (p) REVERT: C 434 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7437 (mt-10) REVERT: C 462 MET cc_start: 0.6510 (tmm) cc_final: 0.6310 (tmm) REVERT: C 466 MET cc_start: 0.6967 (ttm) cc_final: 0.6732 (ttm) REVERT: C 470 LYS cc_start: 0.8487 (mttt) cc_final: 0.8077 (mttt) REVERT: C 475 LEU cc_start: 0.8199 (mt) cc_final: 0.7903 (mm) REVERT: C 478 TYR cc_start: 0.7999 (t80) cc_final: 0.7796 (t80) outliers start: 1 outliers final: 0 residues processed: 553 average time/residue: 0.3357 time to fit residues: 261.1560 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 : 1.561 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 111 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 398 GLN A 440 ASN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A1202 ASN B 400 GLN B 404 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.122055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.094259 restraints weight = 75469.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099973 restraints weight = 29280.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103781 restraints weight = 15361.034| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16209 Z= 0.182 Angle : 0.555 7.772 22166 Z= 0.287 Chirality : 0.042 0.180 2406 Planarity : 0.004 0.052 2692 Dihedral : 14.223 88.742 2496 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.13 % Allowed : 0.50 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1837 helix: 2.06 (0.19), residues: 786 sheet: 0.37 (0.33), residues: 244 loop : -0.15 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 312 HIS 0.007 0.001 HIS B 216 PHE 0.024 0.002 PHE B 254 TYR 0.022 0.001 TYR B 315 ARG 0.011 0.001 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6533.28 seconds wall clock time: 119 minutes 43.79 seconds (7183.79 seconds total)