Starting phenix.real_space_refine on Fri Feb 16 10:50:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3r_27163/02_2024/8d3r_27163_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3r_27163/02_2024/8d3r_27163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3r_27163/02_2024/8d3r_27163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3r_27163/02_2024/8d3r_27163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3r_27163/02_2024/8d3r_27163_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3r_27163/02_2024/8d3r_27163_updated.pdb" } resolution = 3.04 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= 0.339 sd= 0.597 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 48 5.49 5 S 82 5.16 5 C 9490 2.51 5 N 2647 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A GLU 1136": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "C GLU 394": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15113 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7629 Classifications: {'peptide': 958} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 64, 'TRANS': 893} Chain breaks: 6 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3308 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3222 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.86, per 1000 atoms: 0.52 Number of scatterers: 15113 At special positions: 0 Unit cell: (107.95, 114.75, 151.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 82 16.00 P 48 15.00 O 2845 8.00 N 2647 7.00 C 9490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.5 seconds 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3294 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 10 sheets defined 42.1% alpha, 12.8% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 6.80 Creating SS restraints... Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.865A pdb=" N GLU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 135 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.808A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.299A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 removed outlier: 3.899A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.581A pdb=" N GLU A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 417 removed outlier: 3.618A pdb=" N GLN A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A 399 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 400 " --> pdb=" O CYS A 396 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 439 through 481 removed outlier: 4.109A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 539 through 558 removed outlier: 3.758A pdb=" N VAL A 543 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N THR A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.750A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 602 No H-bonds generated for 'chain 'A' and resid 599 through 602' Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 768 through 776 Proline residue: A 772 - end of helix Processing helix chain 'A' and resid 788 through 809 removed outlier: 4.889A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 872 through 877 removed outlier: 4.524A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 removed outlier: 4.353A pdb=" N ALA A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 907 " --> pdb=" O GLY A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 944 through 954 removed outlier: 3.934A pdb=" N LYS A 947 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 948 " --> pdb=" O HIS A 945 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 951 " --> pdb=" O ILE A 948 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY A 952 " --> pdb=" O PHE A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.865A pdb=" N LEU A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 1053 through 1064 removed outlier: 3.596A pdb=" N GLU A1056 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET A1057 " --> pdb=" O GLU A1054 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A1059 " --> pdb=" O GLU A1056 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A1061 " --> pdb=" O PHE A1058 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU A1062 " --> pdb=" O ASN A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1093 through 1123 removed outlier: 3.783A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1167 removed outlier: 5.653A pdb=" N TYR A1147 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1202 No H-bonds generated for 'chain 'A' and resid 1200 through 1202' Processing helix chain 'A' and resid 1206 through 1209 No H-bonds generated for 'chain 'A' and resid 1206 through 1209' Processing helix chain 'A' and resid 1220 through 1227 Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 150 through 158 removed outlier: 4.029A pdb=" N GLU B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.543A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.576A pdb=" N HIS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 removed outlier: 3.890A pdb=" N ASP B 198 " --> pdb=" O ASN B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 392 through 409 removed outlier: 3.713A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 468 through 483 removed outlier: 4.575A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.698A pdb=" N ASP C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 177 Processing helix chain 'C' and resid 185 through 200 removed outlier: 3.681A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 removed outlier: 5.526A pdb=" N ASN C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 250 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 392 through 409 removed outlier: 3.632A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 425 through 434 Processing helix chain 'C' and resid 445 through 449 Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.486A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.925A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.736A pdb=" N ARG A 290 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLY A 268 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 292 " --> pdb=" O GLY A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 435 through 437 removed outlier: 4.819A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 816 " --> pdb=" O TYR A 837 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 612 through 615 removed outlier: 3.583A pdb=" N SER A 615 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 3.695A pdb=" N ILE A1131 " --> pdb=" O ARG A1138 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.689A pdb=" N GLY B 207 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER B 337 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASN B 305 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN B 339 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU B 303 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP B 341 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU B 301 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 289 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR B 302 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B 287 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP B 304 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS B 285 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 323 through 326 Processing sheet with id= H, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.438A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE B 439 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP B 386 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 441 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.910A pdb=" N GLY C 207 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 289 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR C 302 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN C 287 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP C 304 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LYS C 285 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.505A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE C 439 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASP C 386 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 441 " --> pdb=" O ASP C 386 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 6.10 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: 3059 1.33 - 1.45: 3885 1.45 - 1.57: 8422 1.57 - 1.69: 89 1.69 - 1.81: 130 Bond restraints: 15585 Sorted by residual: bond pdb=" O5' DCP A1301 " pdb=" PA DCP A1301 " ideal model delta sigma weight residual 1.579 1.804 -0.225 1.50e-02 4.44e+03 2.25e+02 bond pdb=" C5' DCP A1301 " pdb=" O5' DCP A1301 " ideal model delta sigma weight residual 1.443 1.322 0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 1.592 1.710 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 1.600 1.652 -0.052 1.10e-02 8.26e+03 2.25e+01 bond pdb=" C4 DCP A1301 " pdb=" N4 DCP A1301 " ideal model delta sigma weight residual 1.334 1.390 -0.056 1.20e-02 6.94e+03 2.17e+01 ... (remaining 15580 not shown) Histogram of bond angle deviations from ideal: 92.41 - 100.86: 26 100.86 - 109.30: 1789 109.30 - 117.74: 10045 117.74 - 126.19: 8966 126.19 - 134.63: 495 Bond angle restraints: 21321 Sorted by residual: angle pdb=" C1' DCP A1301 " pdb=" O4' DCP A1301 " pdb=" C4' DCP A1301 " ideal model delta sigma weight residual 109.55 101.71 7.84 1.31e+00 5.82e-01 3.58e+01 angle pdb=" PB DCP A1301 " pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 139.87 133.96 5.91 1.00e+00 1.00e+00 3.49e+01 angle pdb=" O2G DCP A1301 " pdb=" PG DCP A1301 " pdb=" O3B DCP A1301 " ideal model delta sigma weight residual 104.48 98.01 6.47 1.14e+00 7.76e-01 3.25e+01 angle pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " pdb=" O3B DCP A1301 " ideal model delta sigma weight residual 101.57 93.17 8.40 1.54e+00 4.24e-01 2.99e+01 angle pdb=" O2A DCP A1301 " pdb=" PA DCP A1301 " pdb=" O3A DCP A1301 " ideal model delta sigma weight residual 106.94 116.49 -9.55 1.88e+00 2.83e-01 2.58e+01 ... (remaining 21316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7689 17.99 - 35.97: 1039 35.97 - 53.96: 349 53.96 - 71.95: 85 71.95 - 89.94: 30 Dihedral angle restraints: 9192 sinusoidal: 4090 harmonic: 5102 Sorted by residual: dihedral pdb=" CA GLN A 159 " pdb=" C GLN A 159 " pdb=" N ALA A 160 " pdb=" CA ALA A 160 " ideal model delta harmonic sigma weight residual -180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 123.82 -30.82 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CA VAL A 196 " pdb=" C VAL A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual 180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 9189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1757 0.038 - 0.076: 375 0.076 - 0.114: 134 0.114 - 0.152: 33 0.152 - 0.190: 2 Chirality restraints: 2301 Sorted by residual: chirality pdb=" CA VAL C 228 " pdb=" N VAL C 228 " pdb=" C VAL C 228 " pdb=" CB VAL C 228 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" C1' DCP A1301 " pdb=" C2' DCP A1301 " pdb=" N1 DCP A1301 " pdb=" O4' DCP A1301 " both_signs ideal model delta sigma weight residual False 2.45 2.28 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 2298 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 532 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C PRO A 532 " 0.033 2.00e-02 2.50e+03 pdb=" O PRO A 532 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS A 533 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA P 23 " 0.025 2.00e-02 2.50e+03 1.15e-02 3.64e+00 pdb=" N9 DA P 23 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DA P 23 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA P 23 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA P 23 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA P 23 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA P 23 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA P 23 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA P 23 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA P 23 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA P 23 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1152 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ALA A1152 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA A1152 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A1153 " -0.009 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 120 2.53 - 3.12: 11519 3.12 - 3.72: 23552 3.72 - 4.31: 31477 4.31 - 4.90: 52799 Nonbonded interactions: 119467 Sorted by model distance: nonbonded pdb=" O LEU A1153 " pdb=" OG1 THR A1156 " model vdw 1.941 2.440 nonbonded pdb=" O LEU C 147 " pdb=" OG SER C 178 " model vdw 2.032 2.440 nonbonded pdb=" OG SER A 302 " pdb=" O ILE A 350 " model vdw 2.051 2.440 nonbonded pdb=" OG1 THR C 444 " pdb=" OE1 GLU C 445 " model vdw 2.064 2.440 nonbonded pdb=" OG1 THR A1199 " pdb=" OD1 ASN A1202 " model vdw 2.107 2.440 ... (remaining 119462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 219 or resid 228 through 355 or resid 368 throu \ gh 485)) selection = chain 'C' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.740 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 43.400 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 15585 Z= 0.199 Angle : 0.611 13.020 21321 Z= 0.336 Chirality : 0.039 0.190 2301 Planarity : 0.004 0.061 2577 Dihedral : 18.931 89.937 5895 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.20 % Allowed : 22.37 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.21), residues: 1742 helix: 0.29 (0.20), residues: 710 sheet: 0.50 (0.33), residues: 225 loop : -0.39 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 241 HIS 0.003 0.001 HIS A 71 PHE 0.014 0.001 PHE C 242 TYR 0.014 0.001 TYR A1108 ARG 0.007 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 440 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7336 (t80) cc_final: 0.6866 (t80) REVERT: A 304 LEU cc_start: 0.6400 (mt) cc_final: 0.6037 (mm) REVERT: A 438 ASN cc_start: 0.7586 (t0) cc_final: 0.7225 (t0) REVERT: A 461 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7718 (ptpt) REVERT: A 793 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 875 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8452 (mttp) REVERT: A 877 MET cc_start: 0.8233 (mmm) cc_final: 0.7878 (mmp) REVERT: A 919 MET cc_start: 0.6904 (mtt) cc_final: 0.6691 (mtt) REVERT: A 943 ARG cc_start: 0.5633 (tmt170) cc_final: 0.5396 (ttt-90) REVERT: A 963 GLU cc_start: 0.6446 (tm-30) cc_final: 0.6064 (tm-30) REVERT: A 965 LEU cc_start: 0.4927 (mm) cc_final: 0.4218 (tt) REVERT: A 967 MET cc_start: 0.5754 (mmm) cc_final: 0.5137 (ptt) REVERT: A 1196 ASP cc_start: 0.6939 (t0) cc_final: 0.6724 (t0) REVERT: B 301 GLU cc_start: 0.7672 (tt0) cc_final: 0.7433 (tt0) REVERT: B 305 ASN cc_start: 0.8463 (t0) cc_final: 0.8174 (t0) REVERT: B 373 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8512 (mttt) REVERT: B 408 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7814 (tm-30) REVERT: C 107 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.7005 (ttp-170) REVERT: C 279 GLN cc_start: 0.7717 (mt0) cc_final: 0.7032 (mm-40) REVERT: C 325 ARG cc_start: 0.6716 (mtt-85) cc_final: 0.6351 (mtt90) REVERT: C 394 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6939 (mm-30) outliers start: 3 outliers final: 0 residues processed: 440 average time/residue: 0.3113 time to fit residues: 191.3321 Evaluate side-chains 377 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 975 GLN B 397 GLN C 279 GLN C 313 HIS ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15585 Z= 0.209 Angle : 0.590 8.169 21321 Z= 0.306 Chirality : 0.042 0.207 2301 Planarity : 0.004 0.049 2577 Dihedral : 15.263 81.003 2426 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.72 % Allowed : 20.42 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.20), residues: 1742 helix: 0.46 (0.20), residues: 702 sheet: 0.46 (0.34), residues: 216 loop : -0.37 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 241 HIS 0.005 0.001 HIS A 71 PHE 0.024 0.002 PHE C 242 TYR 0.016 0.002 TYR A 363 ARG 0.005 0.001 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 391 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8173 (mmm-85) REVERT: A 461 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7404 (ptpt) REVERT: A 465 ASP cc_start: 0.8108 (m-30) cc_final: 0.7900 (m-30) REVERT: A 875 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8350 (mttp) REVERT: A 919 MET cc_start: 0.6975 (mtt) cc_final: 0.6520 (mtp) REVERT: A 937 THR cc_start: 0.7879 (t) cc_final: 0.7656 (p) REVERT: A 943 ARG cc_start: 0.5851 (tmt170) cc_final: 0.5621 (ttt-90) REVERT: A 965 LEU cc_start: 0.4904 (OUTLIER) cc_final: 0.4421 (tt) REVERT: A 966 LEU cc_start: 0.7240 (mm) cc_final: 0.7009 (mm) REVERT: A 967 MET cc_start: 0.5583 (mmm) cc_final: 0.5024 (ptt) REVERT: A 986 TYR cc_start: 0.7224 (m-80) cc_final: 0.6876 (m-80) REVERT: A 1136 GLU cc_start: 0.6610 (mp0) cc_final: 0.6152 (mp0) REVERT: A 1196 ASP cc_start: 0.7134 (t0) cc_final: 0.6922 (t0) REVERT: B 301 GLU cc_start: 0.7580 (tt0) cc_final: 0.7239 (tt0) REVERT: B 373 LYS cc_start: 0.8880 (mtmt) cc_final: 0.8491 (mttt) REVERT: B 408 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7700 (tm-30) REVERT: B 421 MET cc_start: 0.4404 (ttt) cc_final: 0.4120 (ttt) REVERT: C 107 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.6964 (ttp-170) REVERT: C 325 ARG cc_start: 0.6769 (mtt-85) cc_final: 0.6401 (mtt90) outliers start: 57 outliers final: 36 residues processed: 415 average time/residue: 0.2821 time to fit residues: 169.1134 Evaluate side-chains 408 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 371 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 363 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 476 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A1175 GLN B 132 HIS C 258 HIS C 397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15585 Z= 0.191 Angle : 0.583 11.309 21321 Z= 0.301 Chirality : 0.041 0.187 2301 Planarity : 0.004 0.049 2577 Dihedral : 15.256 78.831 2426 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.17 % Allowed : 20.42 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.21), residues: 1742 helix: 0.48 (0.20), residues: 707 sheet: 0.46 (0.33), residues: 227 loop : -0.37 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 175 HIS 0.005 0.001 HIS A 298 PHE 0.030 0.002 PHE B 403 TYR 0.015 0.001 TYR A 622 ARG 0.006 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 386 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7628 (m-80) cc_final: 0.7368 (m-10) REVERT: A 461 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7345 (ptpt) REVERT: A 465 ASP cc_start: 0.8122 (m-30) cc_final: 0.7861 (m-30) REVERT: A 875 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8339 (mttp) REVERT: A 919 MET cc_start: 0.6920 (mtt) cc_final: 0.6681 (mtt) REVERT: A 937 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7702 (p) REVERT: A 943 ARG cc_start: 0.5829 (tmt170) cc_final: 0.5570 (ttt-90) REVERT: A 965 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4342 (tt) REVERT: A 966 LEU cc_start: 0.7266 (mm) cc_final: 0.7031 (mm) REVERT: A 967 MET cc_start: 0.5402 (mmm) cc_final: 0.4983 (ptt) REVERT: A 986 TYR cc_start: 0.7265 (m-80) cc_final: 0.6836 (m-80) REVERT: A 1136 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: A 1196 ASP cc_start: 0.7098 (t0) cc_final: 0.6859 (t0) REVERT: B 373 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8482 (mttt) REVERT: B 421 MET cc_start: 0.4414 (ttt) cc_final: 0.4154 (ttt) REVERT: C 107 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.6968 (ttp-170) REVERT: C 325 ARG cc_start: 0.6703 (mtt-85) cc_final: 0.6291 (mtt90) REVERT: C 453 ILE cc_start: 0.8419 (pt) cc_final: 0.7988 (mt) outliers start: 64 outliers final: 44 residues processed: 420 average time/residue: 0.2849 time to fit residues: 174.3542 Evaluate side-chains 418 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 371 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 0.1980 chunk 122 optimal weight: 6.9990 chunk 84 optimal weight: 0.0980 chunk 18 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN A1175 GLN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15585 Z= 0.181 Angle : 0.589 11.999 21321 Z= 0.299 Chirality : 0.041 0.180 2301 Planarity : 0.004 0.050 2577 Dihedral : 15.293 78.563 2426 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.76 % Allowed : 21.07 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.20), residues: 1742 helix: 0.49 (0.20), residues: 708 sheet: 0.50 (0.32), residues: 231 loop : -0.39 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 175 HIS 0.004 0.001 HIS A 298 PHE 0.026 0.001 PHE C 242 TYR 0.014 0.001 TYR A 363 ARG 0.004 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 383 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 461 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7552 (ptpt) REVERT: A 553 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.7050 (pttm) REVERT: A 875 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8313 (mttp) REVERT: A 919 MET cc_start: 0.6979 (mtt) cc_final: 0.6658 (mtt) REVERT: A 937 THR cc_start: 0.7905 (t) cc_final: 0.7692 (p) REVERT: A 943 ARG cc_start: 0.5878 (tmt170) cc_final: 0.5630 (ttt-90) REVERT: A 965 LEU cc_start: 0.4902 (OUTLIER) cc_final: 0.4346 (tt) REVERT: A 966 LEU cc_start: 0.7287 (mm) cc_final: 0.7040 (mm) REVERT: A 967 MET cc_start: 0.5295 (mmm) cc_final: 0.5046 (ptt) REVERT: A 1136 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6134 (mp0) REVERT: A 1196 ASP cc_start: 0.7101 (t0) cc_final: 0.6875 (t0) REVERT: B 385 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 421 MET cc_start: 0.4479 (ttt) cc_final: 0.4217 (ttt) REVERT: C 107 ARG cc_start: 0.7335 (ttp-170) cc_final: 0.6969 (ttp-170) REVERT: C 175 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5466 (mt) REVERT: C 325 ARG cc_start: 0.6745 (mtt-85) cc_final: 0.6262 (mtt90) outliers start: 73 outliers final: 54 residues processed: 422 average time/residue: 0.2828 time to fit residues: 174.6807 Evaluate side-chains 429 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 369 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 0.0770 chunk 2 optimal weight: 4.9990 chunk 128 optimal weight: 0.0770 chunk 71 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 43 optimal weight: 0.0020 overall best weight: 0.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 GLN B 279 GLN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15585 Z= 0.142 Angle : 0.565 10.946 21321 Z= 0.286 Chirality : 0.040 0.172 2301 Planarity : 0.004 0.045 2577 Dihedral : 15.271 77.877 2426 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.24 % Allowed : 22.05 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.21), residues: 1742 helix: 0.58 (0.20), residues: 705 sheet: 0.59 (0.32), residues: 234 loop : -0.35 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 175 HIS 0.008 0.001 HIS B 454 PHE 0.027 0.001 PHE B 403 TYR 0.012 0.001 TYR A 150 ARG 0.004 0.000 ARG A1148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 382 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 386 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.8077 (mtt-85) REVERT: A 461 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7408 (ptpt) REVERT: A 553 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.7011 (pttm) REVERT: A 875 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8302 (mttp) REVERT: A 919 MET cc_start: 0.6971 (mtt) cc_final: 0.6663 (mtt) REVERT: A 937 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7677 (p) REVERT: A 943 ARG cc_start: 0.5861 (tmt170) cc_final: 0.5623 (ttt-90) REVERT: A 965 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4289 (tt) REVERT: A 966 LEU cc_start: 0.7226 (mm) cc_final: 0.7009 (mm) REVERT: A 1139 TYR cc_start: 0.7088 (m-80) cc_final: 0.6856 (m-80) REVERT: A 1148 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7971 (mtp85) REVERT: A 1196 ASP cc_start: 0.7074 (t0) cc_final: 0.6842 (t0) REVERT: B 70 LEU cc_start: 0.8250 (mm) cc_final: 0.7770 (mm) REVERT: B 421 MET cc_start: 0.4341 (ttt) cc_final: 0.4082 (ttt) REVERT: B 468 ILE cc_start: 0.8327 (tt) cc_final: 0.8104 (mm) REVERT: C 71 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: C 107 ARG cc_start: 0.7322 (ttp-170) cc_final: 0.6950 (ttp-170) REVERT: C 325 ARG cc_start: 0.6746 (mtt-85) cc_final: 0.6303 (mtt90) REVERT: C 409 ASN cc_start: 0.7558 (m110) cc_final: 0.7293 (m-40) outliers start: 65 outliers final: 43 residues processed: 417 average time/residue: 0.2788 time to fit residues: 169.2457 Evaluate side-chains 420 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 372 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 173 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 80 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 454 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15585 Z= 0.226 Angle : 0.614 10.181 21321 Z= 0.313 Chirality : 0.042 0.253 2301 Planarity : 0.005 0.049 2577 Dihedral : 15.403 77.223 2426 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.15 % Allowed : 21.46 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.20), residues: 1742 helix: 0.43 (0.20), residues: 704 sheet: 0.35 (0.32), residues: 241 loop : -0.49 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 175 HIS 0.017 0.001 HIS B 454 PHE 0.021 0.002 PHE C 242 TYR 0.019 0.002 TYR A 622 ARG 0.005 0.000 ARG A1148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 376 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7639 (m-80) cc_final: 0.7348 (m-10) REVERT: A 195 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 461 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7556 (ptpt) REVERT: A 553 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7090 (pttm) REVERT: A 875 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8319 (mttp) REVERT: A 919 MET cc_start: 0.6978 (mtt) cc_final: 0.6647 (mtt) REVERT: A 937 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7654 (p) REVERT: A 943 ARG cc_start: 0.5912 (tmt170) cc_final: 0.5684 (ttt-90) REVERT: A 965 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4225 (tt) REVERT: A 966 LEU cc_start: 0.7174 (mm) cc_final: 0.6967 (mm) REVERT: A 1117 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7792 (ttmm) REVERT: A 1196 ASP cc_start: 0.7115 (t0) cc_final: 0.6877 (t0) REVERT: B 70 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7759 (mm) REVERT: B 301 GLU cc_start: 0.7610 (tt0) cc_final: 0.7294 (tt0) REVERT: B 421 MET cc_start: 0.4411 (ttt) cc_final: 0.4174 (ttt) REVERT: C 71 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: C 107 ARG cc_start: 0.7361 (ttp-170) cc_final: 0.6974 (ttp-170) REVERT: C 175 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5466 (mt) REVERT: C 325 ARG cc_start: 0.6738 (mtt-85) cc_final: 0.6304 (mtt90) outliers start: 79 outliers final: 56 residues processed: 418 average time/residue: 0.2710 time to fit residues: 164.6696 Evaluate side-chains 427 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 363 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.1980 chunk 19 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 79 optimal weight: 0.0020 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15585 Z= 0.169 Angle : 0.582 9.674 21321 Z= 0.296 Chirality : 0.040 0.170 2301 Planarity : 0.004 0.047 2577 Dihedral : 15.338 75.793 2426 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.57 % Allowed : 22.50 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.20), residues: 1742 helix: 0.43 (0.20), residues: 706 sheet: 0.56 (0.32), residues: 233 loop : -0.50 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 175 HIS 0.008 0.001 HIS B 454 PHE 0.022 0.001 PHE B 403 TYR 0.017 0.001 TYR C 432 ARG 0.006 0.000 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 381 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7603 (m-80) cc_final: 0.7320 (m-10) REVERT: A 195 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8475 (mp) REVERT: A 382 MET cc_start: 0.6906 (tpp) cc_final: 0.6626 (tpp) REVERT: A 461 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7388 (ptpt) REVERT: A 553 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7079 (pttm) REVERT: A 826 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7715 (tt) REVERT: A 875 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8296 (mttp) REVERT: A 919 MET cc_start: 0.6966 (mtt) cc_final: 0.6626 (mtt) REVERT: A 943 ARG cc_start: 0.5884 (tmt170) cc_final: 0.5667 (ttt-90) REVERT: A 965 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4596 (tt) REVERT: A 1081 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.6931 (mtm-85) REVERT: A 1196 ASP cc_start: 0.7084 (t0) cc_final: 0.6849 (t0) REVERT: B 70 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7790 (mm) REVERT: B 421 MET cc_start: 0.4332 (ttt) cc_final: 0.4069 (ttt) REVERT: C 71 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: C 107 ARG cc_start: 0.7351 (ttp-170) cc_final: 0.6970 (ttp-170) REVERT: C 175 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5380 (mt) REVERT: C 325 ARG cc_start: 0.6727 (mtt-85) cc_final: 0.6303 (mtt90) REVERT: C 409 ASN cc_start: 0.7636 (m110) cc_final: 0.7376 (m-40) outliers start: 70 outliers final: 53 residues processed: 418 average time/residue: 0.2898 time to fit residues: 174.4311 Evaluate side-chains 424 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 364 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.0470 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15585 Z= 0.307 Angle : 0.689 9.956 21321 Z= 0.354 Chirality : 0.044 0.198 2301 Planarity : 0.005 0.052 2577 Dihedral : 15.635 75.509 2426 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.15 % Allowed : 22.50 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.20), residues: 1742 helix: 0.10 (0.19), residues: 707 sheet: 0.25 (0.32), residues: 232 loop : -0.80 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 175 HIS 0.005 0.001 HIS A 298 PHE 0.023 0.002 PHE C 242 TYR 0.022 0.002 TYR C 432 ARG 0.006 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 368 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 553 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7143 (pttm) REVERT: A 875 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8385 (mttp) REVERT: A 919 MET cc_start: 0.7072 (mtt) cc_final: 0.6673 (mtt) REVERT: A 943 ARG cc_start: 0.5910 (tmt170) cc_final: 0.5696 (ttt-90) REVERT: A 1081 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.6973 (mtm-85) REVERT: A 1117 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7885 (ttmm) REVERT: A 1196 ASP cc_start: 0.7230 (t0) cc_final: 0.7029 (t0) REVERT: B 70 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8077 (mm) REVERT: B 301 GLU cc_start: 0.7668 (tt0) cc_final: 0.7338 (tt0) REVERT: B 421 MET cc_start: 0.4528 (ttt) cc_final: 0.4270 (ttt) REVERT: C 71 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: C 107 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.6974 (ttp-170) REVERT: C 325 ARG cc_start: 0.6748 (mtt-85) cc_final: 0.6318 (mtt90) REVERT: C 425 LEU cc_start: 0.7974 (mt) cc_final: 0.7664 (mt) outliers start: 79 outliers final: 63 residues processed: 409 average time/residue: 0.2999 time to fit residues: 180.4197 Evaluate side-chains 430 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 362 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15585 Z= 0.231 Angle : 0.648 10.504 21321 Z= 0.331 Chirality : 0.042 0.190 2301 Planarity : 0.005 0.051 2577 Dihedral : 15.583 74.838 2426 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.83 % Allowed : 22.96 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.20), residues: 1742 helix: 0.12 (0.19), residues: 706 sheet: 0.24 (0.33), residues: 226 loop : -0.79 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 175 HIS 0.012 0.001 HIS B 454 PHE 0.024 0.002 PHE C 242 TYR 0.015 0.002 TYR C 206 ARG 0.006 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 372 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 438 ASN cc_start: 0.7796 (t0) cc_final: 0.7555 (t0) REVERT: A 553 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7146 (pttm) REVERT: A 826 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 875 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8346 (mttp) REVERT: A 919 MET cc_start: 0.7044 (mtt) cc_final: 0.6658 (mtt) REVERT: A 965 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4452 (tt) REVERT: A 1081 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.6932 (mtm-85) REVERT: A 1117 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7829 (ttmm) REVERT: A 1196 ASP cc_start: 0.7183 (t0) cc_final: 0.6933 (t0) REVERT: B 70 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8016 (mm) REVERT: C 71 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: C 107 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.6978 (ttp-170) REVERT: C 325 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.6300 (mtt90) REVERT: C 425 LEU cc_start: 0.7955 (mt) cc_final: 0.7670 (mt) outliers start: 74 outliers final: 64 residues processed: 412 average time/residue: 0.2677 time to fit residues: 160.3474 Evaluate side-chains 432 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 361 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15585 Z= 0.258 Angle : 0.665 10.746 21321 Z= 0.340 Chirality : 0.042 0.190 2301 Planarity : 0.005 0.052 2577 Dihedral : 15.630 74.346 2426 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.83 % Allowed : 23.29 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.20), residues: 1742 helix: 0.07 (0.19), residues: 706 sheet: 0.21 (0.32), residues: 236 loop : -0.86 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 175 HIS 0.005 0.001 HIS A 298 PHE 0.025 0.002 PHE C 242 TYR 0.033 0.002 TYR C 432 ARG 0.006 0.001 ARG A 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 367 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 TRP cc_start: 0.7827 (m100) cc_final: 0.7599 (m100) REVERT: A 195 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 438 ASN cc_start: 0.7817 (t0) cc_final: 0.7581 (t0) REVERT: A 553 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7136 (pttm) REVERT: A 826 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7859 (tt) REVERT: A 875 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8354 (mttp) REVERT: A 919 MET cc_start: 0.7128 (mtt) cc_final: 0.6741 (mtt) REVERT: A 965 LEU cc_start: 0.4864 (OUTLIER) cc_final: 0.4077 (tt) REVERT: A 1081 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.6919 (mtm-85) REVERT: A 1117 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7873 (ttmm) REVERT: A 1196 ASP cc_start: 0.7199 (t0) cc_final: 0.6948 (t0) REVERT: B 70 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8051 (mm) REVERT: B 465 MET cc_start: 0.8489 (mmm) cc_final: 0.8125 (mmp) REVERT: C 71 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: C 107 ARG cc_start: 0.7373 (ttp-170) cc_final: 0.6977 (ttp-170) REVERT: C 325 ARG cc_start: 0.6693 (mtt-85) cc_final: 0.6286 (mtt90) REVERT: C 425 LEU cc_start: 0.7914 (mt) cc_final: 0.7607 (mt) outliers start: 74 outliers final: 64 residues processed: 407 average time/residue: 0.2785 time to fit residues: 165.0825 Evaluate side-chains 436 residues out of total 1539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 365 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 chunk 142 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.137239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.123514 restraints weight = 33076.551| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.54 r_work: 0.3669 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15585 Z= 0.204 Angle : 0.642 11.749 21321 Z= 0.325 Chirality : 0.041 0.193 2301 Planarity : 0.005 0.051 2577 Dihedral : 15.552 73.358 2426 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.89 % Allowed : 23.61 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.20), residues: 1742 helix: 0.18 (0.19), residues: 706 sheet: 0.25 (0.33), residues: 230 loop : -0.79 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 175 HIS 0.005 0.001 HIS A 71 PHE 0.022 0.001 PHE C 242 TYR 0.031 0.002 TYR C 432 ARG 0.006 0.000 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4026.75 seconds wall clock time: 73 minutes 0.81 seconds (4380.81 seconds total)