Starting phenix.real_space_refine on Wed Jun 25 18:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d42_27172/06_2025/8d42_27172_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d42_27172/06_2025/8d42_27172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d42_27172/06_2025/8d42_27172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d42_27172/06_2025/8d42_27172.map" model { file = "/net/cci-nas-00/data/ceres_data/8d42_27172/06_2025/8d42_27172_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d42_27172/06_2025/8d42_27172_neut_trim.cif" } resolution = 2.91 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= -0.121 sd= 0.790 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 45 5.49 5 S 82 5.16 5 C 9546 2.51 5 N 2665 2.21 5 O 2852 1.98 5 H 14610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 15393 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6613 Classifications: {'peptide': 411} Modifications used: {'COO': 1} 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: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6431 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 666 Classifications: {'DNA': 21} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 669 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {' CA': 3, 'DCP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 14.24, per 1000 atoms: 0.48 Number of scatterers: 29803 At special positions: 0 Unit cell: (115.6, 105.4, 145.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 82 16.00 P 45 15.00 O 2852 8.00 N 2665 7.00 C 9546 6.00 H 14610 1.00 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 13 sheets defined 48.3% alpha, 13.7% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 11.75 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.633A pdb=" N GLN A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.661A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 278 No H-bonds generated for 'chain 'A' and resid 277 through 278' Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.751A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.530A pdb=" N ILE A 350 " --> pdb=" O TRP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.419A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 4.102A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 5.268A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 554 removed outlier: 3.562A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.919A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.011A pdb=" N LYS A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 661 removed outlier: 3.725A pdb=" N ARG A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 787 through 810 removed outlier: 4.767A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 871 through 878 removed outlier: 3.819A pdb=" N LEU A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 923 Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 955 Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.731A pdb=" N ASN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.985A pdb=" N GLU A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.686A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 165 through 178 removed outlier: 4.195A pdb=" N ALA B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.547A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 247 through 266 removed outlier: 3.941A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.508A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.541A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 468 through 485 removed outlier: 4.626A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.893A pdb=" N GLU C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 156' Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 163 through 166 removed outlier: 4.427A pdb=" N GLN C 166 " --> pdb=" O SER C 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.916A pdb=" N LEU C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.634A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.870A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.188A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.716A pdb=" N LYS C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 391 through 409 removed outlier: 4.484A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.583A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 485 removed outlier: 4.323A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.804A pdb=" N ILE A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.721A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 438 removed outlier: 4.826A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA5, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.704A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A1186 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.292A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.614A pdb=" N LYS B 180 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 149 removed outlier: 3.611A pdb=" N ARG B 146 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.688A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.090A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB4, first strand: chain 'C' and resid 413 through 414 removed outlier: 7.132A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 11.08 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14576 1.03 - 1.23: 66 1.23 - 1.42: 6671 1.42 - 1.62: 8825 1.62 - 1.81: 131 Bond restraints: 30269 Sorted by residual: bond pdb=" O5' DCP A1304 " pdb=" PA DCP A1304 " ideal model delta sigma weight residual 1.579 1.805 -0.226 1.50e-02 4.44e+03 2.27e+02 bond pdb=" C5' DCP A1304 " pdb=" O5' DCP A1304 " ideal model delta sigma weight residual 1.443 1.323 0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" O3A DCP A1304 " pdb=" PB DCP A1304 " ideal model delta sigma weight residual 1.592 1.710 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" C4' DCP A1304 " pdb=" C5' DCP A1304 " ideal model delta sigma weight residual 1.508 1.563 -0.055 1.10e-02 8.26e+03 2.52e+01 bond pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 1.600 1.651 -0.051 1.10e-02 8.26e+03 2.19e+01 ... (remaining 30264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 54564 2.56 - 5.12: 150 5.12 - 7.67: 6 7.67 - 10.23: 5 10.23 - 12.79: 3 Bond angle restraints: 54728 Sorted by residual: angle pdb=" O1G DCP A1304 " pdb=" PG DCP A1304 " pdb=" O3B DCP A1304 " ideal model delta sigma weight residual 110.47 98.05 12.42 1.64e+00 3.70e-01 5.71e+01 angle pdb=" PB DCP A1304 " pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 139.87 133.43 6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" O2A DCP A1304 " pdb=" PA DCP A1304 " pdb=" O3A DCP A1304 " ideal model delta sigma weight residual 106.94 116.95 -10.01 1.88e+00 2.83e-01 2.84e+01 angle pdb=" C1' DCP A1304 " pdb=" N1 DCP A1304 " pdb=" C6 DCP A1304 " ideal model delta sigma weight residual 121.66 114.29 7.37 1.39e+00 5.21e-01 2.82e+01 angle pdb=" O3A DCP A1304 " pdb=" PB DCP A1304 " pdb=" O3B DCP A1304 " ideal model delta sigma weight residual 101.57 93.51 8.06 1.54e+00 4.24e-01 2.76e+01 ... (remaining 54723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 13596 34.74 - 69.48: 459 69.48 - 104.22: 9 104.22 - 138.95: 0 138.95 - 173.69: 1 Dihedral angle restraints: 14065 sinusoidal: 7902 harmonic: 6163 Sorted by residual: dihedral pdb=" CA LYS C 164 " pdb=" C LYS C 164 " pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASP B 159 " pdb=" C ASP B 159 " pdb=" N LYS B 160 " pdb=" CA LYS B 160 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DG T 5 " pdb=" C3' DG T 5 " pdb=" O3' DG T 5 " pdb=" P DT T 6 " ideal model delta sinusoidal sigma weight residual -140.00 33.69 -173.69 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 14062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1550 0.029 - 0.058: 497 0.058 - 0.087: 143 0.087 - 0.116: 96 0.116 - 0.145: 20 Chirality restraints: 2306 Sorted by residual: chirality pdb=" C1' DCP A1304 " pdb=" C2' DCP A1304 " pdb=" N1 DCP A1304 " pdb=" O4' DCP A1304 " both_signs ideal model delta sigma weight residual False 2.45 2.30 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE B 437 " pdb=" N ILE B 437 " pdb=" C ILE B 437 " pdb=" CB ILE B 437 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL C 338 " pdb=" N VAL C 338 " pdb=" C VAL C 338 " pdb=" CB VAL C 338 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2303 not shown) Planarity restraints: 4303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 485 " 0.029 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C VAL C 485 " -0.103 2.00e-02 2.50e+03 pdb=" O VAL C 485 " 0.037 2.00e-02 2.50e+03 pdb=" OXT VAL C 485 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 448 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C ALA A 448 " 0.027 2.00e-02 2.50e+03 pdb=" O ALA A 448 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 449 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 457 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ARG A 457 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG A 457 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 458 " 0.008 2.00e-02 2.50e+03 ... (remaining 4300 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 989 2.16 - 2.77: 56145 2.77 - 3.38: 81540 3.38 - 3.99: 104571 3.99 - 4.60: 163799 Nonbonded interactions: 407044 Sorted by model distance: nonbonded pdb=" OE1 GLU A1144 " pdb=" H GLU A1144 " model vdw 1.552 2.450 nonbonded pdb=" H VAL A 201 " pdb=" O3' DT P 24 " model vdw 1.564 2.450 nonbonded pdb=" HH TYR A 150 " pdb=" O ARG A 288 " model vdw 1.587 2.450 nonbonded pdb=" OE1 GLU C 310 " pdb=" H GLU C 310 " model vdw 1.617 2.450 nonbonded pdb=" OE1 GLU A 231 " pdb=" H GLU A 231 " model vdw 1.623 2.450 ... (remaining 407039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 67 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 68 through 218 or (resid 219 and (name N or \ name CA or name C or name O or name CB or name H or name HA or name HB2 or name \ HB3)) or (resid 228 and (name N or name CA or name C or name O or name CB or nam \ e HA or name HB )) or resid 229 through 355 or (resid 368 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 o \ r name NE2 or name HA or name HB2 or name HB3)) or resid 369 through 485)) selection = (chain 'C' and (resid 67 through 215 or (resid 216 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 217 through 355 or (resid 368 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name HA or name HB2 or name HB3)) or resid 369 through 485)) } 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: 1.800 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: 0.490 Extract box with map and model: 1.090 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 68.570 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 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:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 0.226 15660 Z= 0.225 Angle : 0.555 12.790 21408 Z= 0.310 Chirality : 0.037 0.145 2306 Planarity : 0.004 0.059 2600 Dihedral : 14.520 173.693 5921 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.84 % Allowed : 5.81 % Favored : 93.35 % 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: 0.49 (0.21), residues: 1758 helix: 0.92 (0.21), residues: 713 sheet: 0.56 (0.31), residues: 258 loop : -0.20 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 620 HIS 0.003 0.001 HIS B 313 PHE 0.012 0.001 PHE C 403 TYR 0.008 0.001 TYR A 434 ARG 0.002 0.000 ARG C 257 Details of bonding type rmsd hydrogen bonds : bond 0.14215 ( 703) hydrogen bonds : angle 6.63000 ( 1933) SS BOND : bond 0.00432 ( 1) SS BOND : angle 0.56495 ( 2) covalent geometry : bond 0.00351 (15659) covalent geometry : angle 0.55501 (21406) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 435 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8163 (t0) cc_final: 0.7825 (t0) REVERT: A 361 ARG cc_start: 0.7615 (tmt-80) cc_final: 0.7139 (tpm170) REVERT: A 610 PHE cc_start: 0.7513 (m-80) cc_final: 0.7261 (m-80) REVERT: A 743 ASP cc_start: 0.7133 (p0) cc_final: 0.6831 (p0) REVERT: A 793 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8038 (mp0) REVERT: A 797 MET cc_start: 0.8071 (mtt) cc_final: 0.7762 (mtp) REVERT: A 994 TRP cc_start: 0.4383 (m-90) cc_final: 0.3987 (m-10) REVERT: A 1138 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8083 (mmt-90) REVERT: A 1192 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7514 (mm-30) REVERT: B 249 ASN cc_start: 0.8076 (m-40) cc_final: 0.7773 (t0) REVERT: C 107 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7414 (mtm110) REVERT: C 129 ASP cc_start: 0.8193 (t70) cc_final: 0.7965 (t0) outliers start: 13 outliers final: 5 residues processed: 443 average time/residue: 2.1973 time to fit residues: 1096.7714 Evaluate side-chains 396 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 390 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 264 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN A1202 ASN B 124 GLN B 192 HIS B 250 GLN B 258 HIS B 292 ASN B 339 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120490 restraints weight = 81500.950| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.15 r_work: 0.3558 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15660 Z= 0.247 Angle : 0.612 4.801 21408 Z= 0.332 Chirality : 0.042 0.154 2306 Planarity : 0.005 0.084 2600 Dihedral : 14.709 172.098 2427 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.17 % Allowed : 14.66 % Favored : 82.17 % 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: 0.27 (0.20), residues: 1758 helix: 1.03 (0.20), residues: 720 sheet: 0.30 (0.32), residues: 251 loop : -0.59 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 262 HIS 0.006 0.001 HIS B 313 PHE 0.015 0.002 PHE A1180 TYR 0.015 0.002 TYR C 206 ARG 0.006 0.001 ARG A1128 Details of bonding type rmsd hydrogen bonds : bond 0.05628 ( 703) hydrogen bonds : angle 5.24391 ( 1933) SS BOND : bond 0.00624 ( 1) SS BOND : angle 2.80314 ( 2) covalent geometry : bond 0.00542 (15659) covalent geometry : angle 0.61125 (21406) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 399 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8329 (t0) cc_final: 0.7821 (t0) REVERT: A 443 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7969 (ttm-80) REVERT: A 610 PHE cc_start: 0.7744 (m-80) cc_final: 0.7488 (m-80) REVERT: A 793 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8142 (mp0) REVERT: A 797 MET cc_start: 0.8317 (mtt) cc_final: 0.8005 (mtp) REVERT: A 1091 GLU cc_start: 0.7164 (tt0) cc_final: 0.6942 (tt0) REVERT: A 1116 MET cc_start: 0.7806 (mmm) cc_final: 0.7591 (mmm) REVERT: A 1138 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7922 (mmt90) REVERT: A 1192 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 1226 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8630 (mt) REVERT: C 107 ARG cc_start: 0.8356 (mtm110) cc_final: 0.7924 (mtm110) REVERT: C 129 ASP cc_start: 0.8390 (t70) cc_final: 0.8133 (t0) REVERT: C 201 ASN cc_start: 0.8852 (t0) cc_final: 0.8618 (t0) outliers start: 49 outliers final: 30 residues processed: 419 average time/residue: 2.1217 time to fit residues: 1009.2985 Evaluate side-chains 404 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 143 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 803 ASN A 843 GLN B 192 HIS B 250 GLN B 292 ASN C 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.129664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118554 restraints weight = 82139.743| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.14 r_work: 0.3530 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15660 Z= 0.262 Angle : 0.636 5.620 21408 Z= 0.346 Chirality : 0.042 0.150 2306 Planarity : 0.006 0.063 2600 Dihedral : 14.823 170.981 2422 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.20 % Allowed : 15.63 % Favored : 80.17 % 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: -0.18 (0.20), residues: 1758 helix: 0.78 (0.19), residues: 718 sheet: 0.27 (0.32), residues: 238 loop : -1.05 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 262 HIS 0.008 0.002 HIS B 313 PHE 0.016 0.002 PHE A 197 TYR 0.017 0.002 TYR C 206 ARG 0.007 0.001 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.05703 ( 703) hydrogen bonds : angle 5.23438 ( 1933) SS BOND : bond 0.00106 ( 1) SS BOND : angle 3.85429 ( 2) covalent geometry : bond 0.00579 (15659) covalent geometry : angle 0.63486 (21406) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 443 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 378 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.4668 (OUTLIER) cc_final: 0.4451 (t0) REVERT: A 270 ASN cc_start: 0.8361 (t0) cc_final: 0.8013 (t0) REVERT: A 610 PHE cc_start: 0.7768 (m-80) cc_final: 0.7423 (m-80) REVERT: A 659 HIS cc_start: 0.2808 (OUTLIER) cc_final: 0.2451 (m90) REVERT: A 793 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8216 (mp0) REVERT: A 797 MET cc_start: 0.8351 (mtt) cc_final: 0.8061 (mtp) REVERT: A 1138 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7990 (mmt90) REVERT: A 1192 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 1226 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8634 (mt) REVERT: A 1233 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6063 (tptp) REVERT: B 122 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8598 (mtt-85) REVERT: C 107 ARG cc_start: 0.8443 (mtm110) cc_final: 0.8061 (mmm-85) REVERT: C 129 ASP cc_start: 0.8433 (t70) cc_final: 0.8064 (t70) REVERT: C 201 ASN cc_start: 0.8902 (t0) cc_final: 0.8599 (t0) REVERT: C 400 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: C 465 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.4816 (mpp) outliers start: 65 outliers final: 37 residues processed: 406 average time/residue: 2.0765 time to fit residues: 956.0098 Evaluate side-chains 409 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 169 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS B 292 ASN B 305 ASN C 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119382 restraints weight = 81889.599| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.15 r_work: 0.3542 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15660 Z= 0.196 Angle : 0.602 5.943 21408 Z= 0.324 Chirality : 0.040 0.147 2306 Planarity : 0.005 0.056 2600 Dihedral : 14.716 171.256 2422 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.68 % Allowed : 17.64 % Favored : 78.68 % 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 (0.20), residues: 1758 helix: 0.96 (0.19), residues: 724 sheet: 0.26 (0.32), residues: 238 loop : -1.08 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 897 HIS 0.007 0.001 HIS B 313 PHE 0.016 0.002 PHE A 197 TYR 0.014 0.002 TYR C 206 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 703) hydrogen bonds : angle 5.03537 ( 1933) SS BOND : bond 0.00779 ( 1) SS BOND : angle 3.56217 ( 2) covalent geometry : bond 0.00436 (15659) covalent geometry : angle 0.60091 (21406) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 379 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: A 270 ASN cc_start: 0.8359 (t0) cc_final: 0.7899 (t0) REVERT: A 430 MET cc_start: 0.8110 (tpt) cc_final: 0.7776 (tpt) REVERT: A 608 ASP cc_start: 0.7960 (t0) cc_final: 0.7732 (t0) REVERT: A 610 PHE cc_start: 0.7656 (m-80) cc_final: 0.7229 (m-80) REVERT: A 793 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8194 (mp0) REVERT: A 797 MET cc_start: 0.8384 (mtt) cc_final: 0.8074 (mtp) REVERT: A 1138 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7921 (mmt90) REVERT: A 1192 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 1226 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8637 (mt) REVERT: C 107 ARG cc_start: 0.8439 (mtm110) cc_final: 0.8102 (mmm-85) REVERT: C 129 ASP cc_start: 0.8436 (t70) cc_final: 0.8091 (t0) REVERT: C 201 ASN cc_start: 0.8902 (t0) cc_final: 0.8637 (t0) REVERT: C 400 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: C 404 ASN cc_start: 0.7855 (m110) cc_final: 0.7403 (m110) outliers start: 57 outliers final: 40 residues processed: 408 average time/residue: 2.0874 time to fit residues: 971.3546 Evaluate side-chains 416 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 372 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 10 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 258 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116123 restraints weight = 82559.108| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.12 r_work: 0.3491 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 15660 Z= 0.349 Angle : 0.740 15.079 21408 Z= 0.401 Chirality : 0.045 0.204 2306 Planarity : 0.007 0.063 2600 Dihedral : 15.168 169.688 2422 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.56 % Allowed : 17.12 % Favored : 77.33 % 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: -0.88 (0.19), residues: 1758 helix: 0.20 (0.19), residues: 730 sheet: 0.17 (0.33), residues: 225 loop : -1.53 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 262 HIS 0.010 0.002 HIS B 313 PHE 0.022 0.003 PHE A1092 TYR 0.019 0.003 TYR C 206 ARG 0.015 0.001 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.06322 ( 703) hydrogen bonds : angle 5.37479 ( 1933) SS BOND : bond 0.03453 ( 1) SS BOND : angle 10.16780 ( 2) covalent geometry : bond 0.00774 (15659) covalent geometry : angle 0.73366 (21406) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 378 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8508 (mmm) cc_final: 0.8270 (mmm) REVERT: A 81 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8420 (ttm110) REVERT: A 105 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7609 (tp30) REVERT: A 270 ASN cc_start: 0.8385 (t0) cc_final: 0.8150 (t0) REVERT: A 430 MET cc_start: 0.8141 (tpt) cc_final: 0.7833 (tpt) REVERT: A 610 PHE cc_start: 0.7662 (m-80) cc_final: 0.7330 (m-80) REVERT: A 793 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8331 (mp0) REVERT: A 797 MET cc_start: 0.8376 (mtt) cc_final: 0.7985 (mtp) REVERT: A 1138 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8074 (mmt90) REVERT: A 1192 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 1233 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6777 (tptp) REVERT: B 139 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5271 (pt) REVERT: B 161 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5301 (tm-30) REVERT: C 107 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8041 (mtp180) REVERT: C 201 ASN cc_start: 0.8899 (t0) cc_final: 0.8613 (t0) REVERT: C 344 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7356 (mmt-90) REVERT: C 400 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: C 404 ASN cc_start: 0.7915 (m110) cc_final: 0.7487 (m110) REVERT: C 465 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.4935 (mpp) outliers start: 86 outliers final: 49 residues processed: 422 average time/residue: 2.0973 time to fit residues: 1005.1503 Evaluate side-chains 437 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 380 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1142 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 78 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN B 192 HIS B 258 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.129577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118818 restraints weight = 81912.189| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.12 r_work: 0.3535 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15660 Z= 0.167 Angle : 0.618 15.445 21408 Z= 0.330 Chirality : 0.040 0.163 2306 Planarity : 0.005 0.055 2600 Dihedral : 14.866 172.115 2422 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.75 % Allowed : 19.25 % Favored : 77.00 % 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: -0.28 (0.20), residues: 1758 helix: 0.83 (0.19), residues: 728 sheet: 0.26 (0.33), residues: 232 loop : -1.27 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 897 HIS 0.008 0.001 HIS B 313 PHE 0.015 0.001 PHE A 197 TYR 0.012 0.001 TYR C 206 ARG 0.004 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 703) hydrogen bonds : angle 4.97135 ( 1933) SS BOND : bond 0.02913 ( 1) SS BOND : angle 6.50349 ( 2) covalent geometry : bond 0.00371 (15659) covalent geometry : angle 0.61435 (21406) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 440 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 382 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8426 (ttm110) REVERT: A 270 ASN cc_start: 0.8358 (t0) cc_final: 0.7932 (t0) REVERT: A 430 MET cc_start: 0.8158 (tpt) cc_final: 0.7843 (tpt) REVERT: A 793 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8195 (mp0) REVERT: A 797 MET cc_start: 0.8359 (mtt) cc_final: 0.8041 (mtp) REVERT: A 896 LEU cc_start: 0.7963 (mt) cc_final: 0.7757 (mp) REVERT: A 1138 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7908 (mmt90) REVERT: A 1233 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.5972 (tptp) REVERT: B 139 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5252 (pt) REVERT: B 161 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.5248 (tm-30) REVERT: C 107 ARG cc_start: 0.8439 (mtm110) cc_final: 0.8009 (mtp180) REVERT: C 201 ASN cc_start: 0.8874 (t0) cc_final: 0.8602 (t0) REVERT: C 400 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: C 404 ASN cc_start: 0.7871 (m110) cc_final: 0.7425 (m110) outliers start: 58 outliers final: 35 residues processed: 410 average time/residue: 2.4692 time to fit residues: 1181.7059 Evaluate side-chains 415 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 374 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 106 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 68 optimal weight: 0.0870 chunk 59 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS B 292 ASN B 305 ASN C 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116804 restraints weight = 81763.480| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.11 r_work: 0.3505 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15660 Z= 0.269 Angle : 0.677 13.571 21408 Z= 0.364 Chirality : 0.043 0.150 2306 Planarity : 0.006 0.055 2600 Dihedral : 15.086 171.914 2422 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.46 % Allowed : 19.06 % Favored : 76.49 % 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: -0.61 (0.20), residues: 1758 helix: 0.55 (0.19), residues: 729 sheet: 0.16 (0.33), residues: 233 loop : -1.49 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 262 HIS 0.009 0.002 HIS B 313 PHE 0.016 0.002 PHE A1092 TYR 0.020 0.002 TYR B 291 ARG 0.006 0.001 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.05572 ( 703) hydrogen bonds : angle 5.13718 ( 1933) SS BOND : bond 0.02513 ( 1) SS BOND : angle 6.55764 ( 2) covalent geometry : bond 0.00599 (15659) covalent geometry : angle 0.67425 (21406) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 446 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 377 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8422 (ttm110) REVERT: A 270 ASN cc_start: 0.8343 (t0) cc_final: 0.8050 (t0) REVERT: A 430 MET cc_start: 0.8198 (tpt) cc_final: 0.7870 (tpt) REVERT: A 793 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8310 (mp0) REVERT: A 797 MET cc_start: 0.8359 (mtt) cc_final: 0.7959 (mtp) REVERT: A 896 LEU cc_start: 0.8049 (mt) cc_final: 0.7831 (mp) REVERT: A 1138 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7903 (mmt90) REVERT: A 1233 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6710 (tptp) REVERT: B 139 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5124 (pp) REVERT: B 161 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5329 (tm-30) REVERT: B 310 GLU cc_start: 0.8336 (mp0) cc_final: 0.8126 (mp0) REVERT: B 371 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (p) REVERT: C 107 ARG cc_start: 0.8432 (mtm110) cc_final: 0.8012 (mtp180) REVERT: C 201 ASN cc_start: 0.8852 (t0) cc_final: 0.8583 (t0) REVERT: C 344 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7264 (mmt-90) REVERT: C 400 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: C 404 ASN cc_start: 0.7823 (m110) cc_final: 0.7406 (m110) REVERT: C 465 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.4912 (mpp) outliers start: 69 outliers final: 50 residues processed: 412 average time/residue: 2.2661 time to fit residues: 1063.7257 Evaluate side-chains 430 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 371 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 99 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 68 optimal weight: 0.0050 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.127838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117286 restraints weight = 81976.491| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.11 r_work: 0.3511 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15660 Z= 0.236 Angle : 0.663 12.350 21408 Z= 0.355 Chirality : 0.042 0.161 2306 Planarity : 0.006 0.055 2600 Dihedral : 15.081 172.251 2422 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.46 % Allowed : 20.09 % Favored : 75.45 % 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: 1758 helix: 0.68 (0.19), residues: 722 sheet: 0.12 (0.33), residues: 236 loop : -1.52 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 897 HIS 0.008 0.001 HIS B 313 PHE 0.020 0.002 PHE C 254 TYR 0.018 0.002 TYR B 291 ARG 0.005 0.001 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.05313 ( 703) hydrogen bonds : angle 5.07470 ( 1933) SS BOND : bond 0.02294 ( 1) SS BOND : angle 5.74871 ( 2) covalent geometry : bond 0.00527 (15659) covalent geometry : angle 0.66096 (21406) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 450 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 381 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8408 (ttm110) REVERT: A 270 ASN cc_start: 0.8337 (t0) cc_final: 0.8008 (t0) REVERT: A 430 MET cc_start: 0.8192 (tpt) cc_final: 0.7863 (tpt) REVERT: A 793 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8299 (mp0) REVERT: A 797 MET cc_start: 0.8393 (mtt) cc_final: 0.7994 (mtp) REVERT: A 896 LEU cc_start: 0.8027 (mt) cc_final: 0.7781 (mp) REVERT: A 1138 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7872 (mmt90) REVERT: A 1233 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6691 (tptp) REVERT: B 139 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5105 (pp) REVERT: B 161 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5374 (tm-30) REVERT: B 310 GLU cc_start: 0.8337 (mp0) cc_final: 0.8126 (mp0) REVERT: B 371 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 418 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9053 (mt) REVERT: C 107 ARG cc_start: 0.8443 (mtm110) cc_final: 0.8046 (mtp180) REVERT: C 201 ASN cc_start: 0.8866 (t0) cc_final: 0.8602 (t0) REVERT: C 310 GLU cc_start: 0.8229 (mp0) cc_final: 0.7958 (mp0) REVERT: C 344 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7270 (mmt-90) REVERT: C 400 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: C 404 ASN cc_start: 0.7830 (m110) cc_final: 0.7406 (m110) outliers start: 69 outliers final: 46 residues processed: 418 average time/residue: 2.1693 time to fit residues: 1043.7755 Evaluate side-chains 429 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 374 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 6 optimal weight: 0.0670 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.120805 restraints weight = 81193.915| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.13 r_work: 0.3564 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15660 Z= 0.122 Angle : 0.598 10.693 21408 Z= 0.315 Chirality : 0.039 0.158 2306 Planarity : 0.005 0.052 2600 Dihedral : 14.709 173.849 2422 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.91 % Allowed : 21.83 % Favored : 75.26 % 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: 0.10 (0.20), residues: 1758 helix: 1.26 (0.20), residues: 720 sheet: 0.24 (0.32), residues: 241 loop : -1.11 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 897 HIS 0.005 0.001 HIS B 313 PHE 0.016 0.001 PHE A 197 TYR 0.011 0.001 TYR A 150 ARG 0.004 0.000 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 703) hydrogen bonds : angle 4.72486 ( 1933) SS BOND : bond 0.01703 ( 1) SS BOND : angle 4.13250 ( 2) covalent geometry : bond 0.00276 (15659) covalent geometry : angle 0.59703 (21406) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 396 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8354 (t0) cc_final: 0.7946 (t0) REVERT: A 430 MET cc_start: 0.8172 (tpt) cc_final: 0.7829 (tpt) REVERT: A 793 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8154 (mp0) REVERT: A 797 MET cc_start: 0.8385 (mtt) cc_final: 0.8057 (mtp) REVERT: A 896 LEU cc_start: 0.7975 (mt) cc_final: 0.7737 (mp) REVERT: A 967 MET cc_start: 0.8203 (mtp) cc_final: 0.7990 (mtt) REVERT: A 1138 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8019 (mmt90) REVERT: B 139 LEU cc_start: 0.5952 (OUTLIER) cc_final: 0.5156 (pt) REVERT: B 371 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8667 (p) REVERT: B 418 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9021 (mt) REVERT: C 107 ARG cc_start: 0.8404 (mtm110) cc_final: 0.8024 (mtp180) REVERT: C 129 ASP cc_start: 0.8425 (t0) cc_final: 0.8132 (t0) REVERT: C 201 ASN cc_start: 0.8831 (t0) cc_final: 0.8596 (t0) REVERT: C 400 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: C 404 ASN cc_start: 0.7791 (m110) cc_final: 0.7371 (m110) REVERT: C 465 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.4905 (mpp) outliers start: 45 outliers final: 27 residues processed: 418 average time/residue: 2.0790 time to fit residues: 984.6939 Evaluate side-chains 413 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 380 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 121 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS B 292 ASN B 305 ASN C 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120184 restraints weight = 81396.025| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.13 r_work: 0.3556 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15660 Z= 0.136 Angle : 0.605 10.501 21408 Z= 0.318 Chirality : 0.039 0.156 2306 Planarity : 0.005 0.051 2600 Dihedral : 14.697 174.026 2422 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.20 % Allowed : 22.80 % Favored : 75.00 % 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: 0.18 (0.20), residues: 1758 helix: 1.35 (0.20), residues: 721 sheet: 0.34 (0.32), residues: 235 loop : -1.10 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 897 HIS 0.005 0.001 HIS C 77 PHE 0.019 0.001 PHE C 254 TYR 0.012 0.001 TYR A1108 ARG 0.009 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 703) hydrogen bonds : angle 4.70323 ( 1933) SS BOND : bond 0.01833 ( 1) SS BOND : angle 4.26409 ( 2) covalent geometry : bond 0.00311 (15659) covalent geometry : angle 0.60358 (21406) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 388 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8353 (t0) cc_final: 0.7940 (t0) REVERT: A 430 MET cc_start: 0.8182 (tpt) cc_final: 0.7830 (tpt) REVERT: A 793 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8184 (mp0) REVERT: A 797 MET cc_start: 0.8384 (mtt) cc_final: 0.8065 (mtp) REVERT: A 896 LEU cc_start: 0.7987 (mt) cc_final: 0.7733 (mp) REVERT: A 967 MET cc_start: 0.8247 (mtp) cc_final: 0.8016 (mtt) REVERT: A 1138 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8008 (mmt90) REVERT: B 139 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5144 (pt) REVERT: B 371 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8667 (p) REVERT: B 396 ARG cc_start: 0.8168 (mmt90) cc_final: 0.7892 (mmt90) REVERT: B 418 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9008 (mt) REVERT: C 107 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8053 (mtp180) REVERT: C 129 ASP cc_start: 0.8449 (t0) cc_final: 0.8201 (t0) REVERT: C 201 ASN cc_start: 0.8819 (t0) cc_final: 0.8594 (t0) REVERT: C 400 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: C 404 ASN cc_start: 0.7769 (m110) cc_final: 0.7300 (m110) outliers start: 34 outliers final: 27 residues processed: 405 average time/residue: 2.2475 time to fit residues: 1057.5677 Evaluate side-chains 415 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 383 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS C 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118755 restraints weight = 81741.561| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.12 r_work: 0.3534 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15660 Z= 0.189 Angle : 0.628 10.567 21408 Z= 0.333 Chirality : 0.040 0.160 2306 Planarity : 0.005 0.051 2600 Dihedral : 14.838 173.810 2422 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.20 % Allowed : 23.00 % Favored : 74.81 % 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: 0.02 (0.20), residues: 1758 helix: 1.28 (0.20), residues: 715 sheet: 0.32 (0.33), residues: 235 loop : -1.26 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 897 HIS 0.006 0.001 HIS B 313 PHE 0.017 0.002 PHE A 197 TYR 0.014 0.002 TYR B 291 ARG 0.008 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 703) hydrogen bonds : angle 4.80339 ( 1933) SS BOND : bond 0.02024 ( 1) SS BOND : angle 4.69582 ( 2) covalent geometry : bond 0.00425 (15659) covalent geometry : angle 0.62671 (21406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23243.22 seconds wall clock time: 397 minutes 34.31 seconds (23854.31 seconds total)