Starting phenix.real_space_refine on Wed Jun 18 12:24:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p28_17359/06_2025/8p28_17359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p28_17359/06_2025/8p28_17359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p28_17359/06_2025/8p28_17359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p28_17359/06_2025/8p28_17359.map" model { file = "/net/cci-nas-00/data/ceres_data/8p28_17359/06_2025/8p28_17359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p28_17359/06_2025/8p28_17359.cif" } resolution = 2.77 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 4 5.21 5 S 136 5.16 5 C 13238 2.51 5 N 3688 2.21 5 O 4039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21141 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5187 Classifications: {'peptide': 645} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 624} Chain breaks: 3 Chain: "B" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "C" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5186 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 624} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 92 Unusual residues: {' MG': 2, 'DTP': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'DTP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 15.07, per 1000 atoms: 0.71 Number of scatterers: 21141 At special positions: 0 Unit cell: (106.715, 170.05, 130.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 36 15.00 Mg 4 11.99 O 4039 8.00 N 3688 7.00 C 13238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 171 " - pdb=" SG CYS A 416 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 2.9 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4856 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 15 sheets defined 52.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.640A pdb=" N ARG A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.771A pdb=" N THR A 31 " --> pdb=" O MET A 28 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP A 32 " --> pdb=" O LEU A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.907A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.554A pdb=" N LEU A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.694A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.857A pdb=" N MET A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 142 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 175 through 182 removed outlier: 4.119A pdb=" N ILE A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 removed outlier: 4.038A pdb=" N VAL A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 245 Proline residue: A 230 - end of helix removed outlier: 4.351A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.815A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.701A pdb=" N TYR A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.850A pdb=" N ALA A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.681A pdb=" N LYS A 408 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 455 through 486 removed outlier: 3.725A pdb=" N ILE A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 462 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.695A pdb=" N ASN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 535 removed outlier: 3.686A pdb=" N CYS A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.967A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.967A pdb=" N VAL A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.721A pdb=" N ALA B 22 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 51 removed outlier: 4.289A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 70 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.791A pdb=" N SER B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 103' Processing helix chain 'B' and resid 121 through 142 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.506A pdb=" N HIS B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.817A pdb=" N TYR B 163 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.963A pdb=" N HIS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.517A pdb=" N ALA B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 223 through 229 removed outlier: 4.067A pdb=" N LEU B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.948A pdb=" N TYR B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.807A pdb=" N GLU B 274 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 305 removed outlier: 3.998A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 339 removed outlier: 3.525A pdb=" N CYS B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.889A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.662A pdb=" N LYS B 408 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 451 Processing helix chain 'B' and resid 455 through 486 removed outlier: 3.525A pdb=" N ARG B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 528 through 535 removed outlier: 3.828A pdb=" N CYS B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 570 removed outlier: 3.843A pdb=" N GLN B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 549 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 596 removed outlier: 3.620A pdb=" N GLN B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 635 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.991A pdb=" N GLU B 657 " --> pdb=" O PRO B 653 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.517A pdb=" N ALA C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 57 through 69 removed outlier: 3.606A pdb=" N MET C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.834A pdb=" N ALA C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 121 through 142 removed outlier: 3.580A pdb=" N ALA C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 175 through 182 removed outlier: 4.127A pdb=" N ILE C 179 " --> pdb=" O PRO C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.915A pdb=" N ASN C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 235 through 247 removed outlier: 3.712A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 301 removed outlier: 3.700A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 322 through 339 removed outlier: 3.911A pdb=" N ARG C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.707A pdb=" N LYS C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 458 through 486 removed outlier: 3.681A pdb=" N PHE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 Processing helix chain 'C' and resid 516 through 520 Processing helix chain 'C' and resid 528 through 538 removed outlier: 3.550A pdb=" N CYS C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 570 removed outlier: 3.635A pdb=" N GLN C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 549 " --> pdb=" O GLU C 545 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 552 " --> pdb=" O GLN C 548 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 596 removed outlier: 3.852A pdb=" N LYS C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 628 Processing helix chain 'C' and resid 653 through 666 removed outlier: 3.511A pdb=" N ASP C 664 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR C 666 " --> pdb=" O MET C 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 removed outlier: 4.104A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 4.607A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 73 through 92 removed outlier: 4.311A pdb=" N ALA D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 84 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.811A pdb=" N SER D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 103' Processing helix chain 'D' and resid 121 through 142 Proline residue: D 136 - end of helix Processing helix chain 'D' and resid 144 through 153 removed outlier: 3.588A pdb=" N HIS D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 removed outlier: 4.366A pdb=" N ILE D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.576A pdb=" N ALA D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 201' Processing helix chain 'D' and resid 201 through 213 removed outlier: 4.023A pdb=" N SER D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.927A pdb=" N LEU D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 removed outlier: 4.185A pdb=" N ARG D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR D 236 " --> pdb=" O VAL D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.692A pdb=" N TYR D 255 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.920A pdb=" N GLU D 274 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 305 removed outlier: 3.634A pdb=" N ILE D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER D 304 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.951A pdb=" N ARG D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 removed outlier: 3.542A pdb=" N TYR D 371 " --> pdb=" O ASN D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.536A pdb=" N LYS D 408 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.891A pdb=" N CYS D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 486 removed outlier: 3.674A pdb=" N ASP D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 493 Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.607A pdb=" N HIS D 519 " --> pdb=" O VAL D 516 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 520 " --> pdb=" O ILE D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 520' Processing helix chain 'D' and resid 528 through 537 removed outlier: 4.118A pdb=" N CYS D 532 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 570 removed outlier: 3.730A pdb=" N LEU D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 552 " --> pdb=" O GLN D 548 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 596 removed outlier: 3.689A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 630 through 635 removed outlier: 4.503A pdb=" N ASP D 633 " --> pdb=" O PRO D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 666 removed outlier: 4.014A pdb=" N GLU D 657 " --> pdb=" O PRO D 653 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 658 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.982A pdb=" N THR A 4 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.817A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.594A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A 219 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASN A 316 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 221 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLN A 351 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 387 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TRP A 353 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 7.281A pdb=" N VAL A 643 " --> pdb=" O ASN A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 158 removed outlier: 5.226A pdb=" N ASN B 435 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLY B 523 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 437 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLY B 525 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B 439 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE B 527 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 441 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AA8, first strand: chain 'B' and resid 314 through 317 removed outlier: 3.574A pdb=" N TYR B 317 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLN B 351 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU B 387 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP B 353 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=AB1, first strand: chain 'C' and resid 156 through 158 removed outlier: 5.673A pdb=" N THR C 521 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER C 437 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 523 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER C 439 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 522 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU C 576 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 524 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 172 through 173 removed outlier: 6.709A pdb=" N VAL C 172 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN C 219 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN C 316 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 221 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER C 313 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE C 352 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 315 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS C 354 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR C 317 " --> pdb=" O LYS C 354 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLN C 351 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU C 387 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TRP C 353 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 386 " --> pdb=" O GLY C 671 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 643 " --> pdb=" O ASN C 674 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.489A pdb=" N THR D 4 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 156 through 158 removed outlier: 7.023A pdb=" N SER D 437 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLY D 525 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER D 439 " --> pdb=" O GLY D 525 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE D 526 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AB6, first strand: chain 'D' and resid 220 through 221 removed outlier: 3.512A pdb=" N ASN D 316 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLN D 351 " --> pdb=" O ASN D 385 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU D 387 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP D 353 " --> pdb=" O LEU D 387 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6944 1.34 - 1.47: 4998 1.47 - 1.60: 9395 1.60 - 1.73: 0 1.73 - 1.85: 236 Bond restraints: 21573 Sorted by residual: bond pdb=" N VAL A 377 " pdb=" CA VAL A 377 " ideal model delta sigma weight residual 1.462 1.508 -0.046 1.18e-02 7.18e+03 1.49e+01 bond pdb=" N VAL C 502 " pdb=" CA VAL C 502 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N ASN A 385 " pdb=" CA ASN A 385 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.27e-02 6.20e+03 1.03e+01 bond pdb=" N THR B 588 " pdb=" CA THR B 588 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.85e+00 ... (remaining 21568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 28387 1.69 - 3.38: 617 3.38 - 5.08: 121 5.08 - 6.77: 26 6.77 - 8.46: 2 Bond angle restraints: 29153 Sorted by residual: angle pdb=" CA PHE C 184 " pdb=" CB PHE C 184 " pdb=" CG PHE C 184 " ideal model delta sigma weight residual 113.80 118.62 -4.82 1.00e+00 1.00e+00 2.32e+01 angle pdb=" N GLN A 334 " pdb=" CA GLN A 334 " pdb=" C GLN A 334 " ideal model delta sigma weight residual 113.55 107.79 5.76 1.26e+00 6.30e-01 2.09e+01 angle pdb=" CA ASN A 385 " pdb=" C ASN A 385 " pdb=" O ASN A 385 " ideal model delta sigma weight residual 121.88 116.99 4.89 1.13e+00 7.83e-01 1.87e+01 angle pdb=" N PRO C 175 " pdb=" CA PRO C 175 " pdb=" C PRO C 175 " ideal model delta sigma weight residual 112.47 104.01 8.46 2.06e+00 2.36e-01 1.69e+01 angle pdb=" CA TRP C 501 " pdb=" C TRP C 501 " pdb=" O TRP C 501 " ideal model delta sigma weight residual 121.25 116.86 4.39 1.09e+00 8.42e-01 1.62e+01 ... (remaining 29148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.33: 12402 20.33 - 40.66: 607 40.66 - 60.99: 131 60.99 - 81.32: 54 81.32 - 101.65: 10 Dihedral angle restraints: 13204 sinusoidal: 5660 harmonic: 7544 Sorted by residual: dihedral pdb=" CA TYR B 606 " pdb=" C TYR B 606 " pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER D 71 " pdb=" C SER D 71 " pdb=" N ALA D 72 " pdb=" CA ALA D 72 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ASP A 603 " pdb=" C ASP A 603 " pdb=" N ARG A 604 " pdb=" CA ARG A 604 " ideal model delta harmonic sigma weight residual -180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 13201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2517 0.054 - 0.108: 477 0.108 - 0.161: 106 0.161 - 0.215: 3 0.215 - 0.269: 25 Chirality restraints: 3128 Sorted by residual: chirality pdb=" C4' DTP A 802 " pdb=" C3' DTP A 802 " pdb=" C5' DTP A 802 " pdb=" O4' DTP A 802 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLU C 505 " pdb=" N GLU C 505 " pdb=" C GLU C 505 " pdb=" CB GLU C 505 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C3' DTP D 801 " pdb=" C2' DTP D 801 " pdb=" C4' DTP D 801 " pdb=" O3' DTP D 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.94 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3125 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 604 " 0.321 9.50e-02 1.11e+02 1.44e-01 1.28e+01 pdb=" NE ARG B 604 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 604 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 604 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 604 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 182 " -0.013 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C HIS C 182 " 0.043 2.00e-02 2.50e+03 pdb=" O HIS C 182 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY C 183 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 173 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C GLN C 173 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN C 173 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS C 174 " -0.012 2.00e-02 2.50e+03 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 84 2.42 - 3.04: 13891 3.04 - 3.66: 28783 3.66 - 4.28: 44667 4.28 - 4.90: 76553 Nonbonded interactions: 163978 Sorted by model distance: nonbonded pdb=" O3A DTP C 801 " pdb="MG MG C 804 " model vdw 1.795 2.170 nonbonded pdb=" O2B DTP A 801 " pdb="MG MG B 804 " model vdw 1.817 2.170 nonbonded pdb="MG MG A 804 " pdb=" O2B DTP B 801 " model vdw 1.842 2.170 nonbonded pdb=" OE2 GLU C 293 " pdb="MG MG C 805 " model vdw 1.859 2.170 nonbonded pdb="MG MG C 805 " pdb=" O2B DTP D 801 " model vdw 1.876 2.170 ... (remaining 163973 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 'A' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 674 or resid 801 through 803)) selection = (chain 'B' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 674 or resid 801 through 803)) selection = (chain 'C' and (resid 1 through 674 or resid 801 through 803)) selection = (chain 'D' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 674 or resid 801 through 803)) } 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: 6.070 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: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 51.850 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.110 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:17.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.859 21575 Z= 0.638 Angle : 0.642 8.461 29155 Z= 0.379 Chirality : 0.049 0.269 3128 Planarity : 0.005 0.144 3712 Dihedral : 13.734 101.650 8345 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.99 % Favored : 89.81 % Rotamer: Outliers : 2.15 % Allowed : 7.02 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2552 helix: 0.39 (0.16), residues: 1162 sheet: 0.03 (0.37), residues: 250 loop : -2.60 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 353 HIS 0.006 0.001 HIS A 289 PHE 0.020 0.002 PHE B 184 TYR 0.021 0.002 TYR A 262 ARG 0.004 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.18424 ( 807) hydrogen bonds : angle 6.16260 ( 2325) SS BOND : bond 0.02359 ( 1) SS BOND : angle 5.04644 ( 2) covalent geometry : bond 0.00528 (21573) covalent geometry : angle 0.64080 (29153) Misc. bond : bond 0.85863 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 567 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8205 (tp) cc_final: 0.7898 (tt) REVERT: A 154 ASN cc_start: 0.8141 (t0) cc_final: 0.7869 (t0) REVERT: A 468 ASP cc_start: 0.6788 (t0) cc_final: 0.6525 (t0) REVERT: A 533 LEU cc_start: 0.8020 (mp) cc_final: 0.7749 (mp) REVERT: A 670 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.8101 (t80) REVERT: B 41 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6524 (mm-30) REVERT: B 160 ASP cc_start: 0.7102 (t70) cc_final: 0.6824 (t70) REVERT: B 296 ILE cc_start: 0.6872 (mt) cc_final: 0.6662 (mp) REVERT: B 369 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.6721 (p0) REVERT: B 388 ASN cc_start: 0.7784 (t0) cc_final: 0.7451 (t0) REVERT: B 446 LEU cc_start: 0.8332 (mt) cc_final: 0.8118 (mt) REVERT: B 449 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6912 (tm-30) REVERT: B 521 THR cc_start: 0.7680 (p) cc_final: 0.7449 (m) REVERT: B 560 ASP cc_start: 0.7995 (m-30) cc_final: 0.7646 (m-30) REVERT: B 665 LYS cc_start: 0.8649 (tppp) cc_final: 0.8286 (mtpp) REVERT: C 2 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7369 (mp) REVERT: C 41 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6673 (mt-10) REVERT: C 45 ASP cc_start: 0.7098 (m-30) cc_final: 0.6805 (m-30) REVERT: C 65 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 67 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 79 LYS cc_start: 0.7220 (mmtt) cc_final: 0.6784 (mttt) REVERT: C 188 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8044 (p-80) REVERT: C 344 GLU cc_start: 0.6884 (pm20) cc_final: 0.6528 (pm20) REVERT: C 454 GLU cc_start: 0.7263 (tm-30) cc_final: 0.7021 (tm-30) REVERT: D 29 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (tt) REVERT: D 192 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6970 (ptt90) REVERT: D 369 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.7444 (p0) REVERT: D 420 VAL cc_start: 0.8428 (p) cc_final: 0.8221 (p) REVERT: D 560 ASP cc_start: 0.8018 (m-30) cc_final: 0.7789 (m-30) outliers start: 48 outliers final: 10 residues processed: 601 average time/residue: 1.3032 time to fit residues: 888.9774 Evaluate side-chains 527 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 510 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 494 PRO Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 369 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.1980 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 61 GLN A 213 ASN A 455 ASN A 518 ASN B 279 HIS B 385 ASN B 388 ASN B 396 ASN C 30 HIS C 154 ASN C 213 ASN D 572 ASN D 639 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.136436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125274 restraints weight = 30801.662| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.89 r_work: 0.3657 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21575 Z= 0.153 Angle : 0.620 12.038 29155 Z= 0.327 Chirality : 0.044 0.188 3128 Planarity : 0.005 0.052 3712 Dihedral : 12.202 91.717 3227 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.04 % Allowed : 14.81 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.17), residues: 2552 helix: 0.72 (0.16), residues: 1188 sheet: 0.14 (0.37), residues: 252 loop : -2.55 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 409 HIS 0.009 0.001 HIS D 297 PHE 0.027 0.002 PHE B 526 TYR 0.014 0.001 TYR B 607 ARG 0.005 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.05967 ( 807) hydrogen bonds : angle 4.69429 ( 2325) SS BOND : bond 0.01740 ( 1) SS BOND : angle 2.97091 ( 2) covalent geometry : bond 0.00342 (21573) covalent geometry : angle 0.61995 (29153) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 532 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 18 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7792 (tp40) REVERT: A 60 ILE cc_start: 0.8383 (tp) cc_final: 0.8068 (tt) REVERT: A 154 ASN cc_start: 0.8304 (t0) cc_final: 0.8076 (t0) REVERT: A 423 ASP cc_start: 0.7994 (t70) cc_final: 0.7793 (t0) REVERT: B 41 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 160 ASP cc_start: 0.7538 (t70) cc_final: 0.7274 (t70) REVERT: B 420 VAL cc_start: 0.8217 (p) cc_final: 0.7984 (m) REVERT: B 446 LEU cc_start: 0.8410 (mt) cc_final: 0.8196 (mt) REVERT: B 449 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7265 (tm-30) REVERT: B 464 PHE cc_start: 0.8237 (m-80) cc_final: 0.8019 (m-80) REVERT: B 479 ASP cc_start: 0.8057 (t0) cc_final: 0.7856 (t0) REVERT: B 560 ASP cc_start: 0.8469 (m-30) cc_final: 0.8085 (m-30) REVERT: B 631 TYR cc_start: 0.7919 (m-80) cc_final: 0.7595 (m-80) REVERT: C 2 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7660 (mp) REVERT: C 41 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7456 (mt-10) REVERT: C 45 ASP cc_start: 0.7618 (m-30) cc_final: 0.7301 (m-30) REVERT: C 52 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7515 (mmmm) REVERT: C 67 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 79 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7212 (mttt) REVERT: C 140 ASP cc_start: 0.7790 (m-30) cc_final: 0.7535 (m-30) REVERT: C 208 LEU cc_start: 0.7687 (mp) cc_final: 0.7378 (mp) REVERT: C 238 GLU cc_start: 0.6707 (pp20) cc_final: 0.6461 (pp20) REVERT: C 344 GLU cc_start: 0.7553 (pm20) cc_final: 0.7084 (pm20) REVERT: C 454 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7781 (tm-30) REVERT: C 592 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7639 (ttm170) REVERT: C 604 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7803 (mtt180) REVERT: D 185 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8351 (p) REVERT: D 274 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6468 (tm-30) REVERT: D 311 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7765 (t) REVERT: D 420 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8242 (p) REVERT: D 468 ASP cc_start: 0.6342 (OUTLIER) cc_final: 0.5996 (t70) outliers start: 68 outliers final: 22 residues processed: 564 average time/residue: 1.3480 time to fit residues: 859.6507 Evaluate side-chains 532 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 504 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 225 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 206 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 88 ASN A 213 ASN B 385 ASN B 540 HIS C 30 HIS C 213 ASN D 594 GLN D 639 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.135197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123912 restraints weight = 30631.661| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.90 r_work: 0.3640 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21575 Z= 0.191 Angle : 0.628 12.601 29155 Z= 0.330 Chirality : 0.045 0.193 3128 Planarity : 0.005 0.058 3712 Dihedral : 11.723 89.342 3203 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.34 % Allowed : 15.75 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2552 helix: 0.62 (0.16), residues: 1204 sheet: 0.18 (0.36), residues: 254 loop : -2.44 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 425 HIS 0.009 0.001 HIS D 297 PHE 0.029 0.002 PHE B 526 TYR 0.018 0.002 TYR A 236 ARG 0.010 0.001 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.06172 ( 807) hydrogen bonds : angle 4.58519 ( 2325) SS BOND : bond 0.01569 ( 1) SS BOND : angle 2.71032 ( 2) covalent geometry : bond 0.00446 (21573) covalent geometry : angle 0.62716 (29153) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 513 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 41 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 45 ASP cc_start: 0.7983 (m-30) cc_final: 0.7552 (m-30) REVERT: A 60 ILE cc_start: 0.8362 (tp) cc_final: 0.8053 (tt) REVERT: A 154 ASN cc_start: 0.8361 (t0) cc_final: 0.8149 (t0) REVERT: A 423 ASP cc_start: 0.8044 (t70) cc_final: 0.7844 (t0) REVERT: A 592 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7596 (ttm170) REVERT: A 603 ASP cc_start: 0.7217 (m-30) cc_final: 0.6985 (m-30) REVERT: B 41 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 42 GLN cc_start: 0.7941 (mt0) cc_final: 0.7656 (mp10) REVERT: B 160 ASP cc_start: 0.7624 (t70) cc_final: 0.7351 (t70) REVERT: B 185 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 420 VAL cc_start: 0.8276 (p) cc_final: 0.8076 (p) REVERT: B 446 LEU cc_start: 0.8427 (mt) cc_final: 0.8219 (mt) REVERT: B 449 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7190 (tm-30) REVERT: B 479 ASP cc_start: 0.8066 (t0) cc_final: 0.7860 (t0) REVERT: B 560 ASP cc_start: 0.8470 (m-30) cc_final: 0.8104 (m-30) REVERT: B 631 TYR cc_start: 0.7989 (m-80) cc_final: 0.7567 (m-80) REVERT: C 41 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 45 ASP cc_start: 0.7687 (m-30) cc_final: 0.7348 (m-30) REVERT: C 67 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 79 LYS cc_start: 0.7559 (mmtt) cc_final: 0.7232 (mttt) REVERT: C 238 GLU cc_start: 0.6784 (pp20) cc_final: 0.6501 (pp20) REVERT: C 344 GLU cc_start: 0.7501 (pm20) cc_final: 0.7020 (pm20) REVERT: C 454 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 592 ARG cc_start: 0.7959 (ttp-170) cc_final: 0.7635 (ttm170) REVERT: C 644 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7017 (mm-30) REVERT: D 35 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6138 (tp30) REVERT: D 160 ASP cc_start: 0.7142 (p0) cc_final: 0.6901 (p0) REVERT: D 185 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8318 (p) REVERT: D 188 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7932 (p-80) REVERT: D 274 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6567 (tm-30) REVERT: D 420 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8189 (p) REVERT: D 468 ASP cc_start: 0.6394 (OUTLIER) cc_final: 0.6073 (t70) REVERT: D 595 PHE cc_start: 0.8649 (m-80) cc_final: 0.8420 (m-10) outliers start: 97 outliers final: 39 residues processed: 560 average time/residue: 1.3784 time to fit residues: 873.2353 Evaluate side-chains 547 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 501 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 183 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 25 optimal weight: 0.0770 chunk 189 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS B 16 ASN B 385 ASN B 540 HIS ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS D 540 HIS D 639 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.124929 restraints weight = 31135.240| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.91 r_work: 0.3651 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21575 Z= 0.158 Angle : 0.592 13.941 29155 Z= 0.312 Chirality : 0.044 0.173 3128 Planarity : 0.005 0.055 3712 Dihedral : 11.149 89.166 3201 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.98 % Allowed : 17.49 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.85 (0.17), residues: 2552 helix: 0.76 (0.16), residues: 1194 sheet: 0.21 (0.36), residues: 254 loop : -2.33 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 425 HIS 0.007 0.001 HIS B 540 PHE 0.032 0.002 PHE B 526 TYR 0.015 0.002 TYR A 236 ARG 0.009 0.000 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.05548 ( 807) hydrogen bonds : angle 4.44320 ( 2325) SS BOND : bond 0.01521 ( 1) SS BOND : angle 2.77427 ( 2) covalent geometry : bond 0.00362 (21573) covalent geometry : angle 0.59160 (29153) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 513 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 24 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7506 (mp) REVERT: A 41 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7590 (mt-10) REVERT: A 45 ASP cc_start: 0.7964 (m-30) cc_final: 0.7514 (m-30) REVERT: A 60 ILE cc_start: 0.8363 (tp) cc_final: 0.8065 (tt) REVERT: A 154 ASN cc_start: 0.8322 (t0) cc_final: 0.8114 (t0) REVERT: A 423 ASP cc_start: 0.8021 (t70) cc_final: 0.7818 (t0) REVERT: A 507 LEU cc_start: 0.8721 (mt) cc_final: 0.8426 (mp) REVERT: A 606 TYR cc_start: 0.7490 (p90) cc_final: 0.7126 (p90) REVERT: B 41 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7237 (mm-30) REVERT: B 42 GLN cc_start: 0.7912 (mt0) cc_final: 0.7689 (mp10) REVERT: B 160 ASP cc_start: 0.7649 (t70) cc_final: 0.7363 (t70) REVERT: B 185 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8275 (p) REVERT: B 249 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6622 (tt0) REVERT: B 385 ASN cc_start: 0.8283 (m-40) cc_final: 0.8082 (m-40) REVERT: B 446 LEU cc_start: 0.8402 (mt) cc_final: 0.8189 (mt) REVERT: B 449 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 521 THR cc_start: 0.7987 (p) cc_final: 0.7730 (m) REVERT: B 560 ASP cc_start: 0.8505 (m-30) cc_final: 0.8113 (m-30) REVERT: B 631 TYR cc_start: 0.7992 (m-80) cc_final: 0.7615 (m-80) REVERT: C 2 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7629 (mp) REVERT: C 41 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7452 (mt-10) REVERT: C 45 ASP cc_start: 0.7679 (m-30) cc_final: 0.7356 (m-30) REVERT: C 52 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7553 (mmmm) REVERT: C 67 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7882 (tm-30) REVERT: C 79 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7199 (mttt) REVERT: C 238 GLU cc_start: 0.6753 (pp20) cc_final: 0.6447 (pp20) REVERT: C 344 GLU cc_start: 0.7533 (pm20) cc_final: 0.7068 (pm20) REVERT: C 454 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 592 ARG cc_start: 0.7904 (ttp-170) cc_final: 0.7593 (ttm170) REVERT: D 17 GLU cc_start: 0.7237 (tp30) cc_final: 0.6981 (mm-30) REVERT: D 35 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6100 (tm-30) REVERT: D 185 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8307 (p) REVERT: D 188 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7859 (p-80) REVERT: D 192 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7648 (mtt90) REVERT: D 252 SER cc_start: 0.8281 (t) cc_final: 0.8053 (m) REVERT: D 274 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6592 (tm-30) REVERT: D 468 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.6025 (t70) outliers start: 89 outliers final: 37 residues processed: 558 average time/residue: 1.4906 time to fit residues: 942.1691 Evaluate side-chains 561 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 515 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 84 optimal weight: 0.7980 chunk 236 optimal weight: 2.9990 chunk 205 optimal weight: 0.0770 chunk 201 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 199 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 388 ASN B 16 ASN B 540 HIS B 541 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 540 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125746 restraints weight = 30896.841| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.90 r_work: 0.3663 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21575 Z= 0.144 Angle : 0.574 14.644 29155 Z= 0.303 Chirality : 0.043 0.162 3128 Planarity : 0.004 0.054 3712 Dihedral : 10.592 87.364 3201 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.45 % Allowed : 19.42 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.69 (0.17), residues: 2552 helix: 0.91 (0.16), residues: 1192 sheet: 0.29 (0.35), residues: 254 loop : -2.26 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 425 HIS 0.006 0.001 HIS A 30 PHE 0.033 0.002 PHE B 526 TYR 0.014 0.001 TYR A 236 ARG 0.010 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.05152 ( 807) hydrogen bonds : angle 4.32275 ( 2325) SS BOND : bond 0.01290 ( 1) SS BOND : angle 2.39784 ( 2) covalent geometry : bond 0.00325 (21573) covalent geometry : angle 0.57397 (29153) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 517 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8343 (p) REVERT: A 41 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 45 ASP cc_start: 0.7933 (m-30) cc_final: 0.7657 (m-30) REVERT: A 60 ILE cc_start: 0.8358 (tp) cc_final: 0.8057 (tt) REVERT: A 154 ASN cc_start: 0.8288 (t0) cc_final: 0.8082 (t0) REVERT: A 423 ASP cc_start: 0.7989 (t70) cc_final: 0.7787 (t0) REVERT: A 592 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7387 (ttm170) REVERT: A 606 TYR cc_start: 0.7497 (p90) cc_final: 0.7123 (p90) REVERT: B 41 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 160 ASP cc_start: 0.7670 (t70) cc_final: 0.7387 (t70) REVERT: B 185 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 249 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6605 (tt0) REVERT: B 446 LEU cc_start: 0.8399 (mt) cc_final: 0.8191 (mp) REVERT: B 449 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7189 (tm-30) REVERT: B 560 ASP cc_start: 0.8509 (m-30) cc_final: 0.8113 (m-30) REVERT: B 631 TYR cc_start: 0.7997 (m-80) cc_final: 0.7580 (m-80) REVERT: C 28 MET cc_start: 0.8286 (tpp) cc_final: 0.8079 (mtt) REVERT: C 39 LEU cc_start: 0.8795 (tp) cc_final: 0.8533 (tt) REVERT: C 41 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 45 ASP cc_start: 0.7682 (m-30) cc_final: 0.7358 (m-30) REVERT: C 52 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7730 (mmmm) REVERT: C 65 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: C 67 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7890 (tm-30) REVERT: C 79 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7186 (mttt) REVERT: C 225 ASP cc_start: 0.6650 (p0) cc_final: 0.6103 (p0) REVERT: C 238 GLU cc_start: 0.6755 (pp20) cc_final: 0.6428 (pp20) REVERT: C 344 GLU cc_start: 0.7538 (pm20) cc_final: 0.7077 (pm20) REVERT: C 454 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 522 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7909 (mt) REVERT: C 592 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7593 (ttm170) REVERT: D 42 GLN cc_start: 0.7808 (mt0) cc_final: 0.7559 (mp10) REVERT: D 160 ASP cc_start: 0.7052 (p0) cc_final: 0.6682 (p0) REVERT: D 185 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8297 (p) REVERT: D 188 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7864 (p-80) REVERT: D 274 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6654 (tm-30) REVERT: D 468 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.6020 (t70) outliers start: 77 outliers final: 45 residues processed: 555 average time/residue: 1.3554 time to fit residues: 851.9568 Evaluate side-chains 563 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 511 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 233 optimal weight: 0.0010 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 213 ASN A 388 ASN A 455 ASN B 16 ASN B 88 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS B 541 HIS ** B 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124824 restraints weight = 30673.864| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.89 r_work: 0.3653 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21575 Z= 0.173 Angle : 0.600 16.293 29155 Z= 0.317 Chirality : 0.044 0.157 3128 Planarity : 0.005 0.054 3712 Dihedral : 10.519 87.254 3196 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.43 % Allowed : 19.73 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.76 (0.17), residues: 2552 helix: 0.82 (0.16), residues: 1190 sheet: 0.26 (0.35), residues: 254 loop : -2.25 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 425 HIS 0.006 0.001 HIS A 289 PHE 0.035 0.002 PHE A 383 TYR 0.017 0.002 TYR A 236 ARG 0.012 0.001 ARG A 419 Details of bonding type rmsd hydrogen bonds : bond 0.05561 ( 807) hydrogen bonds : angle 4.33463 ( 2325) SS BOND : bond 0.01456 ( 1) SS BOND : angle 2.59934 ( 2) covalent geometry : bond 0.00402 (21573) covalent geometry : angle 0.59981 (29153) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 511 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8351 (p) REVERT: A 21 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7737 (mpp) REVERT: A 32 ASP cc_start: 0.7938 (p0) cc_final: 0.7557 (p0) REVERT: A 41 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 45 ASP cc_start: 0.7980 (m-30) cc_final: 0.7671 (m-30) REVERT: A 60 ILE cc_start: 0.8341 (tp) cc_final: 0.8024 (tt) REVERT: A 79 LYS cc_start: 0.7962 (ptpt) cc_final: 0.7692 (ptmt) REVERT: A 154 ASN cc_start: 0.8324 (t0) cc_final: 0.8115 (t0) REVERT: A 423 ASP cc_start: 0.7989 (t70) cc_final: 0.7767 (t0) REVERT: A 606 TYR cc_start: 0.7533 (p90) cc_final: 0.7172 (p90) REVERT: B 41 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 160 ASP cc_start: 0.7630 (t70) cc_final: 0.7343 (t70) REVERT: B 185 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 420 VAL cc_start: 0.8222 (p) cc_final: 0.7992 (m) REVERT: B 446 LEU cc_start: 0.8398 (mt) cc_final: 0.8188 (mp) REVERT: B 449 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 560 ASP cc_start: 0.8491 (m-30) cc_final: 0.8087 (m-30) REVERT: B 631 TYR cc_start: 0.7994 (m-80) cc_final: 0.7604 (m-80) REVERT: C 39 LEU cc_start: 0.8780 (tp) cc_final: 0.8421 (tt) REVERT: C 41 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7496 (mt-10) REVERT: C 45 ASP cc_start: 0.7706 (m-30) cc_final: 0.7380 (m-30) REVERT: C 52 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7736 (mmmm) REVERT: C 67 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7900 (tm-30) REVERT: C 79 LYS cc_start: 0.7519 (mmtt) cc_final: 0.7190 (mttt) REVERT: C 208 LEU cc_start: 0.7634 (mp) cc_final: 0.7363 (mp) REVERT: C 209 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: C 238 GLU cc_start: 0.6772 (pp20) cc_final: 0.6464 (pp20) REVERT: C 344 GLU cc_start: 0.7509 (pm20) cc_final: 0.7030 (pm20) REVERT: C 454 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 527 ILE cc_start: 0.8665 (tt) cc_final: 0.8438 (pt) REVERT: D 17 GLU cc_start: 0.7209 (tp30) cc_final: 0.6986 (mm-30) REVERT: D 160 ASP cc_start: 0.7073 (p0) cc_final: 0.6721 (p0) REVERT: D 188 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7827 (p-80) REVERT: D 274 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6649 (tm-30) REVERT: D 468 ASP cc_start: 0.6337 (OUTLIER) cc_final: 0.6029 (t70) outliers start: 99 outliers final: 55 residues processed: 561 average time/residue: 1.3925 time to fit residues: 886.1844 Evaluate side-chains 569 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 508 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 chunk 88 optimal weight: 0.0270 chunk 244 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 213 ASN A 351 GLN A 388 ASN A 455 ASN B 16 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124611 restraints weight = 30741.294| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.89 r_work: 0.3649 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21575 Z= 0.183 Angle : 0.618 17.005 29155 Z= 0.325 Chirality : 0.045 0.169 3128 Planarity : 0.005 0.055 3712 Dihedral : 10.504 85.823 3196 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.25 % Allowed : 19.82 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.83 (0.17), residues: 2552 helix: 0.73 (0.16), residues: 1202 sheet: 0.22 (0.35), residues: 254 loop : -2.28 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 425 HIS 0.006 0.001 HIS A 289 PHE 0.036 0.002 PHE A 383 TYR 0.017 0.002 TYR A 236 ARG 0.010 0.001 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 807) hydrogen bonds : angle 4.32919 ( 2325) SS BOND : bond 0.01246 ( 1) SS BOND : angle 2.57700 ( 2) covalent geometry : bond 0.00426 (21573) covalent geometry : angle 0.61790 (29153) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 514 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8357 (p) REVERT: A 32 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7621 (p0) REVERT: A 41 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7689 (mt-10) REVERT: A 45 ASP cc_start: 0.7996 (m-30) cc_final: 0.7665 (m-30) REVERT: A 60 ILE cc_start: 0.8332 (tp) cc_final: 0.8000 (tt) REVERT: A 79 LYS cc_start: 0.7901 (ptpt) cc_final: 0.7610 (ptmt) REVERT: A 423 ASP cc_start: 0.7994 (t70) cc_final: 0.7752 (t0) REVERT: A 592 ARG cc_start: 0.7684 (ttp-170) cc_final: 0.7374 (ttm170) REVERT: A 606 TYR cc_start: 0.7559 (p90) cc_final: 0.7194 (p90) REVERT: B 41 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 160 ASP cc_start: 0.7635 (t70) cc_final: 0.7341 (t70) REVERT: B 185 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8285 (p) REVERT: B 420 VAL cc_start: 0.8245 (p) cc_final: 0.8001 (m) REVERT: B 446 LEU cc_start: 0.8397 (mt) cc_final: 0.8184 (mp) REVERT: B 449 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7150 (tm-30) REVERT: B 549 GLU cc_start: 0.7821 (mp0) cc_final: 0.7586 (pm20) REVERT: B 560 ASP cc_start: 0.8477 (m-30) cc_final: 0.8075 (m-30) REVERT: C 39 LEU cc_start: 0.8743 (tp) cc_final: 0.8505 (tt) REVERT: C 41 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7499 (mt-10) REVERT: C 45 ASP cc_start: 0.7732 (m-30) cc_final: 0.7403 (m-30) REVERT: C 52 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7726 (mmmm) REVERT: C 67 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 79 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7187 (mttt) REVERT: C 208 LEU cc_start: 0.7723 (mp) cc_final: 0.7420 (mp) REVERT: C 238 GLU cc_start: 0.6767 (pp20) cc_final: 0.6464 (pp20) REVERT: C 344 GLU cc_start: 0.7530 (pm20) cc_final: 0.7052 (pm20) REVERT: C 454 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7760 (tm-30) REVERT: C 527 ILE cc_start: 0.8663 (tt) cc_final: 0.8441 (pt) REVERT: C 644 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7153 (mm-30) REVERT: D 160 ASP cc_start: 0.7111 (p0) cc_final: 0.6748 (p0) REVERT: D 188 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7829 (p-80) REVERT: D 274 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6631 (tm-30) REVERT: D 468 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6164 (t70) outliers start: 95 outliers final: 61 residues processed: 561 average time/residue: 1.2690 time to fit residues: 809.3767 Evaluate side-chains 568 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 502 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 567 GLU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 239 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 254 optimal weight: 0.0170 chunk 223 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 213 ASN A 388 ASN A 455 ASN B 16 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS C 213 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125498 restraints weight = 30805.883| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.90 r_work: 0.3661 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21575 Z= 0.153 Angle : 0.618 17.309 29155 Z= 0.325 Chirality : 0.045 0.447 3128 Planarity : 0.004 0.055 3712 Dihedral : 10.314 84.724 3196 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.71 % Allowed : 20.72 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.78 (0.17), residues: 2552 helix: 0.81 (0.16), residues: 1192 sheet: 0.24 (0.35), residues: 254 loop : -2.28 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 425 HIS 0.005 0.001 HIS A 30 PHE 0.036 0.002 PHE B 526 TYR 0.015 0.001 TYR A 236 ARG 0.010 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.05293 ( 807) hydrogen bonds : angle 4.28595 ( 2325) SS BOND : bond 0.01250 ( 1) SS BOND : angle 2.22407 ( 2) covalent geometry : bond 0.00348 (21573) covalent geometry : angle 0.61789 (29153) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 513 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8347 (p) REVERT: A 32 ASP cc_start: 0.8034 (p0) cc_final: 0.7729 (p0) REVERT: A 41 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 45 ASP cc_start: 0.7997 (m-30) cc_final: 0.7645 (m-30) REVERT: A 60 ILE cc_start: 0.8318 (tp) cc_final: 0.7985 (tt) REVERT: A 79 LYS cc_start: 0.7872 (ptpt) cc_final: 0.7609 (ptmt) REVERT: A 423 ASP cc_start: 0.7988 (t70) cc_final: 0.7752 (t0) REVERT: A 592 ARG cc_start: 0.7661 (ttp-170) cc_final: 0.7347 (ttm170) REVERT: A 606 TYR cc_start: 0.7521 (p90) cc_final: 0.7177 (p90) REVERT: B 41 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 160 ASP cc_start: 0.7656 (t70) cc_final: 0.7358 (t70) REVERT: B 185 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 249 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6584 (tt0) REVERT: B 283 LYS cc_start: 0.7650 (mtmm) cc_final: 0.7216 (ptmt) REVERT: B 420 VAL cc_start: 0.8252 (p) cc_final: 0.7998 (m) REVERT: B 446 LEU cc_start: 0.8384 (mt) cc_final: 0.8168 (mp) REVERT: B 449 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 496 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (tp) REVERT: B 560 ASP cc_start: 0.8491 (m-30) cc_final: 0.8079 (m-30) REVERT: B 631 TYR cc_start: 0.7863 (m-80) cc_final: 0.7544 (m-80) REVERT: C 41 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 45 ASP cc_start: 0.7691 (m-30) cc_final: 0.7363 (m-30) REVERT: C 52 LYS cc_start: 0.8145 (mmmm) cc_final: 0.7730 (mmmm) REVERT: C 67 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7876 (tm-30) REVERT: C 79 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7151 (mttt) REVERT: C 208 LEU cc_start: 0.7660 (mp) cc_final: 0.7346 (mp) REVERT: C 238 GLU cc_start: 0.6764 (pp20) cc_final: 0.6444 (pp20) REVERT: C 344 GLU cc_start: 0.7543 (pm20) cc_final: 0.7078 (pm20) REVERT: C 411 ILE cc_start: 0.7947 (pt) cc_final: 0.7571 (tt) REVERT: C 454 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7758 (tm-30) REVERT: C 456 GLU cc_start: 0.7243 (tp30) cc_final: 0.6979 (tp30) REVERT: C 644 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7166 (mm-30) REVERT: D 42 GLN cc_start: 0.7807 (mt0) cc_final: 0.7574 (mp10) REVERT: D 160 ASP cc_start: 0.7090 (p0) cc_final: 0.6713 (p0) REVERT: D 188 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7819 (p-80) REVERT: D 274 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6665 (tm-30) REVERT: D 468 ASP cc_start: 0.6286 (OUTLIER) cc_final: 0.6013 (t70) outliers start: 83 outliers final: 59 residues processed: 554 average time/residue: 1.3556 time to fit residues: 851.6549 Evaluate side-chains 563 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 499 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 165 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 chunk 152 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 229 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 226 optimal weight: 0.0980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 61 GLN A 388 ASN B 16 ASN B 540 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.139250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.127928 restraints weight = 30691.822| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.91 r_work: 0.3690 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21575 Z= 0.120 Angle : 0.586 17.497 29155 Z= 0.307 Chirality : 0.044 0.366 3128 Planarity : 0.004 0.054 3712 Dihedral : 9.791 88.478 3196 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.55 % Allowed : 22.19 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.52 (0.17), residues: 2552 helix: 1.02 (0.16), residues: 1200 sheet: 0.38 (0.34), residues: 254 loop : -2.16 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 425 HIS 0.008 0.001 HIS C 30 PHE 0.037 0.001 PHE B 526 TYR 0.012 0.001 TYR A 236 ARG 0.010 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 807) hydrogen bonds : angle 4.13649 ( 2325) SS BOND : bond 0.00974 ( 1) SS BOND : angle 1.49031 ( 2) covalent geometry : bond 0.00261 (21573) covalent geometry : angle 0.58571 (29153) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 512 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 32 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7594 (p0) REVERT: A 41 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 45 ASP cc_start: 0.7960 (m-30) cc_final: 0.7498 (m-30) REVERT: A 60 ILE cc_start: 0.8324 (tp) cc_final: 0.7993 (tt) REVERT: A 423 ASP cc_start: 0.7963 (t70) cc_final: 0.7736 (t0) REVERT: A 592 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7455 (ttm170) REVERT: A 606 TYR cc_start: 0.7444 (p90) cc_final: 0.7125 (p90) REVERT: B 154 ASN cc_start: 0.8278 (t0) cc_final: 0.7782 (t0) REVERT: B 160 ASP cc_start: 0.7698 (t70) cc_final: 0.7414 (t70) REVERT: B 185 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 249 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6509 (tt0) REVERT: B 274 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6742 (tm-30) REVERT: B 420 VAL cc_start: 0.8234 (p) cc_final: 0.7977 (m) REVERT: B 446 LEU cc_start: 0.8346 (mt) cc_final: 0.8133 (mp) REVERT: B 449 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7147 (tm-30) REVERT: B 496 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8205 (tp) REVERT: B 560 ASP cc_start: 0.8457 (m-30) cc_final: 0.8094 (m-30) REVERT: B 631 TYR cc_start: 0.7776 (m-80) cc_final: 0.7433 (m-80) REVERT: C 41 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7529 (mt-10) REVERT: C 45 ASP cc_start: 0.7659 (m-30) cc_final: 0.7394 (m-30) REVERT: C 52 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7900 (mmmm) REVERT: C 67 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 79 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7127 (mttt) REVERT: C 208 LEU cc_start: 0.7418 (mp) cc_final: 0.7189 (mp) REVERT: C 238 GLU cc_start: 0.6759 (pp20) cc_final: 0.6382 (pp20) REVERT: C 324 GLU cc_start: 0.7007 (mp0) cc_final: 0.6781 (mp0) REVERT: C 344 GLU cc_start: 0.7563 (pm20) cc_final: 0.7096 (pm20) REVERT: C 411 ILE cc_start: 0.7932 (pt) cc_final: 0.7652 (tt) REVERT: C 413 THR cc_start: 0.8333 (m) cc_final: 0.7982 (t) REVERT: C 454 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 456 GLU cc_start: 0.7329 (tp30) cc_final: 0.7014 (tp30) REVERT: D 3 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: D 160 ASP cc_start: 0.7025 (p0) cc_final: 0.6595 (p0) REVERT: D 274 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6613 (tm-30) REVERT: D 292 MET cc_start: 0.8050 (mpp) cc_final: 0.7765 (mmp) REVERT: D 344 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7188 (mp0) REVERT: D 453 ILE cc_start: 0.8158 (mt) cc_final: 0.7953 (mp) REVERT: D 468 ASP cc_start: 0.6223 (OUTLIER) cc_final: 0.5995 (t70) REVERT: D 623 LYS cc_start: 0.8051 (mptt) cc_final: 0.7764 (pmmt) outliers start: 57 outliers final: 37 residues processed: 543 average time/residue: 1.6547 time to fit residues: 1023.1545 Evaluate side-chains 544 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 501 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 122 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 149 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 219 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 46 optimal weight: 0.0670 chunk 222 optimal weight: 0.7980 chunk 228 optimal weight: 0.3980 chunk 9 optimal weight: 0.3980 chunk 119 optimal weight: 0.4980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 213 ASN A 388 ASN A 455 ASN B 16 ASN B 88 ASN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.128904 restraints weight = 30932.654| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.92 r_work: 0.3701 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21575 Z= 0.120 Angle : 0.592 17.400 29155 Z= 0.308 Chirality : 0.044 0.306 3128 Planarity : 0.004 0.056 3712 Dihedral : 9.524 88.935 3196 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.15 % Allowed : 23.04 % Favored : 74.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.75 % 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: -0.36 (0.17), residues: 2552 helix: 1.15 (0.16), residues: 1200 sheet: 0.49 (0.34), residues: 256 loop : -2.09 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 425 HIS 0.006 0.001 HIS C 30 PHE 0.021 0.001 PHE A 383 TYR 0.015 0.001 TYR D 670 ARG 0.013 0.000 ARG C 419 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 807) hydrogen bonds : angle 4.09118 ( 2325) SS BOND : bond 0.00590 ( 1) SS BOND : angle 1.34229 ( 2) covalent geometry : bond 0.00260 (21573) covalent geometry : angle 0.59228 (29153) Misc. bond : bond 0.00017 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 513 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 32 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7565 (p0) REVERT: A 33 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7312 (mtmm) REVERT: A 41 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 45 ASP cc_start: 0.7943 (m-30) cc_final: 0.7476 (m-30) REVERT: A 60 ILE cc_start: 0.8299 (tp) cc_final: 0.7974 (tt) REVERT: A 376 LYS cc_start: 0.7481 (tppt) cc_final: 0.7271 (tppt) REVERT: A 423 ASP cc_start: 0.7933 (t70) cc_final: 0.7709 (t0) REVERT: A 606 TYR cc_start: 0.7453 (p90) cc_final: 0.7132 (p90) REVERT: B 154 ASN cc_start: 0.8227 (t0) cc_final: 0.7775 (t0) REVERT: B 160 ASP cc_start: 0.7685 (t70) cc_final: 0.7401 (t70) REVERT: B 185 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 208 LEU cc_start: 0.7822 (tp) cc_final: 0.7617 (tp) REVERT: B 249 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6513 (tt0) REVERT: B 274 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6728 (tm-30) REVERT: B 420 VAL cc_start: 0.8218 (p) cc_final: 0.7967 (m) REVERT: B 446 LEU cc_start: 0.8300 (mt) cc_final: 0.8038 (mp) REVERT: B 449 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 560 ASP cc_start: 0.8447 (m-30) cc_final: 0.8092 (m-30) REVERT: B 631 TYR cc_start: 0.7712 (m-80) cc_final: 0.7393 (m-80) REVERT: C 41 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7480 (mt-10) REVERT: C 45 ASP cc_start: 0.7619 (m-30) cc_final: 0.7319 (m-30) REVERT: C 52 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7709 (mmmm) REVERT: C 67 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 79 LYS cc_start: 0.7386 (mmtt) cc_final: 0.7092 (mttt) REVERT: C 88 ASN cc_start: 0.8270 (m-40) cc_final: 0.8056 (m-40) REVERT: C 208 LEU cc_start: 0.7462 (mp) cc_final: 0.7170 (mp) REVERT: C 324 GLU cc_start: 0.7037 (mp0) cc_final: 0.6799 (mp0) REVERT: C 344 GLU cc_start: 0.7562 (pm20) cc_final: 0.7094 (pm20) REVERT: C 411 ILE cc_start: 0.7931 (pt) cc_final: 0.7700 (tt) REVERT: C 454 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7713 (tm-30) REVERT: C 456 GLU cc_start: 0.7241 (tp30) cc_final: 0.6990 (tp30) REVERT: D 3 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: D 17 GLU cc_start: 0.7222 (mm-30) cc_final: 0.7017 (mm-30) REVERT: D 160 ASP cc_start: 0.6992 (p0) cc_final: 0.6603 (p0) REVERT: D 209 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: D 274 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6557 (tm-30) REVERT: D 453 ILE cc_start: 0.8117 (mt) cc_final: 0.7898 (mp) REVERT: D 468 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5917 (t70) REVERT: D 623 LYS cc_start: 0.8057 (mptt) cc_final: 0.7791 (pmmt) outliers start: 48 outliers final: 33 residues processed: 537 average time/residue: 1.4135 time to fit residues: 860.7403 Evaluate side-chains 540 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 501 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 146 optimal weight: 0.5980 chunk 178 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 chunk 209 optimal weight: 0.0470 chunk 208 optimal weight: 0.6980 chunk 148 optimal weight: 0.0270 chunk 197 optimal weight: 3.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 213 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN B 16 ASN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 540 HIS C 213 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 394 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.139851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128550 restraints weight = 30999.741| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.92 r_work: 0.3695 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21575 Z= 0.126 Angle : 0.598 17.227 29155 Z= 0.312 Chirality : 0.044 0.421 3128 Planarity : 0.004 0.054 3712 Dihedral : 9.457 89.527 3196 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.10 % Allowed : 23.62 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.31 (0.17), residues: 2552 helix: 1.22 (0.16), residues: 1194 sheet: 0.60 (0.34), residues: 254 loop : -2.10 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 425 HIS 0.005 0.001 HIS C 30 PHE 0.036 0.001 PHE B 526 TYR 0.016 0.001 TYR D 670 ARG 0.011 0.000 ARG C 419 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 807) hydrogen bonds : angle 4.11582 ( 2325) SS BOND : bond 0.01003 ( 1) SS BOND : angle 2.84026 ( 2) covalent geometry : bond 0.00283 (21573) covalent geometry : angle 0.59736 (29153) Misc. bond : bond 0.00028 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20054.99 seconds wall clock time: 345 minutes 35.17 seconds (20735.17 seconds total)