Starting phenix.real_space_refine on Wed May 21 08:55:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p28_17359/05_2025/8p28_17359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p28_17359/05_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_17359/05_2025/8p28_17359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p28_17359/05_2025/8p28_17359.map" model { file = "/net/cci-nas-00/data/ceres_data/8p28_17359/05_2025/8p28_17359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p28_17359/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.87, per 1000 atoms: 0.70 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: 6.20 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: 2.59 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: 7.18 Time building geometry restraints manager: 7.07 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: 6.190 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: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 52.690 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.790 ------------------------------------------------------------------------------- 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 : 2.497 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: 0.7900 (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: 0.6661 (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: 0.7368 (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: 1.2854 time to fit residues: 876.4235 Evaluate side-chains 528 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 511 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.136431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125271 restraints weight = 30808.112| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.89 r_work: 0.3657 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21575 Z= 0.152 Angle : 0.621 12.038 29155 Z= 0.327 Chirality : 0.044 0.188 3128 Planarity : 0.005 0.053 3712 Dihedral : 12.231 91.863 3227 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.09 % Allowed : 14.81 % Favored : 82.10 % 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 0.007 0.001 HIS D 297 PHE 0.028 0.002 PHE B 526 TYR 0.016 0.001 TYR B 607 ARG 0.010 0.001 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.05971 ( 807) hydrogen bonds : angle 4.69657 ( 2325) SS BOND : bond 0.01566 ( 1) SS BOND : angle 2.96382 ( 2) covalent geometry : bond 0.00342 (21573) covalent geometry : angle 0.62070 (29153) Misc. bond : bond 0.00031 ( 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 602 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 533 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 18 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7788 (tp40) REVERT: A 60 ILE cc_start: 0.8431 (tp) cc_final: 0.8117 (tt) REVERT: A 154 ASN cc_start: 0.8308 (t0) cc_final: 0.8078 (t0) REVERT: A 423 ASP cc_start: 0.7988 (t70) cc_final: 0.7785 (t0) REVERT: B 41 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 148 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7493 (ttt90) REVERT: B 152 MET cc_start: 0.7625 (mtm) cc_final: 0.7282 (mtm) REVERT: B 160 ASP cc_start: 0.7534 (t70) cc_final: 0.7270 (t70) REVERT: B 420 VAL cc_start: 0.8216 (p) cc_final: 0.7982 (m) REVERT: B 446 LEU cc_start: 0.8413 (mt) cc_final: 0.8199 (mt) REVERT: B 449 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 560 ASP cc_start: 0.8469 (m-30) cc_final: 0.8092 (m-30) REVERT: B 631 TYR cc_start: 0.7920 (m-80) cc_final: 0.7597 (m-80) REVERT: C 2 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7658 (mp) REVERT: C 41 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 45 ASP cc_start: 0.7616 (m-30) cc_final: 0.7301 (m-30) REVERT: C 52 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7520 (mmmm) REVERT: C 67 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 79 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7214 (mttt) REVERT: C 140 ASP cc_start: 0.7792 (m-30) cc_final: 0.7537 (m-30) REVERT: C 178 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8172 (m) REVERT: C 208 LEU cc_start: 0.7685 (mp) cc_final: 0.7368 (mp) REVERT: C 238 GLU cc_start: 0.6722 (pp20) cc_final: 0.6476 (pp20) REVERT: C 344 GLU cc_start: 0.7547 (pm20) cc_final: 0.7078 (pm20) REVERT: C 454 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 592 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7638 (ttm170) REVERT: C 604 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7799 (mtt180) REVERT: D 185 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8353 (p) REVERT: D 274 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6476 (tm-30) REVERT: D 311 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7769 (t) REVERT: D 420 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8242 (p) REVERT: D 468 ASP cc_start: 0.6343 (OUTLIER) cc_final: 0.5996 (t70) outliers start: 69 outliers final: 23 residues processed: 566 average time/residue: 1.3107 time to fit residues: 838.4701 Evaluate side-chains 534 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 504 time to evaluate : 2.088 ------------------------------------------------------------------------------- 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 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 38 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 178 VAL 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: 0.9980 chunk 18 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 206 optimal weight: 0.6980 chunk 101 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.135673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124413 restraints weight = 30625.585| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.89 r_work: 0.3647 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21575 Z= 0.175 Angle : 0.615 12.527 29155 Z= 0.323 Chirality : 0.045 0.182 3128 Planarity : 0.005 0.055 3712 Dihedral : 11.587 88.324 3203 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.07 % Allowed : 15.88 % Favored : 80.04 % 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: -0.94 (0.17), residues: 2552 helix: 0.70 (0.16), residues: 1192 sheet: 0.19 (0.36), residues: 254 loop : -2.39 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 425 HIS 0.008 0.001 HIS D 297 PHE 0.029 0.002 PHE B 526 TYR 0.017 0.002 TYR A 236 ARG 0.009 0.001 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.05924 ( 807) hydrogen bonds : angle 4.54024 ( 2325) SS BOND : bond 0.00515 ( 1) SS BOND : angle 2.97699 ( 2) covalent geometry : bond 0.00406 (21573) covalent geometry : angle 0.61436 (29153) Misc. bond : bond 0.00092 ( 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 602 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 511 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8356 (p) REVERT: A 41 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 45 ASP cc_start: 0.7949 (m-30) cc_final: 0.7512 (m-30) REVERT: A 60 ILE cc_start: 0.8375 (tp) cc_final: 0.8059 (tt) REVERT: A 154 ASN cc_start: 0.8347 (t0) cc_final: 0.8131 (t0) REVERT: A 423 ASP cc_start: 0.8032 (t70) cc_final: 0.7799 (t0) REVERT: A 592 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7585 (ttm170) REVERT: B 41 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7263 (mm-30) REVERT: B 42 GLN cc_start: 0.7932 (mt0) cc_final: 0.7637 (mp10) REVERT: B 160 ASP cc_start: 0.7608 (t70) cc_final: 0.7328 (t70) REVERT: B 185 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 249 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6610 (tt0) REVERT: B 420 VAL cc_start: 0.8263 (p) cc_final: 0.7988 (m) REVERT: B 446 LEU cc_start: 0.8415 (mt) cc_final: 0.8205 (mt) REVERT: B 449 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7190 (tm-30) REVERT: B 560 ASP cc_start: 0.8501 (m-30) cc_final: 0.8118 (m-30) REVERT: B 631 TYR cc_start: 0.7974 (m-80) cc_final: 0.7568 (m-80) REVERT: C 41 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7433 (mt-10) REVERT: C 45 ASP cc_start: 0.7674 (m-30) cc_final: 0.7331 (m-30) REVERT: C 67 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7876 (tm-30) REVERT: C 79 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7219 (mttt) REVERT: C 88 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8097 (m-40) REVERT: C 178 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8160 (m) REVERT: C 208 LEU cc_start: 0.7695 (mp) cc_final: 0.7362 (mp) REVERT: C 238 GLU cc_start: 0.6780 (pp20) cc_final: 0.6477 (pp20) REVERT: C 344 GLU cc_start: 0.7509 (pm20) cc_final: 0.7019 (pm20) REVERT: C 454 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7793 (tm-30) REVERT: C 592 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7631 (ttm170) REVERT: D 35 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6155 (tp30) REVERT: D 160 ASP cc_start: 0.7123 (p0) cc_final: 0.6902 (p0) REVERT: D 185 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8321 (p) REVERT: D 188 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7853 (p-80) REVERT: D 274 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6545 (tm-30) REVERT: D 311 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7691 (t) REVERT: D 468 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.6008 (t70) REVERT: D 487 THR cc_start: 0.8313 (p) cc_final: 0.8091 (p) REVERT: D 595 PHE cc_start: 0.8647 (m-80) cc_final: 0.8426 (m-10) outliers start: 91 outliers final: 36 residues processed: 557 average time/residue: 1.3547 time to fit residues: 853.4840 Evaluate side-chains 548 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 503 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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 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 29 LEU 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 607 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 88 ASN Chi-restraints excluded: chain C residue 178 VAL 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 311 VAL Chi-restraints excluded: chain D residue 373 LEU 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: 0.7980 chunk 215 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 214 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 226 optimal weight: 0.0270 chunk 76 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 455 ASN B 16 ASN B 385 ASN B 540 HIS B 541 HIS C 30 HIS D 639 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.136466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125202 restraints weight = 31155.988| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.91 r_work: 0.3655 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21575 Z= 0.150 Angle : 0.583 14.140 29155 Z= 0.308 Chirality : 0.043 0.169 3128 Planarity : 0.004 0.055 3712 Dihedral : 11.009 87.548 3201 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.76 % Allowed : 17.49 % Favored : 78.75 % 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: -0.80 (0.17), residues: 2552 helix: 0.81 (0.16), residues: 1194 sheet: 0.24 (0.36), residues: 254 loop : -2.32 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 425 HIS 0.007 0.001 HIS B 540 PHE 0.031 0.002 PHE B 526 TYR 0.015 0.001 TYR A 236 ARG 0.010 0.000 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 807) hydrogen bonds : angle 4.40101 ( 2325) SS BOND : bond 0.01358 ( 1) SS BOND : angle 2.55220 ( 2) covalent geometry : bond 0.00341 (21573) covalent geometry : angle 0.58296 (29153) Misc. bond : bond 0.00054 ( 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 606 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 522 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8359 (p) REVERT: A 24 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7507 (mp) REVERT: A 41 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 45 ASP cc_start: 0.7936 (m-30) cc_final: 0.7717 (m-30) REVERT: A 60 ILE cc_start: 0.8365 (tp) cc_final: 0.8069 (tt) REVERT: A 423 ASP cc_start: 0.8006 (t70) cc_final: 0.7797 (t0) REVERT: A 507 LEU cc_start: 0.8708 (mt) cc_final: 0.8425 (mp) REVERT: A 606 TYR cc_start: 0.7469 (p90) cc_final: 0.7102 (p90) REVERT: B 41 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7216 (mm-30) REVERT: B 42 GLN cc_start: 0.7904 (mt0) cc_final: 0.7684 (mp10) REVERT: B 160 ASP cc_start: 0.7635 (t70) cc_final: 0.7355 (t70) REVERT: B 185 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8281 (p) REVERT: B 249 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6592 (tt0) REVERT: B 420 VAL cc_start: 0.8270 (p) cc_final: 0.7998 (m) REVERT: B 446 LEU cc_start: 0.8404 (mt) cc_final: 0.8192 (mt) REVERT: B 449 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7227 (tm-30) REVERT: B 521 THR cc_start: 0.7986 (p) cc_final: 0.7740 (m) REVERT: B 548 GLN cc_start: 0.8159 (tp40) cc_final: 0.7954 (mm-40) REVERT: B 560 ASP cc_start: 0.8508 (m-30) cc_final: 0.8117 (m-30) REVERT: B 631 TYR cc_start: 0.7954 (m-80) cc_final: 0.7544 (m-80) REVERT: C 2 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7654 (mp) REVERT: C 41 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7446 (mt-10) REVERT: C 45 ASP cc_start: 0.7683 (m-30) cc_final: 0.7362 (m-30) REVERT: C 52 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7549 (mmmm) REVERT: C 67 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7879 (tm-30) REVERT: C 79 LYS cc_start: 0.7510 (mmtt) cc_final: 0.7190 (mttt) REVERT: C 208 LEU cc_start: 0.7652 (mp) cc_final: 0.7322 (mp) REVERT: C 238 GLU cc_start: 0.6748 (pp20) cc_final: 0.6443 (pp20) REVERT: C 344 GLU cc_start: 0.7541 (pm20) cc_final: 0.7075 (pm20) REVERT: C 454 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 592 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7603 (ttm170) REVERT: D 35 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6057 (tm-30) REVERT: D 185 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8313 (p) REVERT: D 188 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7876 (p-80) REVERT: D 252 SER cc_start: 0.8281 (t) cc_final: 0.8056 (m) REVERT: D 274 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6562 (tm-30) REVERT: D 311 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7621 (t) REVERT: D 420 VAL cc_start: 0.8287 (p) cc_final: 0.8062 (m) REVERT: D 468 ASP cc_start: 0.6355 (OUTLIER) cc_final: 0.6002 (t70) outliers start: 84 outliers final: 42 residues processed: 561 average time/residue: 1.2650 time to fit residues: 803.5226 Evaluate side-chains 559 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 508 time to evaluate : 2.096 ------------------------------------------------------------------------------- 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 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 56 SER 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 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 663 MET 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 55 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 127 MET 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 429 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER 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 240 VAL Chi-restraints excluded: chain D residue 311 VAL 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: 0.9990 chunk 236 optimal weight: 3.9990 chunk 205 optimal weight: 0.1980 chunk 201 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 199 optimal weight: 0.5980 chunk 206 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.136441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125250 restraints weight = 30951.293| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.90 r_work: 0.3656 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1998 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= 0.160 Angle : 0.587 14.886 29155 Z= 0.309 Chirality : 0.044 0.164 3128 Planarity : 0.004 0.054 3712 Dihedral : 10.664 87.455 3197 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.12 % Allowed : 18.61 % Favored : 77.27 % 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: -0.73 (0.17), residues: 2552 helix: 0.86 (0.16), residues: 1192 sheet: 0.30 (0.35), residues: 254 loop : -2.29 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 425 HIS 0.005 0.001 HIS A 30 PHE 0.032 0.002 PHE B 526 TYR 0.016 0.002 TYR A 236 ARG 0.011 0.001 ARG D 25 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 807) hydrogen bonds : angle 4.35996 ( 2325) SS BOND : bond 0.01369 ( 1) SS BOND : angle 2.58284 ( 2) covalent geometry : bond 0.00368 (21573) covalent geometry : angle 0.58615 (29153) Misc. bond : bond 0.00051 ( 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 606 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 514 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 41 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 45 ASP cc_start: 0.7947 (m-30) cc_final: 0.7672 (m-30) REVERT: A 60 ILE cc_start: 0.8346 (tp) cc_final: 0.8038 (tt) REVERT: A 79 LYS cc_start: 0.8156 (ptpt) cc_final: 0.7842 (ptmt) REVERT: A 423 ASP cc_start: 0.8003 (t70) cc_final: 0.7785 (t0) REVERT: A 592 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7418 (ttm170) REVERT: A 606 TYR cc_start: 0.7520 (p90) cc_final: 0.7152 (p90) REVERT: B 41 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7198 (mm-30) REVERT: B 185 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 249 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6617 (tt0) REVERT: B 446 LEU cc_start: 0.8412 (mt) cc_final: 0.8201 (mp) REVERT: B 449 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7227 (tm-30) REVERT: B 521 THR cc_start: 0.7985 (p) cc_final: 0.7735 (m) REVERT: B 560 ASP cc_start: 0.8524 (m-30) cc_final: 0.8115 (m-30) REVERT: B 631 TYR cc_start: 0.8004 (m-80) cc_final: 0.7594 (m-80) REVERT: C 41 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7489 (mt-10) REVERT: C 45 ASP cc_start: 0.7713 (m-30) cc_final: 0.7381 (m-30) REVERT: C 52 LYS cc_start: 0.8117 (mmmm) cc_final: 0.7728 (mmmm) REVERT: C 67 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7905 (tm-30) REVERT: C 79 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7227 (mttt) REVERT: C 208 LEU cc_start: 0.7676 (mp) cc_final: 0.7378 (mp) REVERT: C 238 GLU cc_start: 0.6783 (pp20) cc_final: 0.6451 (pp20) REVERT: C 344 GLU cc_start: 0.7515 (pm20) cc_final: 0.7057 (pm20) REVERT: C 454 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7785 (tm-30) REVERT: C 522 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 527 ILE cc_start: 0.8680 (tt) cc_final: 0.8445 (pt) REVERT: C 592 ARG cc_start: 0.7886 (ttp-170) cc_final: 0.7587 (ttm170) REVERT: D 160 ASP cc_start: 0.7077 (p0) cc_final: 0.6777 (p0) REVERT: D 185 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8296 (p) REVERT: D 188 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7856 (p-80) REVERT: D 252 SER cc_start: 0.8256 (t) cc_final: 0.8048 (m) REVERT: D 274 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6643 (tm-30) REVERT: D 311 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7623 (t) REVERT: D 468 ASP cc_start: 0.6372 (OUTLIER) cc_final: 0.6054 (t70) outliers start: 92 outliers final: 50 residues processed: 560 average time/residue: 1.3049 time to fit residues: 826.8826 Evaluate side-chains 566 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 509 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 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 502 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 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 540 HIS 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 522 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 662 MET 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 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 311 VAL 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: 0.0470 chunk 59 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 233 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 215 optimal weight: 0.0980 chunk 102 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 B 16 ASN B 540 HIS ** B 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.137083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.125844 restraints weight = 30667.954| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.89 r_work: 0.3665 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21575 Z= 0.147 Angle : 0.579 16.220 29155 Z= 0.306 Chirality : 0.043 0.158 3128 Planarity : 0.005 0.054 3712 Dihedral : 10.415 85.992 3197 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.12 % Allowed : 19.55 % Favored : 76.33 % 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: 0.90 (0.16), residues: 1190 sheet: 0.28 (0.35), residues: 254 loop : -2.24 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 425 HIS 0.014 0.001 HIS B 540 PHE 0.033 0.002 PHE B 526 TYR 0.015 0.001 TYR A 236 ARG 0.012 0.001 ARG A 419 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 807) hydrogen bonds : angle 4.27569 ( 2325) SS BOND : bond 0.01287 ( 1) SS BOND : angle 2.24232 ( 2) covalent geometry : bond 0.00334 (21573) covalent geometry : angle 0.57904 (29153) Misc. bond : bond 0.00035 ( 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: 92 poor density : 518 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8344 (p) REVERT: A 41 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 45 ASP cc_start: 0.7969 (m-30) cc_final: 0.7641 (m-30) REVERT: A 60 ILE cc_start: 0.8348 (tp) cc_final: 0.8043 (tt) REVERT: A 423 ASP cc_start: 0.7993 (t70) cc_final: 0.7765 (t0) REVERT: A 592 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7421 (ttm170) REVERT: A 606 TYR cc_start: 0.7508 (p90) cc_final: 0.7163 (p90) REVERT: B 41 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 185 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8282 (p) REVERT: B 446 LEU cc_start: 0.8399 (mt) cc_final: 0.8189 (mp) REVERT: B 449 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7167 (tm-30) REVERT: B 560 ASP cc_start: 0.8513 (m-30) cc_final: 0.8106 (m-30) REVERT: B 631 TYR cc_start: 0.7948 (m-80) cc_final: 0.7585 (m-80) REVERT: C 39 LEU cc_start: 0.8780 (tp) cc_final: 0.8577 (tt) REVERT: C 41 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 45 ASP cc_start: 0.7703 (m-30) cc_final: 0.7372 (m-30) REVERT: C 52 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7734 (mmmm) REVERT: C 67 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7893 (tm-30) REVERT: C 79 LYS cc_start: 0.7505 (mmtt) cc_final: 0.7202 (mttt) REVERT: C 209 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: C 238 GLU cc_start: 0.6774 (pp20) cc_final: 0.6455 (pp20) REVERT: C 454 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7765 (tm-30) REVERT: C 522 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7919 (mt) REVERT: C 527 ILE cc_start: 0.8657 (tt) cc_final: 0.8415 (pt) REVERT: D 160 ASP cc_start: 0.7070 (p0) cc_final: 0.6714 (p0) REVERT: D 185 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8274 (p) REVERT: D 188 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7851 (p-80) REVERT: D 274 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6640 (tm-30) REVERT: D 311 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7593 (t) REVERT: D 468 ASP cc_start: 0.6305 (OUTLIER) cc_final: 0.6032 (t70) outliers start: 92 outliers final: 52 residues processed: 565 average time/residue: 1.2920 time to fit residues: 828.9344 Evaluate side-chains 568 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 508 time to evaluate : 2.258 ------------------------------------------------------------------------------- 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 40 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 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 567 GLU 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 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 209 GLU 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 522 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain D residue 2 ILE 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 240 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 311 VAL 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 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: 0.8980 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 172 optimal weight: 0.5980 chunk 88 optimal weight: 0.0980 chunk 244 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 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 = 0.3919 r_free = 0.3919 target = 0.137984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126704 restraints weight = 30620.716| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.89 r_work: 0.3678 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21575 Z= 0.130 Angle : 0.574 16.928 29155 Z= 0.301 Chirality : 0.043 0.152 3128 Planarity : 0.004 0.053 3712 Dihedral : 10.083 86.460 3197 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.76 % Allowed : 20.22 % Favored : 76.02 % 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: -0.59 (0.17), residues: 2552 helix: 0.98 (0.16), residues: 1192 sheet: 0.31 (0.35), residues: 254 loop : -2.19 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 425 HIS 0.005 0.001 HIS C 30 PHE 0.036 0.002 PHE B 526 TYR 0.013 0.001 TYR A 236 ARG 0.012 0.000 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 807) hydrogen bonds : angle 4.19329 ( 2325) SS BOND : bond 0.01095 ( 1) SS BOND : angle 1.91476 ( 2) covalent geometry : bond 0.00288 (21573) covalent geometry : angle 0.57367 (29153) Misc. bond : bond 0.00032 ( 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 596 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 512 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 21 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7653 (mpp) REVERT: A 41 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 45 ASP cc_start: 0.7986 (m-30) cc_final: 0.7616 (m-30) REVERT: A 60 ILE cc_start: 0.8342 (tp) cc_final: 0.8028 (tt) REVERT: A 79 LYS cc_start: 0.7817 (ptpt) cc_final: 0.7524 (ptmt) REVERT: A 423 ASP cc_start: 0.7987 (t70) cc_final: 0.7759 (t0) REVERT: A 592 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7340 (ttm170) REVERT: A 606 TYR cc_start: 0.7469 (p90) cc_final: 0.7126 (p90) REVERT: B 41 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 185 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 249 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6566 (tt0) REVERT: B 446 LEU cc_start: 0.8392 (mt) cc_final: 0.8179 (mp) REVERT: B 449 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7167 (tm-30) REVERT: B 560 ASP cc_start: 0.8492 (m-30) cc_final: 0.8116 (m-30) REVERT: B 631 TYR cc_start: 0.7906 (m-80) cc_final: 0.7572 (m-80) REVERT: C 39 LEU cc_start: 0.8778 (tp) cc_final: 0.8379 (tt) REVERT: C 41 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 45 ASP cc_start: 0.7719 (m-30) cc_final: 0.7393 (m-30) REVERT: C 52 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7739 (mmmm) REVERT: C 67 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7880 (tm-30) REVERT: C 79 LYS cc_start: 0.7486 (mmtt) cc_final: 0.7187 (mttt) REVERT: C 238 GLU cc_start: 0.6740 (pp20) cc_final: 0.6397 (pp20) REVERT: C 344 GLU cc_start: 0.7544 (pm20) cc_final: 0.7057 (pm20) REVERT: C 454 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7757 (tm-30) REVERT: C 470 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7058 (tp) REVERT: C 522 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7894 (mt) REVERT: C 527 ILE cc_start: 0.8631 (tt) cc_final: 0.8406 (pt) REVERT: C 592 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7627 (ttp-170) REVERT: D 3 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: D 42 GLN cc_start: 0.7775 (mt0) cc_final: 0.7520 (mp10) REVERT: D 160 ASP cc_start: 0.7041 (p0) cc_final: 0.6660 (p0) REVERT: D 274 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6609 (tm-30) REVERT: D 311 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7541 (t) REVERT: D 468 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.6036 (t70) REVERT: D 491 LYS cc_start: 0.8475 (ptmm) cc_final: 0.8143 (ptpp) outliers start: 84 outliers final: 49 residues processed: 558 average time/residue: 1.2728 time to fit residues: 805.0900 Evaluate side-chains 563 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 506 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 21 MET Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 156 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 567 GLU 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 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 480 GLU 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 57 VAL 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 522 LEU Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 662 MET 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 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 311 VAL 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 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 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: 0.9980 chunk 153 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 540 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.136268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125048 restraints weight = 30914.130| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.90 r_work: 0.3653 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21575 Z= 0.186 Angle : 0.632 17.639 29155 Z= 0.332 Chirality : 0.046 0.446 3128 Planarity : 0.005 0.055 3712 Dihedral : 10.279 85.583 3196 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.07 % Allowed : 20.31 % Favored : 75.62 % 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: -0.74 (0.17), residues: 2552 helix: 0.81 (0.16), residues: 1206 sheet: 0.29 (0.35), residues: 254 loop : -2.27 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 425 HIS 0.006 0.001 HIS A 289 PHE 0.035 0.002 PHE B 526 TYR 0.017 0.002 TYR A 236 ARG 0.011 0.001 ARG D 25 Details of bonding type rmsd hydrogen bonds : bond 0.05592 ( 807) hydrogen bonds : angle 4.29217 ( 2325) SS BOND : bond 0.01235 ( 1) SS BOND : angle 2.51858 ( 2) covalent geometry : bond 0.00437 (21573) covalent geometry : angle 0.63214 (29153) Misc. bond : bond 0.00052 ( 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 601 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 510 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 21 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7645 (mpp) REVERT: A 41 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 45 ASP cc_start: 0.7983 (m-30) cc_final: 0.7619 (m-30) REVERT: A 60 ILE cc_start: 0.8338 (tp) cc_final: 0.8011 (tt) REVERT: A 79 LYS cc_start: 0.7900 (ptpt) cc_final: 0.7692 (ptmt) REVERT: A 423 ASP cc_start: 0.8031 (t70) cc_final: 0.7774 (t0) REVERT: A 592 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7336 (ttm170) REVERT: A 606 TYR cc_start: 0.7533 (p90) cc_final: 0.7190 (p90) REVERT: B 41 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 185 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 446 LEU cc_start: 0.8403 (mt) cc_final: 0.8193 (mp) REVERT: B 449 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7173 (tm-30) REVERT: B 549 GLU cc_start: 0.7956 (mp0) cc_final: 0.7657 (pm20) REVERT: B 560 ASP cc_start: 0.8488 (m-30) cc_final: 0.8062 (m-30) REVERT: B 631 TYR cc_start: 0.7960 (m-80) cc_final: 0.7580 (m-80) REVERT: C 41 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7480 (mt-10) REVERT: C 45 ASP cc_start: 0.7691 (m-30) cc_final: 0.7371 (m-30) REVERT: C 52 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7726 (mmmm) REVERT: C 67 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 79 LYS cc_start: 0.7525 (mmtt) cc_final: 0.7182 (mttt) REVERT: C 88 ASN cc_start: 0.8282 (m-40) cc_final: 0.8071 (m-40) REVERT: C 238 GLU cc_start: 0.6785 (pp20) cc_final: 0.6456 (pp20) REVERT: C 344 GLU cc_start: 0.7525 (pm20) cc_final: 0.7040 (pm20) REVERT: C 454 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7744 (tm-30) REVERT: C 456 GLU cc_start: 0.7210 (tp30) cc_final: 0.6951 (tp30) REVERT: C 592 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7671 (ttm170) REVERT: D 160 ASP cc_start: 0.7100 (p0) cc_final: 0.6723 (p0) REVERT: D 188 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7854 (p-80) REVERT: D 274 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6628 (tm-30) REVERT: D 311 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7616 (t) REVERT: D 468 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.6134 (t70) outliers start: 91 outliers final: 56 residues processed: 562 average time/residue: 1.2604 time to fit residues: 805.1209 Evaluate side-chains 566 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 504 time to evaluate : 2.210 ------------------------------------------------------------------------------- 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 21 MET 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 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 172 VAL 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 28 MET Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 VAL 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 521 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 662 MET 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 188 HIS 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 311 VAL 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 495 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL 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: 0.7980 chunk 200 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 152 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 229 optimal weight: 0.0770 chunk 80 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 226 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 A 455 ASN B 16 ASN B 540 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS D 572 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.138378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.127116 restraints weight = 30734.610| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.90 r_work: 0.3679 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21575 Z= 0.133 Angle : 0.603 17.681 29155 Z= 0.315 Chirality : 0.044 0.400 3128 Planarity : 0.004 0.054 3712 Dihedral : 9.956 87.651 3196 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.04 % Allowed : 21.74 % Favored : 75.21 % 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: -0.54 (0.17), residues: 2552 helix: 1.03 (0.16), residues: 1192 sheet: 0.36 (0.35), residues: 254 loop : -2.18 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 425 HIS 0.005 0.001 HIS C 30 PHE 0.036 0.002 PHE B 526 TYR 0.013 0.001 TYR D 670 ARG 0.010 0.001 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 807) hydrogen bonds : angle 4.18156 ( 2325) SS BOND : bond 0.01119 ( 1) SS BOND : angle 2.66034 ( 2) covalent geometry : bond 0.00298 (21573) covalent geometry : angle 0.60244 (29153) Misc. bond : bond 0.00024 ( 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 581 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 513 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8338 (p) REVERT: A 33 LYS cc_start: 0.7117 (mtmm) cc_final: 0.6904 (mtmt) REVERT: A 41 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 45 ASP cc_start: 0.7932 (m-30) cc_final: 0.7474 (m-30) REVERT: A 60 ILE cc_start: 0.8336 (tp) cc_final: 0.8008 (tt) REVERT: A 62 ASP cc_start: 0.8055 (t0) cc_final: 0.7800 (m-30) REVERT: A 423 ASP cc_start: 0.7983 (t70) cc_final: 0.7727 (t0) REVERT: A 606 TYR cc_start: 0.7481 (p90) cc_final: 0.7143 (p90) REVERT: B 41 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 154 ASN cc_start: 0.8254 (t0) cc_final: 0.7754 (t0) REVERT: B 185 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 249 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6453 (tt0) REVERT: B 446 LEU cc_start: 0.8380 (mt) cc_final: 0.8115 (mt) REVERT: B 449 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 549 GLU cc_start: 0.7914 (mp0) cc_final: 0.7645 (pm20) REVERT: B 560 ASP cc_start: 0.8477 (m-30) cc_final: 0.8103 (m-30) REVERT: B 631 TYR cc_start: 0.7884 (m-80) cc_final: 0.7470 (m-80) REVERT: C 41 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 45 ASP cc_start: 0.7682 (m-30) cc_final: 0.7388 (m-30) REVERT: C 52 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7708 (mmmm) REVERT: C 67 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7844 (tm-30) REVERT: C 79 LYS cc_start: 0.7509 (mmtt) cc_final: 0.7178 (mttt) REVERT: C 88 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.8036 (m-40) REVERT: C 225 ASP cc_start: 0.6622 (p0) cc_final: 0.6339 (p0) REVERT: C 238 GLU cc_start: 0.6753 (pp20) cc_final: 0.6414 (pp20) REVERT: C 324 GLU cc_start: 0.7035 (mp0) cc_final: 0.6769 (mp0) REVERT: C 344 GLU cc_start: 0.7576 (pm20) cc_final: 0.7099 (pm20) REVERT: C 454 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7662 (tm-30) REVERT: C 456 GLU cc_start: 0.7313 (tp30) cc_final: 0.7044 (tp30) REVERT: C 644 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7139 (mm-30) REVERT: D 3 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: D 42 GLN cc_start: 0.7763 (mt0) cc_final: 0.7532 (mp10) REVERT: D 160 ASP cc_start: 0.7050 (p0) cc_final: 0.6673 (p0) REVERT: D 274 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6611 (tm-30) REVERT: D 311 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7546 (t) REVERT: D 468 ASP cc_start: 0.6256 (OUTLIER) cc_final: 0.6049 (t70) outliers start: 68 outliers final: 48 residues processed: 551 average time/residue: 1.2788 time to fit residues: 805.2556 Evaluate side-chains 554 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 500 time to evaluate : 2.496 ------------------------------------------------------------------------------- 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 37 THR Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 56 SER 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 439 SER Chi-restraints excluded: chain A residue 444 VAL 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 286 ASN 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 28 MET 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 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 429 THR 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 C residue 662 MET 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 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 122 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 149 optimal weight: 0.0770 chunk 76 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 222 optimal weight: 0.2980 chunk 228 optimal weight: 0.3980 chunk 9 optimal weight: 0.3980 chunk 119 optimal weight: 0.6980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 A 455 ASN B 16 ASN B 88 ASN B 540 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.139672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.128295 restraints weight = 31036.865| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.93 r_work: 0.3692 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2625 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= 0.122 Angle : 0.591 17.625 29155 Z= 0.309 Chirality : 0.043 0.372 3128 Planarity : 0.004 0.054 3712 Dihedral : 9.594 88.450 3196 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.42 % Allowed : 22.51 % Favored : 75.08 % 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: -0.39 (0.17), residues: 2552 helix: 1.15 (0.16), residues: 1198 sheet: 0.44 (0.34), residues: 256 loop : -2.11 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 425 HIS 0.008 0.001 HIS C 30 PHE 0.037 0.001 PHE B 526 TYR 0.013 0.001 TYR D 670 ARG 0.013 0.001 ARG C 419 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 807) hydrogen bonds : angle 4.08421 ( 2325) SS BOND : bond 0.00175 ( 1) SS BOND : angle 4.34699 ( 2) covalent geometry : bond 0.00268 (21573) covalent geometry : angle 0.58967 (29153) Misc. bond : bond 0.00021 ( 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 568 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 514 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 60 ILE cc_start: 0.8281 (tp) cc_final: 0.7972 (tt) REVERT: A 62 ASP cc_start: 0.8022 (t0) cc_final: 0.7802 (m-30) REVERT: A 376 LYS cc_start: 0.7344 (tppt) cc_final: 0.7077 (tppt) REVERT: A 423 ASP cc_start: 0.7981 (t70) cc_final: 0.7729 (t0) REVERT: A 606 TYR cc_start: 0.7458 (p90) cc_final: 0.7141 (p90) REVERT: B 154 ASN cc_start: 0.8209 (t0) cc_final: 0.7740 (t0) REVERT: B 185 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 249 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6506 (tt0) REVERT: B 446 LEU cc_start: 0.8372 (mt) cc_final: 0.8099 (mt) REVERT: B 449 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 549 GLU cc_start: 0.7869 (mp0) cc_final: 0.7613 (pm20) REVERT: B 560 ASP cc_start: 0.8454 (m-30) cc_final: 0.8094 (m-30) REVERT: B 631 TYR cc_start: 0.7842 (m-80) cc_final: 0.7442 (m-80) REVERT: C 41 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 45 ASP cc_start: 0.7632 (m-30) cc_final: 0.7338 (m-30) REVERT: C 52 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7702 (mmmm) REVERT: C 67 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 79 LYS cc_start: 0.7574 (mmtt) cc_final: 0.7222 (mttt) REVERT: C 88 ASN cc_start: 0.8280 (m-40) cc_final: 0.8062 (m-40) REVERT: C 225 ASP cc_start: 0.6631 (p0) cc_final: 0.5999 (p0) REVERT: C 324 GLU cc_start: 0.7002 (mp0) cc_final: 0.6787 (mp0) REVERT: C 344 GLU cc_start: 0.7601 (pm20) cc_final: 0.7130 (pm20) REVERT: C 454 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 456 GLU cc_start: 0.7280 (tp30) cc_final: 0.7049 (tp30) REVERT: D 3 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: D 160 ASP cc_start: 0.7023 (p0) cc_final: 0.6626 (p0) REVERT: D 274 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6551 (tm-30) REVERT: D 453 ILE cc_start: 0.8116 (mt) cc_final: 0.7888 (mp) REVERT: D 468 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5981 (t70) REVERT: D 623 LYS cc_start: 0.8038 (mptt) cc_final: 0.7770 (pmmt) outliers start: 54 outliers final: 41 residues processed: 548 average time/residue: 1.2224 time to fit residues: 763.6250 Evaluate side-chains 545 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 500 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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 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 286 ASN Chi-restraints excluded: chain B residue 495 LEU 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 28 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 146 ASP 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 491 LYS 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 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 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 146 optimal weight: 0.0980 chunk 178 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 208 optimal weight: 0.5980 chunk 148 optimal weight: 0.3980 chunk 197 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.138735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.127358 restraints weight = 31003.620| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.93 r_work: 0.3677 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2625 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= 0.143 Angle : 0.609 17.330 29155 Z= 0.320 Chirality : 0.045 0.413 3128 Planarity : 0.004 0.054 3712 Dihedral : 9.649 87.432 3196 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.68 % Allowed : 22.73 % Favored : 74.59 % 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: -0.38 (0.17), residues: 2552 helix: 1.15 (0.16), residues: 1194 sheet: 0.53 (0.34), residues: 254 loop : -2.13 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 425 HIS 0.007 0.001 HIS C 30 PHE 0.026 0.002 PHE C 482 TYR 0.017 0.001 TYR D 670 ARG 0.011 0.001 ARG C 419 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 807) hydrogen bonds : angle 4.14174 ( 2325) SS BOND : bond 0.01276 ( 1) SS BOND : angle 3.83627 ( 2) covalent geometry : bond 0.00327 (21573) covalent geometry : angle 0.60789 (29153) Misc. bond : bond 0.00034 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17850.82 seconds wall clock time: 307 minutes 17.35 seconds (18437.35 seconds total)