Starting phenix.real_space_refine on Sun Aug 24 16:17:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p28_17359/08_2025/8p28_17359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p28_17359/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p28_17359/08_2025/8p28_17359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p28_17359/08_2025/8p28_17359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p28_17359/08_2025/8p28_17359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p28_17359/08_2025/8p28_17359.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.34, per 1000 atoms: 0.21 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: 1.45 Conformation dependent library (CDL) restraints added in 580.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.45 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: 3.18 Time building geometry restraints manager: 1.85 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 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 803)) selection = (chain 'C' and resid 1 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 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: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.210 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 604 TYR 0.021 0.002 TYR A 262 PHE 0.020 0.002 PHE B 184 TRP 0.009 0.002 TRP D 353 HIS 0.006 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00528 (21573) covalent geometry : angle 0.64080 (29153) SS BOND : bond 0.02359 ( 1) SS BOND : angle 5.04644 ( 2) hydrogen bonds : bond 0.18424 ( 807) hydrogen bonds : angle 6.16260 ( 2325) 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 : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8205 (tp) cc_final: 0.7898 (tt) REVERT: A 154 ASN cc_start: 0.8141 (t0) cc_final: 0.7869 (t0) REVERT: A 468 ASP cc_start: 0.6788 (t0) cc_final: 0.6525 (t0) REVERT: A 533 LEU cc_start: 0.8020 (mp) cc_final: 0.7749 (mp) REVERT: A 670 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.8101 (t80) REVERT: B 41 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6524 (mm-30) REVERT: B 160 ASP cc_start: 0.7102 (t70) cc_final: 0.6824 (t70) REVERT: B 296 ILE cc_start: 0.6872 (mt) cc_final: 0.6662 (mp) REVERT: B 369 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.6721 (p0) REVERT: B 388 ASN cc_start: 0.7784 (t0) cc_final: 0.7451 (t0) REVERT: B 446 LEU cc_start: 0.8332 (mt) cc_final: 0.8118 (mt) REVERT: B 449 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6912 (tm-30) REVERT: B 521 THR cc_start: 0.7680 (p) cc_final: 0.7449 (m) REVERT: B 560 ASP cc_start: 0.7995 (m-30) cc_final: 0.7646 (m-30) REVERT: B 665 LYS cc_start: 0.8649 (tppp) cc_final: 0.8286 (mtpp) REVERT: C 2 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7369 (mp) REVERT: C 41 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6673 (mt-10) REVERT: C 45 ASP cc_start: 0.7098 (m-30) cc_final: 0.6805 (m-30) REVERT: C 65 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 67 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 79 LYS cc_start: 0.7220 (mmtt) cc_final: 0.6784 (mttt) REVERT: C 188 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8044 (p-80) REVERT: C 344 GLU cc_start: 0.6884 (pm20) cc_final: 0.6528 (pm20) REVERT: C 454 GLU cc_start: 0.7263 (tm-30) cc_final: 0.7021 (tm-30) REVERT: D 29 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (tt) REVERT: D 192 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6970 (ptt90) REVERT: D 369 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.7444 (p0) REVERT: D 420 VAL cc_start: 0.8428 (p) cc_final: 0.8221 (p) REVERT: D 560 ASP cc_start: 0.8018 (m-30) cc_final: 0.7789 (m-30) outliers start: 48 outliers final: 10 residues processed: 601 average time/residue: 0.5741 time to fit residues: 390.7045 Evaluate side-chains 527 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 510 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.3980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.3980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 61 GLN A 213 ASN A 455 ASN A 518 ASN B 279 HIS B 385 ASN B 388 ASN B 396 ASN C 30 HIS C 154 ASN C 213 ASN D 572 ASN D 639 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.135846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124680 restraints weight = 30842.906| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.89 r_work: 0.3649 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1400 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= 0.172 Angle : 0.636 12.367 29155 Z= 0.335 Chirality : 0.045 0.188 3128 Planarity : 0.005 0.054 3712 Dihedral : 12.258 93.466 3227 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.40 % Allowed : 14.85 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.17), residues: 2552 helix: 0.65 (0.16), residues: 1180 sheet: 0.13 (0.37), residues: 252 loop : -2.51 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 148 TYR 0.015 0.002 TYR A 236 PHE 0.028 0.002 PHE B 526 TRP 0.009 0.002 TRP D 409 HIS 0.010 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00389 (21573) covalent geometry : angle 0.63531 (29153) SS BOND : bond 0.01396 ( 1) SS BOND : angle 3.02807 ( 2) hydrogen bonds : bond 0.06124 ( 807) hydrogen bonds : angle 4.71410 ( 2325) Misc. bond : bond 0.00008 ( 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 603 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 527 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 18 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7791 (tp40) REVERT: A 60 ILE cc_start: 0.8386 (tp) cc_final: 0.8068 (tt) REVERT: A 154 ASN cc_start: 0.8322 (t0) cc_final: 0.8099 (t0) REVERT: A 423 ASP cc_start: 0.7999 (t70) cc_final: 0.7781 (t0) REVERT: A 592 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7430 (ttm170) REVERT: B 41 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7163 (mm-30) REVERT: B 160 ASP cc_start: 0.7551 (t70) cc_final: 0.7294 (t70) REVERT: B 420 VAL cc_start: 0.8222 (p) cc_final: 0.7984 (m) REVERT: B 446 LEU cc_start: 0.8419 (mt) cc_final: 0.8204 (mt) REVERT: B 449 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 560 ASP cc_start: 0.8461 (m-30) cc_final: 0.8089 (m-30) REVERT: B 631 TYR cc_start: 0.7954 (m-80) cc_final: 0.7679 (m-80) REVERT: C 2 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7678 (mp) REVERT: C 41 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7445 (mt-10) REVERT: C 45 ASP cc_start: 0.7632 (m-30) cc_final: 0.7308 (m-30) REVERT: C 52 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7532 (mmmm) REVERT: C 67 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 79 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7233 (mttt) REVERT: C 140 ASP cc_start: 0.7797 (m-30) cc_final: 0.7544 (m-30) REVERT: C 208 LEU cc_start: 0.7736 (mp) cc_final: 0.7427 (mp) REVERT: C 238 GLU cc_start: 0.6720 (pp20) cc_final: 0.6455 (pp20) REVERT: C 344 GLU cc_start: 0.7538 (pm20) cc_final: 0.7070 (pm20) REVERT: C 454 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 592 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7627 (ttm170) REVERT: D 185 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8343 (p) REVERT: D 274 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6517 (tm-30) REVERT: D 468 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.6019 (t70) outliers start: 76 outliers final: 28 residues processed: 566 average time/residue: 0.5901 time to fit residues: 377.6978 Evaluate side-chains 533 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 501 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 B residue 29 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 2 ILE 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 240 VAL Chi-restraints excluded: chain D residue 273 ARG 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 52 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 148 optimal weight: 0.0570 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.136081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124798 restraints weight = 31107.481| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.91 r_work: 0.3649 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21575 Z= 0.162 Angle : 0.606 12.667 29155 Z= 0.319 Chirality : 0.044 0.177 3128 Planarity : 0.005 0.056 3712 Dihedral : 11.541 88.280 3205 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.53 % Allowed : 16.51 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.17), residues: 2552 helix: 0.70 (0.16), residues: 1194 sheet: 0.19 (0.36), residues: 254 loop : -2.38 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 419 TYR 0.016 0.002 TYR A 236 PHE 0.029 0.002 PHE B 526 TRP 0.012 0.002 TRP D 425 HIS 0.010 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00371 (21573) covalent geometry : angle 0.60579 (29153) SS BOND : bond 0.00653 ( 1) SS BOND : angle 2.77602 ( 2) hydrogen bonds : bond 0.05737 ( 807) hydrogen bonds : angle 4.52940 ( 2325) Misc. bond : bond 0.00057 ( 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 592 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 513 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 41 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 45 ASP cc_start: 0.7971 (m-30) cc_final: 0.7535 (m-30) REVERT: A 60 ILE cc_start: 0.8363 (tp) cc_final: 0.8055 (tt) REVERT: A 423 ASP cc_start: 0.8045 (t70) cc_final: 0.7806 (t0) REVERT: B 41 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 42 GLN cc_start: 0.7919 (mt0) cc_final: 0.7692 (mp10) REVERT: B 160 ASP cc_start: 0.7610 (t70) cc_final: 0.7333 (t70) REVERT: B 185 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 249 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6526 (tt0) REVERT: B 420 VAL cc_start: 0.8261 (p) cc_final: 0.8000 (m) REVERT: B 446 LEU cc_start: 0.8402 (mt) cc_final: 0.8190 (mt) REVERT: B 449 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7200 (tm-30) REVERT: B 521 THR cc_start: 0.7985 (p) cc_final: 0.7742 (m) REVERT: B 560 ASP cc_start: 0.8508 (m-30) cc_final: 0.8137 (m-30) REVERT: B 631 TYR cc_start: 0.7967 (m-80) cc_final: 0.7582 (m-80) REVERT: C 41 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 45 ASP cc_start: 0.7693 (m-30) cc_final: 0.7388 (m-30) REVERT: C 67 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 79 LYS cc_start: 0.7535 (mmtt) cc_final: 0.7213 (mttt) REVERT: C 88 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8096 (m-40) REVERT: C 208 LEU cc_start: 0.7729 (mp) cc_final: 0.7406 (mp) REVERT: C 225 ASP cc_start: 0.6646 (p0) cc_final: 0.6113 (p0) REVERT: C 238 GLU cc_start: 0.6757 (pp20) cc_final: 0.6450 (pp20) REVERT: C 344 GLU cc_start: 0.7534 (pm20) cc_final: 0.7047 (pm20) REVERT: C 454 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7808 (tm-30) REVERT: C 592 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7691 (ttp-170) REVERT: D 35 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6096 (tm-30) REVERT: D 160 ASP cc_start: 0.7122 (p0) cc_final: 0.6894 (p0) REVERT: D 185 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8327 (p) REVERT: D 188 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7859 (p-80) REVERT: D 274 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6559 (tm-30) REVERT: D 468 ASP cc_start: 0.6371 (OUTLIER) cc_final: 0.6015 (t70) REVERT: D 487 THR cc_start: 0.8313 (p) cc_final: 0.8090 (p) REVERT: D 595 PHE cc_start: 0.8648 (m-80) cc_final: 0.8429 (m-10) outliers start: 79 outliers final: 29 residues processed: 554 average time/residue: 0.6587 time to fit residues: 411.2587 Evaluate side-chains 536 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 500 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 550 LEU 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 273 ARG Chi-restraints excluded: chain D residue 296 ILE 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 118 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 238 optimal weight: 0.0670 chunk 67 optimal weight: 0.7980 chunk 201 optimal weight: 0.0870 chunk 171 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 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 = 0.3902 r_free = 0.3902 target = 0.136734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125462 restraints weight = 30988.588| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.91 r_work: 0.3659 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1916 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= 0.145 Angle : 0.579 13.632 29155 Z= 0.305 Chirality : 0.043 0.168 3128 Planarity : 0.004 0.054 3712 Dihedral : 10.923 87.631 3201 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.85 % Allowed : 17.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.17), residues: 2552 helix: 0.83 (0.16), residues: 1194 sheet: 0.26 (0.36), residues: 254 loop : -2.32 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 419 TYR 0.015 0.001 TYR A 236 PHE 0.030 0.002 PHE B 526 TRP 0.015 0.001 TRP D 425 HIS 0.008 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00329 (21573) covalent geometry : angle 0.57918 (29153) SS BOND : bond 0.01154 ( 1) SS BOND : angle 2.12753 ( 2) hydrogen bonds : bond 0.05277 ( 807) hydrogen bonds : angle 4.39201 ( 2325) Misc. bond : bond 0.00046 ( 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 609 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 523 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8357 (p) REVERT: A 41 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 45 ASP cc_start: 0.7949 (m-30) cc_final: 0.7729 (m-30) REVERT: A 60 ILE cc_start: 0.8359 (tp) cc_final: 0.8059 (tt) REVERT: A 423 ASP cc_start: 0.8013 (t70) cc_final: 0.7809 (t0) REVERT: A 507 LEU cc_start: 0.8708 (mt) cc_final: 0.8419 (mp) REVERT: A 592 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7577 (ttm170) REVERT: A 606 TYR cc_start: 0.7463 (p90) cc_final: 0.7097 (p90) REVERT: B 41 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 42 GLN cc_start: 0.7887 (mt0) cc_final: 0.7684 (mp10) REVERT: B 160 ASP cc_start: 0.7646 (t70) cc_final: 0.7364 (t70) REVERT: B 185 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 249 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6585 (tt0) REVERT: B 420 VAL cc_start: 0.8267 (p) cc_final: 0.7998 (m) REVERT: B 446 LEU cc_start: 0.8395 (mt) cc_final: 0.8189 (mp) REVERT: B 449 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 521 THR cc_start: 0.7981 (p) cc_final: 0.7741 (m) REVERT: B 548 GLN cc_start: 0.8158 (tp40) cc_final: 0.7945 (mm-40) REVERT: B 560 ASP cc_start: 0.8514 (m-30) cc_final: 0.8119 (m-30) REVERT: B 631 TYR cc_start: 0.7954 (m-80) cc_final: 0.7548 (m-80) REVERT: C 41 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7465 (mt-10) REVERT: C 45 ASP cc_start: 0.7686 (m-30) cc_final: 0.7361 (m-30) REVERT: C 52 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7725 (mmmm) REVERT: C 67 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7881 (tm-30) REVERT: C 79 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7180 (mttt) REVERT: C 208 LEU cc_start: 0.7666 (mp) cc_final: 0.7343 (mp) REVERT: C 238 GLU cc_start: 0.6750 (pp20) cc_final: 0.6444 (pp20) REVERT: C 344 GLU cc_start: 0.7534 (pm20) cc_final: 0.7065 (pm20) REVERT: C 454 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7820 (tm-30) REVERT: C 592 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7598 (ttm170) REVERT: D 35 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.6053 (tm-30) REVERT: D 185 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8310 (p) REVERT: D 188 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7863 (p-80) REVERT: D 252 SER cc_start: 0.8278 (t) cc_final: 0.8046 (m) REVERT: D 274 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6596 (tm-30) REVERT: D 420 VAL cc_start: 0.8283 (p) cc_final: 0.8064 (m) REVERT: D 468 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.6003 (t70) outliers start: 86 outliers final: 42 residues processed: 564 average time/residue: 0.6039 time to fit residues: 384.6525 Evaluate side-chains 555 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 507 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 276 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain B residue 29 LEU 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 B residue 663 MET 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 206 ILE Chi-restraints excluded: chain C residue 284 THR 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 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 296 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU 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 253 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 97 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 chunk 238 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 241 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 540 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.137449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.126225 restraints weight = 30819.538| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.90 r_work: 0.3670 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2115 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= 0.134 Angle : 0.567 14.836 29155 Z= 0.299 Chirality : 0.043 0.180 3128 Planarity : 0.004 0.053 3712 Dihedral : 10.385 85.694 3196 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.85 % Allowed : 19.02 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.17), residues: 2552 helix: 0.95 (0.16), residues: 1192 sheet: 0.32 (0.35), residues: 254 loop : -2.23 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 148 TYR 0.014 0.001 TYR A 236 PHE 0.033 0.002 PHE B 526 TRP 0.019 0.002 TRP B 425 HIS 0.005 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00300 (21573) covalent geometry : angle 0.56684 (29153) SS BOND : bond 0.01288 ( 1) SS BOND : angle 2.29870 ( 2) hydrogen bonds : bond 0.04922 ( 807) hydrogen bonds : angle 4.28461 ( 2325) Misc. bond : bond 0.00034 ( 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 595 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 509 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 41 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 45 ASP cc_start: 0.7948 (m-30) cc_final: 0.7652 (m-30) REVERT: A 60 ILE cc_start: 0.8349 (tp) cc_final: 0.8051 (tt) REVERT: A 423 ASP cc_start: 0.7990 (t70) cc_final: 0.7777 (t0) REVERT: A 592 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7480 (ttm170) REVERT: A 606 TYR cc_start: 0.7466 (p90) cc_final: 0.7121 (p90) REVERT: B 41 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 185 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8275 (p) REVERT: B 249 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6547 (tt0) REVERT: B 420 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7974 (m) REVERT: B 446 LEU cc_start: 0.8389 (mt) cc_final: 0.8176 (mp) REVERT: B 449 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7220 (tm-30) REVERT: B 496 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8234 (tp) REVERT: B 521 THR cc_start: 0.7978 (p) cc_final: 0.7743 (m) REVERT: B 560 ASP cc_start: 0.8522 (m-30) cc_final: 0.8136 (m-30) REVERT: B 631 TYR cc_start: 0.7965 (m-80) cc_final: 0.7599 (m-80) REVERT: C 39 LEU cc_start: 0.8782 (tp) cc_final: 0.8533 (tt) REVERT: C 41 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7473 (mt-10) REVERT: C 45 ASP cc_start: 0.7696 (m-30) cc_final: 0.7361 (m-30) REVERT: C 52 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7727 (mmmm) REVERT: C 67 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7882 (tm-30) REVERT: C 79 LYS cc_start: 0.7505 (mmtt) cc_final: 0.7196 (mttt) REVERT: C 208 LEU cc_start: 0.7594 (mp) cc_final: 0.7299 (mp) REVERT: C 225 ASP cc_start: 0.6628 (p0) cc_final: 0.6079 (p0) REVERT: C 238 GLU cc_start: 0.6768 (pp20) cc_final: 0.6443 (pp20) REVERT: C 344 GLU cc_start: 0.7528 (pm20) cc_final: 0.7068 (pm20) REVERT: C 454 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 522 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7899 (mt) REVERT: C 527 ILE cc_start: 0.8676 (tt) cc_final: 0.8433 (pt) REVERT: C 592 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7603 (ttp-170) REVERT: C 604 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7809 (mtt180) REVERT: D 35 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6092 (tm-30) REVERT: D 42 GLN cc_start: 0.7801 (mt0) cc_final: 0.7529 (mp10) REVERT: D 160 ASP cc_start: 0.7083 (p0) cc_final: 0.6733 (p0) REVERT: D 185 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8299 (p) REVERT: D 188 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7867 (p-80) REVERT: D 252 SER cc_start: 0.8254 (t) cc_final: 0.8037 (m) REVERT: D 274 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6626 (tm-30) REVERT: D 344 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7209 (mp0) REVERT: D 468 ASP cc_start: 0.6326 (OUTLIER) cc_final: 0.6012 (t70) outliers start: 86 outliers final: 42 residues processed: 551 average time/residue: 0.5593 time to fit residues: 348.9677 Evaluate side-chains 557 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 506 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain 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 420 VAL Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 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 206 ILE Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain D residue 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 296 ILE 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.5627 > 50: distance: 13 - 18: 19.071 distance: 18 - 19: 5.733 distance: 19 - 20: 11.004 distance: 19 - 22: 9.724 distance: 20 - 21: 8.754 distance: 20 - 28: 10.136 distance: 22 - 23: 15.721 distance: 23 - 24: 4.964 distance: 23 - 25: 24.871 distance: 24 - 26: 22.684 distance: 25 - 27: 11.926 distance: 26 - 27: 22.670 distance: 28 - 29: 6.916 distance: 29 - 30: 14.714 distance: 29 - 32: 10.252 distance: 30 - 31: 8.508 distance: 30 - 35: 6.144 distance: 32 - 33: 10.948 distance: 32 - 34: 16.548 distance: 35 - 36: 17.237 distance: 36 - 37: 18.772 distance: 36 - 39: 21.367 distance: 37 - 43: 9.563 distance: 39 - 40: 26.473 distance: 40 - 41: 11.999 distance: 40 - 42: 17.792 distance: 43 - 44: 17.811 distance: 44 - 45: 24.337 distance: 44 - 47: 22.036 distance: 45 - 46: 14.910 distance: 45 - 52: 26.475 distance: 47 - 48: 16.992 distance: 48 - 49: 14.365 distance: 49 - 50: 27.387 distance: 50 - 51: 15.829 distance: 52 - 53: 17.384 distance: 53 - 54: 11.206 distance: 54 - 55: 6.123 distance: 54 - 56: 7.235 distance: 56 - 57: 4.926 distance: 57 - 60: 10.490 distance: 58 - 59: 8.994 distance: 58 - 65: 19.465 distance: 60 - 61: 10.732 distance: 61 - 62: 9.592 distance: 62 - 63: 7.198 distance: 62 - 64: 7.804 distance: 65 - 66: 15.670 distance: 66 - 67: 25.369 distance: 66 - 69: 10.274 distance: 67 - 68: 17.335 distance: 67 - 73: 12.044 distance: 69 - 70: 7.810 distance: 70 - 72: 6.291 distance: 73 - 74: 5.311 distance: 74 - 75: 8.141 distance: 74 - 77: 9.391 distance: 75 - 80: 4.781 distance: 76 - 103: 17.150 distance: 77 - 78: 9.886 distance: 77 - 79: 8.441 distance: 80 - 81: 12.813 distance: 81 - 82: 10.731 distance: 81 - 84: 19.006 distance: 82 - 83: 9.018 distance: 82 - 87: 6.221 distance: 84 - 85: 6.662 distance: 84 - 86: 11.986 distance: 88 - 89: 4.422 distance: 88 - 91: 7.064 distance: 89 - 90: 3.935 distance: 89 - 95: 3.680 distance: 90 - 120: 6.152 distance: 91 - 92: 11.581 distance: 92 - 93: 8.285 distance: 92 - 94: 5.733