Starting phenix.real_space_refine on Wed Nov 20 07:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/11_2024/8p28_17359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/11_2024/8p28_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/11_2024/8p28_17359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/11_2024/8p28_17359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/11_2024/8p28_17359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/11_2024/8p28_17359.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 4 5.21 5 S 136 5.16 5 C 13238 2.51 5 N 3688 2.21 5 O 4039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 14.54, per 1000 atoms: 0.69 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: 5.01 Conformation dependent library (CDL) restraints added in 2.7 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: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.640A pdb=" N ARG A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.771A pdb=" N THR A 31 " --> pdb=" O MET A 28 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP A 32 " --> pdb=" O LEU A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.907A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.554A pdb=" N LEU A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.694A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.857A pdb=" N MET A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 142 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 175 through 182 removed outlier: 4.119A pdb=" N ILE A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 removed outlier: 4.038A pdb=" N VAL A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 245 Proline residue: A 230 - end of helix removed outlier: 4.351A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.815A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.701A pdb=" N TYR A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.850A pdb=" N ALA A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.681A pdb=" N LYS A 408 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 455 through 486 removed outlier: 3.725A pdb=" N ILE A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 462 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.695A pdb=" N ASN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 535 removed outlier: 3.686A pdb=" N CYS A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.967A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.967A pdb=" N VAL A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.721A pdb=" N ALA B 22 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 51 removed outlier: 4.289A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 70 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.791A pdb=" N SER B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 103' Processing helix chain 'B' and resid 121 through 142 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.506A pdb=" N HIS B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.817A pdb=" N TYR B 163 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.963A pdb=" N HIS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.517A pdb=" N ALA B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 223 through 229 removed outlier: 4.067A pdb=" N LEU B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.948A pdb=" N TYR B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.807A pdb=" N GLU B 274 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 305 removed outlier: 3.998A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 339 removed outlier: 3.525A pdb=" N CYS B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.889A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.662A pdb=" N LYS B 408 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 451 Processing helix chain 'B' and resid 455 through 486 removed outlier: 3.525A pdb=" N ARG B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 528 through 535 removed outlier: 3.828A pdb=" N CYS B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 570 removed outlier: 3.843A pdb=" N GLN B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 549 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 596 removed outlier: 3.620A pdb=" N GLN B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 635 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.991A pdb=" N GLU B 657 " --> pdb=" O PRO B 653 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.517A pdb=" N ALA C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 57 through 69 removed outlier: 3.606A pdb=" N MET C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.834A pdb=" N ALA C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 121 through 142 removed outlier: 3.580A pdb=" N ALA C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 175 through 182 removed outlier: 4.127A pdb=" N ILE C 179 " --> pdb=" O PRO C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.915A pdb=" N ASN C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 235 through 247 removed outlier: 3.712A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 301 removed outlier: 3.700A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 322 through 339 removed outlier: 3.911A pdb=" N ARG C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.707A pdb=" N LYS C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 458 through 486 removed outlier: 3.681A pdb=" N PHE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 Processing helix chain 'C' and resid 516 through 520 Processing helix chain 'C' and resid 528 through 538 removed outlier: 3.550A pdb=" N CYS C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 570 removed outlier: 3.635A pdb=" N GLN C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 549 " --> pdb=" O GLU C 545 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 552 " --> pdb=" O GLN C 548 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 596 removed outlier: 3.852A pdb=" N LYS C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 628 Processing helix chain 'C' and resid 653 through 666 removed outlier: 3.511A pdb=" N ASP C 664 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR C 666 " --> pdb=" O MET C 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 removed outlier: 4.104A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 4.607A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 73 through 92 removed outlier: 4.311A pdb=" N ALA D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 84 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.811A pdb=" N SER D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 103' Processing helix chain 'D' and resid 121 through 142 Proline residue: D 136 - end of helix Processing helix chain 'D' and resid 144 through 153 removed outlier: 3.588A pdb=" N HIS D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 removed outlier: 4.366A pdb=" N ILE D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.576A pdb=" N ALA D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 201' Processing helix chain 'D' and resid 201 through 213 removed outlier: 4.023A pdb=" N SER D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.927A pdb=" N LEU D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 removed outlier: 4.185A pdb=" N ARG D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR D 236 " --> pdb=" O VAL D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.692A pdb=" N TYR D 255 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.920A pdb=" N GLU D 274 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 305 removed outlier: 3.634A pdb=" N ILE D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER D 304 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.951A pdb=" N ARG D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 removed outlier: 3.542A pdb=" N TYR D 371 " --> pdb=" O ASN D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.536A pdb=" N LYS D 408 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.891A pdb=" N CYS D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 486 removed outlier: 3.674A pdb=" N ASP D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 493 Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.607A pdb=" N HIS D 519 " --> pdb=" O VAL D 516 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 520 " --> pdb=" O ILE D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 520' Processing helix chain 'D' and resid 528 through 537 removed outlier: 4.118A pdb=" N CYS D 532 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 570 removed outlier: 3.730A pdb=" N LEU D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 552 " --> pdb=" O GLN D 548 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 596 removed outlier: 3.689A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 630 through 635 removed outlier: 4.503A pdb=" N ASP D 633 " --> pdb=" O PRO D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 666 removed outlier: 4.014A pdb=" N GLU D 657 " --> pdb=" O PRO D 653 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 658 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.982A pdb=" N THR A 4 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.817A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.594A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A 219 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASN A 316 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 221 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLN A 351 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 387 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TRP A 353 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 7.281A pdb=" N VAL A 643 " --> pdb=" O ASN A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 158 removed outlier: 5.226A pdb=" N ASN B 435 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLY B 523 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 437 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLY B 525 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B 439 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE B 527 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 441 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AA8, first strand: chain 'B' and resid 314 through 317 removed outlier: 3.574A pdb=" N TYR B 317 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLN B 351 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU B 387 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP B 353 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=AB1, first strand: chain 'C' and resid 156 through 158 removed outlier: 5.673A pdb=" N THR C 521 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER C 437 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 523 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER C 439 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 522 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU C 576 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 524 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 172 through 173 removed outlier: 6.709A pdb=" N VAL C 172 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN C 219 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN C 316 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 221 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER C 313 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE C 352 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 315 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS C 354 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR C 317 " --> pdb=" O LYS C 354 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLN C 351 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU C 387 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TRP C 353 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 386 " --> pdb=" O GLY C 671 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 643 " --> pdb=" O ASN C 674 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.489A pdb=" N THR D 4 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 156 through 158 removed outlier: 7.023A pdb=" N SER D 437 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLY D 525 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER D 439 " --> pdb=" O GLY D 525 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE D 526 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AB6, first strand: chain 'D' and resid 220 through 221 removed outlier: 3.512A pdb=" N ASN D 316 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLN D 351 " --> pdb=" O ASN D 385 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU D 387 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP D 353 " --> pdb=" O LEU D 387 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 5.85 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 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: 7.610 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: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 47.790 Find NCS groups from input model: 1.460 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:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.520 ------------------------------------------------------------------------------- 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 : 0.005 0.059 21573 Z= 0.344 Angle : 0.641 8.461 29153 Z= 0.378 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 *********************** 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 : 2.405 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: 1.3552 time to fit residues: 922.2894 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 : 2.382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 21573 Z= 0.222 Angle : 0.621 12.038 29153 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 *********************** 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 : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8227 (p) REVERT: A 18 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7599 (tp40) REVERT: A 60 ILE cc_start: 0.8167 (tp) cc_final: 0.7854 (tt) REVERT: A 154 ASN cc_start: 0.8021 (t0) cc_final: 0.7773 (t0) REVERT: B 41 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6523 (mm-30) REVERT: B 152 MET cc_start: 0.6464 (mtm) cc_final: 0.6174 (mtm) REVERT: B 160 ASP cc_start: 0.7132 (t70) cc_final: 0.6847 (t70) REVERT: B 420 VAL cc_start: 0.8127 (p) cc_final: 0.7869 (m) REVERT: B 449 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6956 (tm-30) REVERT: B 560 ASP cc_start: 0.8029 (m-30) cc_final: 0.7705 (m-30) REVERT: B 631 TYR cc_start: 0.7696 (m-80) cc_final: 0.7342 (m-80) REVERT: C 2 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7385 (mp) REVERT: C 41 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6656 (mt-10) REVERT: C 45 ASP cc_start: 0.7017 (m-30) cc_final: 0.6723 (m-30) REVERT: C 52 LYS cc_start: 0.7649 (mmmm) cc_final: 0.7284 (mmmm) REVERT: C 79 LYS cc_start: 0.7269 (mmtt) cc_final: 0.6965 (mttt) REVERT: C 140 ASP cc_start: 0.7288 (m-30) cc_final: 0.7025 (m-30) REVERT: C 208 LEU cc_start: 0.7259 (mp) cc_final: 0.6905 (mp) REVERT: C 238 GLU cc_start: 0.6079 (pp20) cc_final: 0.5856 (pp20) REVERT: C 344 GLU cc_start: 0.7045 (pm20) cc_final: 0.6568 (pm20) REVERT: C 454 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6967 (tm-30) REVERT: C 592 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7262 (ttm170) REVERT: C 604 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7516 (mtt180) REVERT: D 185 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8279 (p) REVERT: D 311 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7772 (t) REVERT: D 420 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8148 (p) REVERT: D 468 ASP cc_start: 0.5738 (OUTLIER) cc_final: 0.5451 (t70) outliers start: 69 outliers final: 23 residues processed: 566 average time/residue: 1.3995 time to fit residues: 894.5695 Evaluate side-chains 530 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 501 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 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 129 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 251 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 230 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 639 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21573 Z= 0.285 Angle : 0.626 12.425 29153 Z= 0.329 Chirality : 0.045 0.192 3128 Planarity : 0.005 0.056 3712 Dihedral : 11.722 89.113 3203 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.16 % Allowed : 16.02 % Favored : 79.82 % 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: -1.00 (0.17), residues: 2552 helix: 0.63 (0.16), residues: 1204 sheet: 0.23 (0.36), residues: 252 loop : -2.45 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 425 HIS 0.009 0.001 HIS D 297 PHE 0.028 0.002 PHE B 526 TYR 0.018 0.002 TYR A 236 ARG 0.009 0.001 ARG D 419 *********************** 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: 93 poor density : 509 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8262 (p) REVERT: A 41 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 45 ASP cc_start: 0.7311 (m-30) cc_final: 0.6925 (m-30) REVERT: A 60 ILE cc_start: 0.8087 (tp) cc_final: 0.7774 (tt) REVERT: A 154 ASN cc_start: 0.8062 (t0) cc_final: 0.7832 (t0) REVERT: A 592 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7248 (ttm170) REVERT: B 41 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6626 (mm-30) REVERT: B 42 GLN cc_start: 0.7500 (mt0) cc_final: 0.7248 (mp10) REVERT: B 160 ASP cc_start: 0.7174 (t70) cc_final: 0.6872 (t70) REVERT: B 185 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 420 VAL cc_start: 0.8194 (p) cc_final: 0.7899 (m) REVERT: B 446 LEU cc_start: 0.8413 (mt) cc_final: 0.8189 (mt) REVERT: B 449 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6954 (tm-30) REVERT: B 560 ASP cc_start: 0.8048 (m-30) cc_final: 0.7729 (m-30) REVERT: B 631 TYR cc_start: 0.7762 (m-80) cc_final: 0.7310 (m-80) REVERT: C 41 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6635 (mt-10) REVERT: C 45 ASP cc_start: 0.7085 (m-30) cc_final: 0.6758 (m-30) REVERT: C 79 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6965 (mttt) REVERT: C 238 GLU cc_start: 0.6132 (pp20) cc_final: 0.5869 (pp20) REVERT: C 344 GLU cc_start: 0.7042 (pm20) cc_final: 0.6545 (pm20) REVERT: C 454 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6999 (tm-30) REVERT: C 592 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.7256 (ttm170) REVERT: C 644 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6572 (mm-30) REVERT: D 35 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5845 (tp30) REVERT: D 160 ASP cc_start: 0.6748 (p0) cc_final: 0.6518 (p0) REVERT: D 185 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8247 (p) REVERT: D 188 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7687 (p-80) REVERT: D 468 ASP cc_start: 0.5755 (OUTLIER) cc_final: 0.5485 (t70) outliers start: 93 outliers final: 38 residues processed: 556 average time/residue: 1.4170 time to fit residues: 889.4240 Evaluate side-chains 542 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 498 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 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 127 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 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 230 optimal weight: 0.3980 chunk 175 optimal weight: 0.0980 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 122 optimal weight: 0.0270 chunk 221 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS B 16 ASN B 385 ASN B 540 HIS B 541 HIS C 30 HIS D 639 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21573 Z= 0.197 Angle : 0.570 13.931 29153 Z= 0.301 Chirality : 0.043 0.169 3128 Planarity : 0.004 0.054 3712 Dihedral : 10.898 86.795 3201 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.22 % Allowed : 18.03 % 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: -0.73 (0.17), residues: 2552 helix: 0.87 (0.16), residues: 1194 sheet: 0.26 (0.36), residues: 254 loop : -2.28 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 425 HIS 0.014 0.001 HIS B 540 PHE 0.030 0.002 PHE B 526 TYR 0.013 0.001 TYR A 236 ARG 0.009 0.000 ARG D 419 *********************** 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 589 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 517 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 41 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7070 (mt-10) REVERT: A 45 ASP cc_start: 0.7270 (m-30) cc_final: 0.7062 (m-30) REVERT: A 60 ILE cc_start: 0.8057 (tp) cc_final: 0.7766 (tt) REVERT: A 154 ASN cc_start: 0.7988 (t0) cc_final: 0.7781 (t0) REVERT: A 507 LEU cc_start: 0.8765 (mt) cc_final: 0.8548 (mp) REVERT: A 606 TYR cc_start: 0.6978 (p90) cc_final: 0.6660 (p90) REVERT: B 41 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6548 (mm-30) REVERT: B 160 ASP cc_start: 0.7196 (t70) cc_final: 0.6885 (t70) REVERT: B 185 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8235 (p) REVERT: B 420 VAL cc_start: 0.8202 (p) cc_final: 0.7906 (m) REVERT: B 446 LEU cc_start: 0.8363 (mt) cc_final: 0.8129 (mt) REVERT: B 449 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6957 (tm-30) REVERT: B 560 ASP cc_start: 0.8076 (m-30) cc_final: 0.7742 (m-30) REVERT: B 631 TYR cc_start: 0.7684 (m-80) cc_final: 0.7255 (m-80) REVERT: C 2 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7462 (mp) REVERT: C 41 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6615 (mt-10) REVERT: C 45 ASP cc_start: 0.7056 (m-30) cc_final: 0.6779 (m-30) REVERT: C 52 LYS cc_start: 0.7641 (mmmm) cc_final: 0.7313 (mmmm) REVERT: C 65 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: C 79 LYS cc_start: 0.7233 (mmtt) cc_final: 0.6944 (mttt) REVERT: C 238 GLU cc_start: 0.6083 (pp20) cc_final: 0.5792 (pp20) REVERT: C 344 GLU cc_start: 0.7068 (pm20) cc_final: 0.6588 (pm20) REVERT: C 454 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6982 (tm-30) REVERT: C 592 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.7227 (ttm170) REVERT: D 35 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5860 (tm-30) REVERT: D 185 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8248 (p) REVERT: D 420 VAL cc_start: 0.8224 (p) cc_final: 0.7957 (m) REVERT: D 468 ASP cc_start: 0.5687 (OUTLIER) cc_final: 0.5393 (t70) outliers start: 72 outliers final: 29 residues processed: 553 average time/residue: 1.2213 time to fit residues: 762.4178 Evaluate side-chains 552 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 516 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 24 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 A residue 382 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 642 TYR 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 495 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 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 55 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 65 GLU 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 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 240 VAL Chi-restraints excluded: chain D residue 273 ARG 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 206 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 chunk 3 optimal weight: 0.0270 chunk 184 optimal weight: 0.0970 chunk 102 optimal weight: 0.0060 chunk 211 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.2652 ------------------------------------------------------------------------------- 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 385 ASN B 540 HIS ** B 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 540 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2282 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: