Starting phenix.real_space_refine on Mon Aug 25 16:15:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j78_61197/08_2025/9j78_61197.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j78_61197/08_2025/9j78_61197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j78_61197/08_2025/9j78_61197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j78_61197/08_2025/9j78_61197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j78_61197/08_2025/9j78_61197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j78_61197/08_2025/9j78_61197.map" } resolution = 3.88 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5212 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 165 5.16 5 C 15945 2.51 5 N 4352 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 25192 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 798 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "B" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5947 Classifications: {'peptide': 725} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 705} Chain breaks: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "F" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "A" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5947 Classifications: {'peptide': 725} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 705} Chain breaks: 1 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 159 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "I" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 113 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.18, per 1000 atoms: 0.25 Number of scatterers: 25192 At special positions: 0 Unit cell: (139.4, 171.38, 199.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 165 16.00 O 4730 8.00 N 4352 7.00 C 15945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6038 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 11 sheets defined 63.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'H' and resid 23 through 36 Processing helix chain 'H' and resid 38 through 42 Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.644A pdb=" N THR B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 Processing helix chain 'B' and resid 53 through 79 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 156 through 173 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 208 through 229 Processing helix chain 'B' and resid 231 through 254 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 271 Processing helix chain 'B' and resid 274 through 289 removed outlier: 4.195A pdb=" N HIS B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 304 removed outlier: 3.546A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 329 removed outlier: 3.981A pdb=" N MET B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 356 removed outlier: 3.802A pdb=" N VAL B 340 " --> pdb=" O PRO B 336 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 377 removed outlier: 3.605A pdb=" N ASN B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 400 removed outlier: 3.691A pdb=" N LEU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 423 Processing helix chain 'B' and resid 427 through 445 Processing helix chain 'B' and resid 450 through 466 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 532 through 547 removed outlier: 4.428A pdb=" N SER B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 removed outlier: 3.720A pdb=" N ASN B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 604 Processing helix chain 'B' and resid 606 through 621 Processing helix chain 'B' and resid 661 through 692 Processing helix chain 'B' and resid 695 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 728 removed outlier: 3.511A pdb=" N ILE B 718 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 83 Processing helix chain 'C' and resid 101 through 110 removed outlier: 4.289A pdb=" N PHE C 109 " --> pdb=" O MET C 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'J' and resid 2 through 14 Processing helix chain 'J' and resid 17 through 24 Processing helix chain 'J' and resid 29 through 37 Processing helix chain 'J' and resid 48 through 56 removed outlier: 3.569A pdb=" N ASN J 56 " --> pdb=" O ILE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 69 removed outlier: 3.950A pdb=" N VAL J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 99 removed outlier: 3.619A pdb=" N GLY J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 110 removed outlier: 3.627A pdb=" N VAL J 104 " --> pdb=" O HIS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 132 Processing helix chain 'J' and resid 133 through 143 Processing helix chain 'J' and resid 156 through 164 removed outlier: 3.681A pdb=" N LYS J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 175 removed outlier: 3.743A pdb=" N VAL J 170 " --> pdb=" O HIS J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 198 removed outlier: 3.560A pdb=" N ALA J 197 " --> pdb=" O PHE J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 221 through 229 Processing helix chain 'J' and resid 231 through 240 Processing helix chain 'J' and resid 245 through 260 Processing helix chain 'J' and resid 268 through 284 Processing helix chain 'J' and resid 299 through 303 Processing helix chain 'J' and resid 310 through 316 Processing helix chain 'J' and resid 320 through 337 Processing helix chain 'J' and resid 343 through 357 removed outlier: 4.262A pdb=" N ILE J 347 " --> pdb=" O VAL J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 377 Processing helix chain 'J' and resid 381 through 398 Processing helix chain 'J' and resid 403 through 428 removed outlier: 3.525A pdb=" N ILE J 407 " --> pdb=" O LYS J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 432 through 457 Processing helix chain 'J' and resid 460 through 476 Processing helix chain 'J' and resid 486 through 493 removed outlier: 3.574A pdb=" N ALA J 491 " --> pdb=" O LEU J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 507 removed outlier: 4.108A pdb=" N VAL J 506 " --> pdb=" O HIS J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 521 Processing helix chain 'J' and resid 534 through 540 removed outlier: 3.567A pdb=" N VAL J 540 " --> pdb=" O LEU J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 563 removed outlier: 3.780A pdb=" N LEU J 552 " --> pdb=" O ASP J 548 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE J 555 " --> pdb=" O THR J 551 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER J 558 " --> pdb=" O SER J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 593 Processing helix chain 'J' and resid 596 through 609 Processing helix chain 'J' and resid 617 through 626 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.562A pdb=" N ALA F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 24 removed outlier: 3.877A pdb=" N ALA F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.730A pdb=" N ILE F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU F 35 " --> pdb=" O ASP F 31 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 36 " --> pdb=" O ILE F 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 36' Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.644A pdb=" N VAL F 62 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'F' and resid 100 through 110 removed outlier: 3.942A pdb=" N VAL F 104 " --> pdb=" O HIS F 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS F 105 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 107 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 removed outlier: 3.573A pdb=" N ALA F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 Processing helix chain 'F' and resid 156 through 164 Processing helix chain 'F' and resid 166 through 174 removed outlier: 4.065A pdb=" N VAL F 170 " --> pdb=" O HIS F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 190 through 195 Processing helix chain 'F' and resid 199 through 209 removed outlier: 4.298A pdb=" N LYS F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TRP F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 229 removed outlier: 3.543A pdb=" N ALA F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 239 removed outlier: 3.657A pdb=" N LEU F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 262 removed outlier: 3.848A pdb=" N ILE F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA F 252 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 284 removed outlier: 3.540A pdb=" N TYR F 273 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 317 removed outlier: 3.516A pdb=" N ILE F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 337 removed outlier: 3.729A pdb=" N LEU F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE F 330 " --> pdb=" O MET F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 357 Processing helix chain 'F' and resid 360 through 377 Processing helix chain 'F' and resid 381 through 398 Processing helix chain 'F' and resid 403 through 428 removed outlier: 3.580A pdb=" N ILE F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 457 Processing helix chain 'F' and resid 460 through 478 Processing helix chain 'F' and resid 486 through 491 Processing helix chain 'F' and resid 501 through 506 Processing helix chain 'F' and resid 511 through 522 removed outlier: 3.554A pdb=" N THR F 515 " --> pdb=" O ASN F 511 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 516 " --> pdb=" O ALA F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 540 Processing helix chain 'F' and resid 548 through 563 Processing helix chain 'F' and resid 582 through 593 Processing helix chain 'F' and resid 596 through 609 Processing helix chain 'F' and resid 617 through 627 removed outlier: 4.084A pdb=" N GLU F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE F 623 " --> pdb=" O THR F 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.605A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 53 through 78 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.739A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.571A pdb=" N GLU A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 230 removed outlier: 3.632A pdb=" N GLU A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 3.535A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.657A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 removed outlier: 4.278A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 308 through 325 removed outlier: 3.677A pdb=" N HIS A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.552A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.678A pdb=" N ALA A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 removed outlier: 3.501A pdb=" N LEU A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 399 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.819A pdb=" N ASP A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.867A pdb=" N HIS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 465 removed outlier: 3.700A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 496 removed outlier: 3.922A pdb=" N LYS A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 579 through 591 removed outlier: 4.180A pdb=" N VAL A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 585 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 603 removed outlier: 3.874A pdb=" N ASP A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'A' and resid 661 through 692 removed outlier: 3.622A pdb=" N MET A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 683 " --> pdb=" O TYR A 679 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 707 removed outlier: 3.880A pdb=" N GLN A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 705 " --> pdb=" O GLN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 3.856A pdb=" N LYS A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS A 721 " --> pdb=" O MET A 717 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 38 Processing helix chain 'G' and resid 40 through 47 Processing helix chain 'G' and resid 66 through 83 Processing helix chain 'G' and resid 102 through 111 Processing helix chain 'K' and resid 132 through 137 Processing helix chain 'L' and resid 132 through 137 removed outlier: 3.629A pdb=" N UNK L 137 " --> pdb=" O UNK L 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 12 through 18 removed outlier: 8.515A pdb=" N VAL H 75 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N MET H 6 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU H 77 " --> pdb=" O MET H 6 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG H 8 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.250A pdb=" N LEU B 512 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N TRP E 35 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 574 through 578 removed outlier: 6.845A pdb=" N THR B 561 " --> pdb=" O TRP E 27 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TRP E 27 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AA7, first strand: chain 'D' and resid 12 through 18 Processing sheet with id=AA8, first strand: chain 'J' and resid 40 through 42 Processing sheet with id=AA9, first strand: chain 'F' and resid 40 through 42 Processing sheet with id=AB1, first strand: chain 'A' and resid 577 through 578 removed outlier: 3.869A pdb=" N ASN I 28 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.788A pdb=" N VAL G 60 " --> pdb=" O LYS G 20 " (cutoff:3.500A) 1330 hydrogen bonds defined for protein. 3912 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: 4.66 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8312 1.34 - 1.46: 3601 1.46 - 1.57: 13491 1.57 - 1.69: 0 1.69 - 1.81: 266 Bond restraints: 25670 Sorted by residual: bond pdb=" C ALA A 522 " pdb=" N PRO A 523 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.64e+00 bond pdb=" CB ASN C 108 " pdb=" CG ASN C 108 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.03e+00 bond pdb=" CG LEU C 104 " pdb=" CD1 LEU C 104 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.00e+00 bond pdb=" C LEU B 3 " pdb=" N LYS B 4 " ideal model delta sigma weight residual 1.329 1.289 0.039 3.03e-02 1.09e+03 1.69e+00 bond pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.58e-02 4.01e+03 1.65e+00 ... (remaining 25665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 34278 2.40 - 4.80: 346 4.80 - 7.21: 57 7.21 - 9.61: 5 9.61 - 12.01: 2 Bond angle restraints: 34688 Sorted by residual: angle pdb=" N ILE J 555 " pdb=" CA ILE J 555 " pdb=" C ILE J 555 " ideal model delta sigma weight residual 112.96 108.92 4.04 1.00e+00 1.00e+00 1.63e+01 angle pdb=" N VAL A 152 " pdb=" CA VAL A 152 " pdb=" C VAL A 152 " ideal model delta sigma weight residual 111.81 108.54 3.27 8.60e-01 1.35e+00 1.45e+01 angle pdb=" N GLN B 463 " pdb=" CA GLN B 463 " pdb=" CB GLN B 463 " ideal model delta sigma weight residual 110.39 116.67 -6.28 1.66e+00 3.63e-01 1.43e+01 angle pdb=" N VAL F 506 " pdb=" CA VAL F 506 " pdb=" C VAL F 506 " ideal model delta sigma weight residual 113.53 109.85 3.68 9.80e-01 1.04e+00 1.41e+01 angle pdb=" C TYR F 84 " pdb=" N VAL F 85 " pdb=" CA VAL F 85 " ideal model delta sigma weight residual 121.97 128.63 -6.66 1.80e+00 3.09e-01 1.37e+01 ... (remaining 34683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13795 17.89 - 35.78: 1511 35.78 - 53.68: 261 53.68 - 71.57: 60 71.57 - 89.46: 22 Dihedral angle restraints: 15649 sinusoidal: 6359 harmonic: 9290 Sorted by residual: dihedral pdb=" CA TYR B 730 " pdb=" C TYR B 730 " pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta harmonic sigma weight residual 180.00 152.26 27.74 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA VAL A 47 " pdb=" C VAL A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PHE A 188 " pdb=" C PHE A 188 " pdb=" N VAL A 189 " pdb=" CA VAL A 189 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 15646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3443 0.063 - 0.126: 431 0.126 - 0.189: 33 0.189 - 0.252: 4 0.252 - 0.315: 1 Chirality restraints: 3912 Sorted by residual: chirality pdb=" CG LEU B 512 " pdb=" CB LEU B 512 " pdb=" CD1 LEU B 512 " pdb=" CD2 LEU B 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL G 31 " pdb=" CA VAL G 31 " pdb=" CG1 VAL G 31 " pdb=" CG2 VAL G 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B 653 " pdb=" CA ILE B 653 " pdb=" CG1 ILE B 653 " pdb=" CG2 ILE B 653 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 3909 not shown) Planarity restraints: 4454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 522 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 523 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 48 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO J 49 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO J 49 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO J 49 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 335 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 336 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " -0.035 5.00e-02 4.00e+02 ... (remaining 4451 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3112 2.75 - 3.29: 26301 3.29 - 3.83: 44238 3.83 - 4.36: 50011 4.36 - 4.90: 84137 Nonbonded interactions: 207799 Sorted by model distance: nonbonded pdb=" OH TYR J 275 " pdb=" O ILE F 546 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 573 " pdb=" O SER B 646 " model vdw 2.215 3.040 nonbonded pdb=" O LEU A 599 " pdb=" OG1 THR A 603 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP A 170 " pdb=" OH TYR A 253 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR C 79 " pdb=" O PRO C 91 " model vdw 2.241 3.040 ... (remaining 207794 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 2 through 81 or resid 85 through 100)) } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 132 through 139) selection = chain 'L' } 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 group one per residue 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: 25.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 24.350 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25670 Z= 0.160 Angle : 0.629 12.009 34688 Z= 0.334 Chirality : 0.043 0.315 3912 Planarity : 0.005 0.067 4454 Dihedral : 15.311 89.461 9611 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.93 (0.14), residues: 3098 helix: 0.06 (0.11), residues: 1837 sheet: -2.24 (0.66), residues: 58 loop : -1.51 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 551 TYR 0.017 0.001 TYR C 79 PHE 0.030 0.002 PHE B 548 TRP 0.020 0.002 TRP A 35 HIS 0.006 0.001 HIS J 369 Details of bonding type rmsd covalent geometry : bond 0.00356 (25670) covalent geometry : angle 0.62850 (34688) hydrogen bonds : bond 0.19027 ( 1330) hydrogen bonds : angle 6.56808 ( 3912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8282 (pttm) REVERT: H 90 ILE cc_start: 0.7910 (mt) cc_final: 0.7491 (pt) REVERT: B 198 PHE cc_start: 0.8283 (p90) cc_final: 0.7407 (p90) REVERT: B 311 MET cc_start: 0.9145 (tpt) cc_final: 0.8582 (tpt) REVERT: B 449 MET cc_start: 0.8433 (ppp) cc_final: 0.8119 (ptm) REVERT: C 17 MET cc_start: 0.7787 (tmm) cc_final: 0.6989 (tmm) REVERT: C 30 ILE cc_start: 0.8964 (mp) cc_final: 0.8685 (mt) REVERT: C 69 VAL cc_start: 0.8886 (t) cc_final: 0.8581 (p) REVERT: C 75 MET cc_start: 0.8615 (mtt) cc_final: 0.8206 (mtt) REVERT: D 2 ASP cc_start: 0.6477 (p0) cc_final: 0.5336 (p0) REVERT: D 79 PHE cc_start: 0.7535 (m-80) cc_final: 0.7203 (m-80) REVERT: J 174 LEU cc_start: 0.9209 (mt) cc_final: 0.8813 (mt) REVERT: J 201 ASP cc_start: 0.8678 (p0) cc_final: 0.8336 (p0) REVERT: J 326 MET cc_start: 0.9054 (mmt) cc_final: 0.8833 (mmp) REVERT: J 357 ASN cc_start: 0.8580 (m-40) cc_final: 0.8225 (t0) REVERT: J 398 LEU cc_start: 0.9227 (mp) cc_final: 0.8952 (tt) REVERT: A 137 MET cc_start: 0.8199 (ptp) cc_final: 0.7832 (ptp) REVERT: A 480 MET cc_start: 0.7962 (tpt) cc_final: 0.7683 (mmm) REVERT: A 657 MET cc_start: 0.7038 (mpp) cc_final: 0.6641 (pmm) REVERT: A 678 MET cc_start: 0.8152 (ppp) cc_final: 0.7771 (ppp) REVERT: A 688 MET cc_start: 0.5470 (tpp) cc_final: 0.4854 (tpt) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.1928 time to fit residues: 137.8563 Evaluate side-chains 267 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 427 ASN J 473 ASN J 611 ASN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 508 GLN A 557 HIS A 600 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.104628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070120 restraints weight = 85534.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071108 restraints weight = 54035.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071392 restraints weight = 36538.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.071851 restraints weight = 34275.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071899 restraints weight = 29034.661| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25670 Z= 0.159 Angle : 0.606 9.198 34688 Z= 0.321 Chirality : 0.040 0.175 3912 Planarity : 0.004 0.056 4454 Dihedral : 4.398 24.899 3413 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.97 % Allowed : 9.88 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.25 (0.15), residues: 3098 helix: 0.73 (0.12), residues: 1883 sheet: -2.62 (0.58), residues: 62 loop : -1.49 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 708 TYR 0.024 0.001 TYR G 79 PHE 0.040 0.002 PHE B 198 TRP 0.019 0.002 TRP F 209 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00347 (25670) covalent geometry : angle 0.60598 (34688) hydrogen bonds : bond 0.04866 ( 1330) hydrogen bonds : angle 4.86695 ( 3912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 310 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 LYS cc_start: 0.8845 (mmpt) cc_final: 0.8497 (ptpp) REVERT: H 90 ILE cc_start: 0.7899 (mt) cc_final: 0.7528 (pt) REVERT: B 449 MET cc_start: 0.8655 (ppp) cc_final: 0.8350 (tmm) REVERT: B 476 MET cc_start: 0.8853 (mtm) cc_final: 0.8612 (mtm) REVERT: B 653 ILE cc_start: 0.8779 (mp) cc_final: 0.8397 (tp) REVERT: C 17 MET cc_start: 0.8133 (tmm) cc_final: 0.7725 (tmm) REVERT: C 18 TYR cc_start: 0.8135 (m-80) cc_final: 0.7525 (m-10) REVERT: C 32 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8762 (tptp) REVERT: C 69 VAL cc_start: 0.9148 (t) cc_final: 0.8877 (p) REVERT: C 76 TYR cc_start: 0.8964 (t80) cc_final: 0.8536 (t80) REVERT: C 79 TYR cc_start: 0.9052 (t80) cc_final: 0.8834 (t80) REVERT: C 105 MET cc_start: 0.8454 (ttm) cc_final: 0.8154 (ttt) REVERT: D 25 PHE cc_start: 0.8034 (t80) cc_final: 0.7664 (t80) REVERT: D 32 GLU cc_start: 0.8388 (tt0) cc_final: 0.8186 (tt0) REVERT: D 79 PHE cc_start: 0.7481 (m-80) cc_final: 0.7252 (m-80) REVERT: J 201 ASP cc_start: 0.8865 (p0) cc_final: 0.8501 (p0) REVERT: J 326 MET cc_start: 0.9151 (mmt) cc_final: 0.8896 (mmp) REVERT: J 357 ASN cc_start: 0.8859 (m-40) cc_final: 0.8486 (t0) REVERT: J 398 LEU cc_start: 0.9430 (mp) cc_final: 0.9159 (tt) REVERT: J 585 SER cc_start: 0.8986 (m) cc_final: 0.8782 (p) REVERT: A 249 ARG cc_start: 0.8571 (ttm110) cc_final: 0.8247 (ttm-80) REVERT: A 311 MET cc_start: 0.8342 (ttp) cc_final: 0.8027 (ttp) REVERT: A 444 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8818 (mt) REVERT: A 480 MET cc_start: 0.8210 (tpt) cc_final: 0.7801 (mmm) REVERT: A 527 PHE cc_start: 0.6430 (p90) cc_final: 0.5253 (p90) REVERT: A 657 MET cc_start: 0.7601 (mpp) cc_final: 0.7120 (pmm) REVERT: A 688 MET cc_start: 0.4755 (tpp) cc_final: 0.4296 (tpt) outliers start: 27 outliers final: 17 residues processed: 326 average time/residue: 0.1683 time to fit residues: 88.3119 Evaluate side-chains 274 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 427 ASN Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 261 optimal weight: 0.5980 chunk 165 optimal weight: 0.4980 chunk 240 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 257 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 HIS ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.104973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.069974 restraints weight = 85394.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071511 restraints weight = 52799.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.071620 restraints weight = 37689.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.072372 restraints weight = 30377.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072189 restraints weight = 26780.156| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25670 Z= 0.147 Angle : 0.567 9.215 34688 Z= 0.300 Chirality : 0.039 0.250 3912 Planarity : 0.004 0.056 4454 Dihedral : 4.273 24.067 3413 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.19 % Allowed : 12.63 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.06 (0.15), residues: 3098 helix: 0.93 (0.12), residues: 1892 sheet: -2.70 (0.55), residues: 62 loop : -1.51 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 177 TYR 0.022 0.001 TYR B 510 PHE 0.028 0.002 PHE A 638 TRP 0.018 0.002 TRP I 35 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00325 (25670) covalent geometry : angle 0.56682 (34688) hydrogen bonds : bond 0.04358 ( 1330) hydrogen bonds : angle 4.61142 ( 3912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 LYS cc_start: 0.8813 (mmpt) cc_final: 0.8485 (ptpp) REVERT: H 57 LEU cc_start: 0.8582 (mt) cc_final: 0.8227 (tp) REVERT: B 449 MET cc_start: 0.8627 (ppp) cc_final: 0.8341 (tmm) REVERT: B 476 MET cc_start: 0.8925 (mtm) cc_final: 0.8532 (mtm) REVERT: B 582 MET cc_start: 0.8858 (ttp) cc_final: 0.8420 (tmm) REVERT: B 702 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: C 17 MET cc_start: 0.8033 (tmm) cc_final: 0.7821 (tmm) REVERT: C 32 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8731 (mmmt) REVERT: C 69 VAL cc_start: 0.9106 (t) cc_final: 0.8794 (p) REVERT: D 25 PHE cc_start: 0.7996 (t80) cc_final: 0.7600 (t80) REVERT: D 32 GLU cc_start: 0.8296 (tt0) cc_final: 0.8036 (tt0) REVERT: J 201 ASP cc_start: 0.8831 (p0) cc_final: 0.8503 (p0) REVERT: J 202 ILE cc_start: 0.9004 (mt) cc_final: 0.8791 (mt) REVERT: J 326 MET cc_start: 0.9147 (mmt) cc_final: 0.8902 (mmp) REVERT: J 357 ASN cc_start: 0.8719 (m-40) cc_final: 0.8353 (t0) REVERT: J 398 LEU cc_start: 0.9335 (mp) cc_final: 0.9074 (tt) REVERT: F 395 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8938 (ptp) REVERT: A 146 MET cc_start: 0.9063 (mmp) cc_final: 0.8568 (mmm) REVERT: A 311 MET cc_start: 0.8288 (ttp) cc_final: 0.7943 (ttp) REVERT: A 475 ARG cc_start: 0.9176 (tpt-90) cc_final: 0.8914 (tpm170) REVERT: A 527 PHE cc_start: 0.6460 (p90) cc_final: 0.5173 (p90) REVERT: A 559 LEU cc_start: 0.9117 (mt) cc_final: 0.8878 (mt) REVERT: A 657 MET cc_start: 0.7633 (mpp) cc_final: 0.7133 (pmm) REVERT: A 688 MET cc_start: 0.4612 (tpp) cc_final: 0.4197 (tpt) REVERT: I 26 LYS cc_start: 0.8535 (tmmt) cc_final: 0.7884 (tptp) outliers start: 33 outliers final: 16 residues processed: 309 average time/residue: 0.1676 time to fit residues: 84.7454 Evaluate side-chains 258 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain F residue 395 MET Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 596 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 80 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 263 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS D 65 GLN ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.103185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068459 restraints weight = 85098.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069835 restraints weight = 54713.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069908 restraints weight = 36067.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070269 restraints weight = 35521.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070351 restraints weight = 30615.410| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25670 Z= 0.217 Angle : 0.613 8.758 34688 Z= 0.320 Chirality : 0.040 0.168 3912 Planarity : 0.004 0.114 4454 Dihedral : 4.341 23.924 3413 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.73 % Allowed : 14.54 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.05 (0.15), residues: 3098 helix: 1.03 (0.12), residues: 1887 sheet: -2.54 (0.54), residues: 68 loop : -1.48 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.036 0.002 TYR C 79 PHE 0.023 0.002 PHE B 548 TRP 0.016 0.002 TRP B 14 HIS 0.009 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00493 (25670) covalent geometry : angle 0.61283 (34688) hydrogen bonds : bond 0.04284 ( 1330) hydrogen bonds : angle 4.61093 ( 3912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 LYS cc_start: 0.8799 (mmpt) cc_final: 0.8226 (ptpp) REVERT: H 57 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8161 (tp) REVERT: B 476 MET cc_start: 0.8790 (mtm) cc_final: 0.8397 (mtm) REVERT: B 605 MET cc_start: 0.8686 (ppp) cc_final: 0.8279 (ppp) REVERT: B 653 ILE cc_start: 0.8803 (mp) cc_final: 0.8284 (tp) REVERT: B 702 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: C 69 VAL cc_start: 0.9148 (t) cc_final: 0.8875 (p) REVERT: C 105 MET cc_start: 0.8621 (ttm) cc_final: 0.8350 (ttt) REVERT: D 25 PHE cc_start: 0.7957 (t80) cc_final: 0.7737 (t80) REVERT: D 32 GLU cc_start: 0.8425 (tt0) cc_final: 0.8120 (tt0) REVERT: J 201 ASP cc_start: 0.8786 (p0) cc_final: 0.8450 (p0) REVERT: J 202 ILE cc_start: 0.9010 (mt) cc_final: 0.8793 (mt) REVERT: J 326 MET cc_start: 0.9175 (mmt) cc_final: 0.8874 (mmp) REVERT: J 357 ASN cc_start: 0.8800 (m-40) cc_final: 0.8419 (t0) REVERT: J 398 LEU cc_start: 0.9395 (mp) cc_final: 0.9142 (tt) REVERT: J 627 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.4641 (m-70) REVERT: A 475 ARG cc_start: 0.9188 (tpt-90) cc_final: 0.8952 (tpm170) REVERT: A 480 MET cc_start: 0.7581 (mmm) cc_final: 0.6926 (mmp) REVERT: A 651 PHE cc_start: 0.8012 (t80) cc_final: 0.7726 (t80) REVERT: A 657 MET cc_start: 0.7654 (mpp) cc_final: 0.7142 (pmm) REVERT: A 688 MET cc_start: 0.4556 (tpp) cc_final: 0.4122 (tpt) outliers start: 48 outliers final: 29 residues processed: 291 average time/residue: 0.1651 time to fit residues: 78.2874 Evaluate side-chains 267 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 390 GLN Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain F residue 209 TRP Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain G residue 52 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 13 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 303 optimal weight: 0.4980 chunk 126 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN D 65 GLN J 340 ASN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 508 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.104462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.068090 restraints weight = 84635.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069866 restraints weight = 49298.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.071061 restraints weight = 34738.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071734 restraints weight = 27818.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072331 restraints weight = 24310.191| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25670 Z= 0.133 Angle : 0.560 9.957 34688 Z= 0.292 Chirality : 0.038 0.172 3912 Planarity : 0.004 0.060 4454 Dihedral : 4.248 23.050 3413 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.59 % Allowed : 15.87 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.21 (0.15), residues: 3098 helix: 1.18 (0.12), residues: 1889 sheet: -2.51 (0.53), residues: 68 loop : -1.47 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 482 TYR 0.034 0.001 TYR C 79 PHE 0.028 0.002 PHE A 527 TRP 0.013 0.001 TRP A 35 HIS 0.004 0.001 HIS J 369 Details of bonding type rmsd covalent geometry : bond 0.00298 (25670) covalent geometry : angle 0.56031 (34688) hydrogen bonds : bond 0.03995 ( 1330) hydrogen bonds : angle 4.40104 ( 3912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 LYS cc_start: 0.8645 (mmpt) cc_final: 0.8031 (ptpp) REVERT: H 57 LEU cc_start: 0.8536 (mt) cc_final: 0.8103 (tp) REVERT: B 86 MET cc_start: 0.8705 (mmp) cc_final: 0.8431 (mmp) REVERT: B 476 MET cc_start: 0.8759 (mtm) cc_final: 0.8314 (mtm) REVERT: B 653 ILE cc_start: 0.8621 (mp) cc_final: 0.8250 (tp) REVERT: B 702 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: C 69 VAL cc_start: 0.9045 (t) cc_final: 0.8729 (p) REVERT: C 105 MET cc_start: 0.8627 (ttm) cc_final: 0.8375 (ttt) REVERT: D 32 GLU cc_start: 0.8209 (tt0) cc_final: 0.7354 (tm-30) REVERT: J 201 ASP cc_start: 0.8691 (p0) cc_final: 0.8371 (p0) REVERT: J 326 MET cc_start: 0.9132 (mmt) cc_final: 0.8852 (mmp) REVERT: J 357 ASN cc_start: 0.8568 (m-40) cc_final: 0.8257 (t0) REVERT: J 386 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8994 (mt) REVERT: J 398 LEU cc_start: 0.9276 (mp) cc_final: 0.8985 (tt) REVERT: J 627 HIS cc_start: 0.6552 (OUTLIER) cc_final: 0.5734 (m-70) REVERT: F 406 ASP cc_start: 0.8125 (m-30) cc_final: 0.7618 (m-30) REVERT: F 416 LEU cc_start: 0.9141 (mp) cc_final: 0.8748 (tp) REVERT: A 476 MET cc_start: 0.8582 (ptp) cc_final: 0.8249 (ptp) REVERT: A 539 MET cc_start: 0.7773 (tpp) cc_final: 0.7366 (tpp) REVERT: A 657 MET cc_start: 0.7551 (mpp) cc_final: 0.7024 (pmm) REVERT: A 688 MET cc_start: 0.4775 (tpp) cc_final: 0.4262 (tpt) outliers start: 44 outliers final: 22 residues processed: 302 average time/residue: 0.1562 time to fit residues: 76.5139 Evaluate side-chains 262 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 146 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 282 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN F 143 ASN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.101942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066838 restraints weight = 86240.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.068365 restraints weight = 53528.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.068625 restraints weight = 36938.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.069183 restraints weight = 30396.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.069101 restraints weight = 27335.065| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25670 Z= 0.252 Angle : 0.656 8.642 34688 Z= 0.338 Chirality : 0.042 0.210 3912 Planarity : 0.004 0.060 4454 Dihedral : 4.362 23.887 3413 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.56 % Allowed : 16.45 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.13 (0.15), residues: 3098 helix: 1.10 (0.12), residues: 1894 sheet: -2.38 (0.58), residues: 59 loop : -1.51 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 43 TYR 0.032 0.002 TYR C 79 PHE 0.030 0.002 PHE B 112 TRP 0.013 0.002 TRP B 14 HIS 0.010 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00569 (25670) covalent geometry : angle 0.65550 (34688) hydrogen bonds : bond 0.04259 ( 1330) hydrogen bonds : angle 4.58865 ( 3912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 243 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 LYS cc_start: 0.8780 (mmpt) cc_final: 0.8191 (ptpp) REVERT: H 57 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 39 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: B 86 MET cc_start: 0.8853 (mmp) cc_final: 0.8546 (mmp) REVERT: B 605 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8246 (ppp) REVERT: B 622 MET cc_start: 0.8352 (tpp) cc_final: 0.7980 (mmm) REVERT: B 702 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: C 17 MET cc_start: 0.8117 (tmm) cc_final: 0.7828 (tmm) REVERT: C 37 LEU cc_start: 0.8882 (tp) cc_final: 0.8672 (tp) REVERT: C 69 VAL cc_start: 0.9136 (t) cc_final: 0.8873 (p) REVERT: D 32 GLU cc_start: 0.8462 (tt0) cc_final: 0.7737 (tm-30) REVERT: D 42 GLN cc_start: 0.7603 (pm20) cc_final: 0.7389 (pm20) REVERT: J 201 ASP cc_start: 0.8806 (p0) cc_final: 0.8471 (p0) REVERT: J 357 ASN cc_start: 0.8757 (m-40) cc_final: 0.8359 (t0) REVERT: J 398 LEU cc_start: 0.9336 (mp) cc_final: 0.9081 (tt) REVERT: F 406 ASP cc_start: 0.8465 (m-30) cc_final: 0.8208 (m-30) REVERT: A 146 MET cc_start: 0.9164 (mmp) cc_final: 0.8587 (mmm) REVERT: A 311 MET cc_start: 0.8562 (ttm) cc_final: 0.8123 (tpp) REVERT: A 476 MET cc_start: 0.8673 (ptp) cc_final: 0.8270 (ptp) REVERT: A 480 MET cc_start: 0.7766 (mmm) cc_final: 0.7072 (mmp) REVERT: A 510 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7818 (t80) REVERT: A 527 PHE cc_start: 0.6684 (p90) cc_final: 0.5890 (p90) REVERT: A 539 MET cc_start: 0.8045 (tpp) cc_final: 0.7601 (tpp) REVERT: A 657 MET cc_start: 0.7692 (mpp) cc_final: 0.7158 (pmm) REVERT: A 688 MET cc_start: 0.4526 (tpp) cc_final: 0.4070 (tpt) REVERT: E 28 ASN cc_start: 0.7350 (t0) cc_final: 0.7103 (t0) outliers start: 71 outliers final: 40 residues processed: 298 average time/residue: 0.1639 time to fit residues: 79.3042 Evaluate side-chains 270 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain F residue 209 TRP Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 510 TYR Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 51 optimal weight: 0.5980 chunk 231 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 269 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 627 HIS F 166 HIS F 565 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.103645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.070016 restraints weight = 85629.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070705 restraints weight = 53000.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070595 restraints weight = 37401.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.070920 restraints weight = 36920.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.071015 restraints weight = 31731.596| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25670 Z= 0.144 Angle : 0.583 11.198 34688 Z= 0.301 Chirality : 0.039 0.211 3912 Planarity : 0.004 0.062 4454 Dihedral : 4.323 25.748 3413 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.70 % Allowed : 17.46 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.27 (0.15), residues: 3098 helix: 1.23 (0.12), residues: 1902 sheet: -2.27 (0.59), residues: 59 loop : -1.49 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 29 TYR 0.041 0.001 TYR A 558 PHE 0.033 0.002 PHE B 112 TRP 0.015 0.002 TRP B 14 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00325 (25670) covalent geometry : angle 0.58319 (34688) hydrogen bonds : bond 0.03962 ( 1330) hydrogen bonds : angle 4.42755 ( 3912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 LYS cc_start: 0.8776 (mmpt) cc_final: 0.8174 (ptpp) REVERT: H 53 ASP cc_start: 0.7696 (m-30) cc_final: 0.6745 (t0) REVERT: H 57 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8077 (tp) REVERT: B 39 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: B 86 MET cc_start: 0.8780 (mmp) cc_final: 0.8479 (mmp) REVERT: B 476 MET cc_start: 0.8740 (mtm) cc_final: 0.8343 (mtm) REVERT: B 576 MET cc_start: 0.8895 (pmm) cc_final: 0.8685 (pmm) REVERT: B 605 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8251 (ppp) REVERT: B 622 MET cc_start: 0.8343 (tpp) cc_final: 0.8048 (mmm) REVERT: B 702 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: C 17 MET cc_start: 0.8224 (tmm) cc_final: 0.7880 (tmm) REVERT: C 37 LEU cc_start: 0.8850 (tp) cc_final: 0.8612 (tp) REVERT: C 56 GLU cc_start: 0.8046 (pm20) cc_final: 0.7637 (pm20) REVERT: C 69 VAL cc_start: 0.9181 (t) cc_final: 0.8915 (p) REVERT: C 108 ASN cc_start: 0.8909 (m-40) cc_final: 0.8680 (m-40) REVERT: D 32 GLU cc_start: 0.8408 (tt0) cc_final: 0.7658 (tm-30) REVERT: D 42 GLN cc_start: 0.7604 (pm20) cc_final: 0.7026 (pm20) REVERT: J 201 ASP cc_start: 0.8763 (p0) cc_final: 0.8452 (p0) REVERT: J 357 ASN cc_start: 0.8811 (m-40) cc_final: 0.8439 (t0) REVERT: J 398 LEU cc_start: 0.9405 (mp) cc_final: 0.9140 (tt) REVERT: J 517 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8436 (tp) REVERT: F 406 ASP cc_start: 0.8503 (m-30) cc_final: 0.8239 (m-30) REVERT: F 416 LEU cc_start: 0.9159 (mp) cc_final: 0.8800 (tp) REVERT: A 151 MET cc_start: 0.8715 (tpp) cc_final: 0.8370 (tpp) REVERT: A 476 MET cc_start: 0.8638 (ptp) cc_final: 0.8189 (ptp) REVERT: A 480 MET cc_start: 0.7683 (mmm) cc_final: 0.7076 (mmp) REVERT: A 527 PHE cc_start: 0.6469 (p90) cc_final: 0.5652 (p90) REVERT: A 539 MET cc_start: 0.8023 (tpp) cc_final: 0.7583 (tpp) REVERT: A 657 MET cc_start: 0.7705 (mpp) cc_final: 0.7181 (pmm) REVERT: A 688 MET cc_start: 0.4620 (tpp) cc_final: 0.4126 (tpt) outliers start: 47 outliers final: 25 residues processed: 281 average time/residue: 0.1406 time to fit residues: 64.6680 Evaluate side-chains 261 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 517 LEU Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 218 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 223 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 HIS F 565 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.102993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068404 restraints weight = 85643.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070053 restraints weight = 53082.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070551 restraints weight = 36101.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070932 restraints weight = 30537.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.070851 restraints weight = 26262.943| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25670 Z= 0.183 Angle : 0.605 11.048 34688 Z= 0.310 Chirality : 0.040 0.192 3912 Planarity : 0.004 0.064 4454 Dihedral : 4.321 25.368 3413 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.28 (0.15), residues: 3098 helix: 1.23 (0.12), residues: 1902 sheet: -2.35 (0.59), residues: 59 loop : -1.49 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 82 TYR 0.035 0.002 TYR C 79 PHE 0.032 0.002 PHE B 112 TRP 0.017 0.002 TRP B 14 HIS 0.015 0.001 HIS F 166 Details of bonding type rmsd covalent geometry : bond 0.00419 (25670) covalent geometry : angle 0.60492 (34688) hydrogen bonds : bond 0.04024 ( 1330) hydrogen bonds : angle 4.47184 ( 3912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 SER cc_start: 0.8902 (t) cc_final: 0.8581 (m) REVERT: H 36 LYS cc_start: 0.8718 (mmpt) cc_final: 0.8107 (ptpp) REVERT: H 53 ASP cc_start: 0.7767 (m-30) cc_final: 0.6821 (t0) REVERT: H 57 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8117 (tp) REVERT: B 39 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: B 86 MET cc_start: 0.8783 (mmp) cc_final: 0.8465 (mmp) REVERT: B 476 MET cc_start: 0.8769 (mtm) cc_final: 0.8368 (mtm) REVERT: B 576 MET cc_start: 0.8905 (pmm) cc_final: 0.8686 (pmm) REVERT: B 605 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8196 (ppp) REVERT: B 702 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: C 56 GLU cc_start: 0.8096 (pm20) cc_final: 0.7647 (pm20) REVERT: C 69 VAL cc_start: 0.9236 (t) cc_final: 0.8950 (p) REVERT: C 108 ASN cc_start: 0.8976 (m-40) cc_final: 0.8730 (m-40) REVERT: D 32 GLU cc_start: 0.8421 (tt0) cc_final: 0.7650 (tm-30) REVERT: D 42 GLN cc_start: 0.7520 (pm20) cc_final: 0.6966 (pm20) REVERT: J 201 ASP cc_start: 0.8716 (p0) cc_final: 0.8390 (p0) REVERT: J 357 ASN cc_start: 0.8713 (m-40) cc_final: 0.8338 (t0) REVERT: J 398 LEU cc_start: 0.9327 (mp) cc_final: 0.9050 (tt) REVERT: J 517 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8477 (tp) REVERT: F 406 ASP cc_start: 0.8384 (m-30) cc_final: 0.8128 (m-30) REVERT: F 416 LEU cc_start: 0.9159 (mp) cc_final: 0.8790 (tp) REVERT: A 146 MET cc_start: 0.9131 (mmp) cc_final: 0.8625 (mmm) REVERT: A 236 MET cc_start: 0.8516 (mtp) cc_final: 0.8120 (mtm) REVERT: A 297 MET cc_start: 0.8297 (ttm) cc_final: 0.8042 (ttp) REVERT: A 311 MET cc_start: 0.8456 (tpp) cc_final: 0.7990 (tpp) REVERT: A 429 ASP cc_start: 0.8102 (m-30) cc_final: 0.7641 (t0) REVERT: A 480 MET cc_start: 0.7757 (mmm) cc_final: 0.6747 (mmp) REVERT: A 510 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 527 PHE cc_start: 0.6480 (p90) cc_final: 0.5649 (p90) REVERT: A 539 MET cc_start: 0.7929 (tpp) cc_final: 0.7515 (tpp) REVERT: A 657 MET cc_start: 0.7699 (mpp) cc_final: 0.7145 (pmm) REVERT: A 665 MET cc_start: 0.7488 (mtt) cc_final: 0.7192 (mpp) REVERT: A 688 MET cc_start: 0.4566 (tpp) cc_final: 0.4072 (tpt) REVERT: G 82 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7478 (mtt180) outliers start: 42 outliers final: 28 residues processed: 267 average time/residue: 0.1566 time to fit residues: 67.9871 Evaluate side-chains 263 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 517 LEU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 537 HIS Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 510 TYR Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 304 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 153 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 238 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.104080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071750 restraints weight = 85743.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.071263 restraints weight = 58737.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071590 restraints weight = 42551.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.071844 restraints weight = 37544.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072011 restraints weight = 34324.262| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25670 Z= 0.133 Angle : 0.582 12.148 34688 Z= 0.299 Chirality : 0.039 0.198 3912 Planarity : 0.004 0.075 4454 Dihedral : 4.282 25.529 3413 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.37 % Allowed : 18.29 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.37 (0.15), residues: 3098 helix: 1.33 (0.12), residues: 1897 sheet: -2.23 (0.61), residues: 59 loop : -1.50 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 29 TYR 0.034 0.001 TYR C 79 PHE 0.037 0.001 PHE B 112 TRP 0.018 0.002 TRP B 14 HIS 0.010 0.001 HIS F 166 Details of bonding type rmsd covalent geometry : bond 0.00302 (25670) covalent geometry : angle 0.58201 (34688) hydrogen bonds : bond 0.03874 ( 1330) hydrogen bonds : angle 4.36329 ( 3912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 SER cc_start: 0.8862 (t) cc_final: 0.8523 (m) REVERT: H 36 LYS cc_start: 0.8708 (mmpt) cc_final: 0.8083 (ptpp) REVERT: H 53 ASP cc_start: 0.7717 (m-30) cc_final: 0.6774 (t0) REVERT: H 57 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8030 (tp) REVERT: B 39 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: B 86 MET cc_start: 0.8757 (mmp) cc_final: 0.8444 (mmp) REVERT: B 576 MET cc_start: 0.8918 (pmm) cc_final: 0.8700 (pmm) REVERT: B 605 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8206 (ppp) REVERT: C 17 MET cc_start: 0.8242 (tmm) cc_final: 0.7441 (tmm) REVERT: C 32 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8567 (mmtt) REVERT: C 69 VAL cc_start: 0.9206 (t) cc_final: 0.8900 (p) REVERT: C 105 MET cc_start: 0.8554 (ttm) cc_final: 0.8135 (ttt) REVERT: C 108 ASN cc_start: 0.8898 (m-40) cc_final: 0.8609 (m-40) REVERT: D 32 GLU cc_start: 0.8399 (tt0) cc_final: 0.7694 (tm-30) REVERT: D 42 GLN cc_start: 0.7548 (pm20) cc_final: 0.7045 (pm20) REVERT: J 201 ASP cc_start: 0.8658 (p0) cc_final: 0.8329 (p0) REVERT: J 357 ASN cc_start: 0.8818 (m-40) cc_final: 0.8421 (t0) REVERT: J 368 LEU cc_start: 0.8859 (mt) cc_final: 0.8585 (tt) REVERT: J 398 LEU cc_start: 0.9390 (mp) cc_final: 0.9131 (tt) REVERT: J 517 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8426 (tp) REVERT: F 406 ASP cc_start: 0.8418 (m-30) cc_final: 0.8216 (m-30) REVERT: F 416 LEU cc_start: 0.9150 (mp) cc_final: 0.8792 (tp) REVERT: A 151 MET cc_start: 0.8778 (tpp) cc_final: 0.8372 (tpp) REVERT: A 236 MET cc_start: 0.8508 (mtp) cc_final: 0.8200 (mtm) REVERT: A 297 MET cc_start: 0.8178 (ttm) cc_final: 0.7978 (ttp) REVERT: A 311 MET cc_start: 0.8442 (tpp) cc_final: 0.7971 (tpp) REVERT: A 429 ASP cc_start: 0.8016 (m-30) cc_final: 0.7601 (t0) REVERT: A 480 MET cc_start: 0.7766 (mmm) cc_final: 0.6919 (mmp) REVERT: A 510 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7651 (t80) REVERT: A 527 PHE cc_start: 0.6437 (p90) cc_final: 0.5630 (p90) REVERT: A 539 MET cc_start: 0.7896 (tpp) cc_final: 0.7461 (tpp) REVERT: A 582 MET cc_start: 0.8049 (ptp) cc_final: 0.6505 (ttt) REVERT: A 657 MET cc_start: 0.7703 (mpp) cc_final: 0.7153 (pmm) REVERT: A 665 MET cc_start: 0.7511 (mtt) cc_final: 0.7193 (mpp) REVERT: A 688 MET cc_start: 0.4644 (tpp) cc_final: 0.4134 (tpt) outliers start: 38 outliers final: 32 residues processed: 265 average time/residue: 0.1390 time to fit residues: 60.5488 Evaluate side-chains 269 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain J residue 517 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 537 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 510 TYR Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 21 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 76 optimal weight: 0.1980 chunk 286 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS A 73 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.101958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066476 restraints weight = 85600.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067953 restraints weight = 53384.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068472 restraints weight = 35986.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069015 restraints weight = 29974.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.068993 restraints weight = 26125.812| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 25670 Z= 0.253 Angle : 0.676 13.147 34688 Z= 0.345 Chirality : 0.042 0.168 3912 Planarity : 0.004 0.066 4454 Dihedral : 4.395 25.771 3413 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.62 % Allowed : 18.33 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.22 (0.15), residues: 3098 helix: 1.19 (0.12), residues: 1902 sheet: -2.36 (0.61), residues: 59 loop : -1.52 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 82 TYR 0.030 0.002 TYR C 76 PHE 0.031 0.002 PHE B 112 TRP 0.012 0.002 TRP A 35 HIS 0.010 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00578 (25670) covalent geometry : angle 0.67588 (34688) hydrogen bonds : bond 0.04195 ( 1330) hydrogen bonds : angle 4.59084 ( 3912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 SER cc_start: 0.8905 (t) cc_final: 0.8594 (m) REVERT: H 36 LYS cc_start: 0.8722 (mmpt) cc_final: 0.8111 (ptpp) REVERT: H 53 ASP cc_start: 0.7725 (m-30) cc_final: 0.6778 (t0) REVERT: H 57 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8067 (tp) REVERT: B 39 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: B 86 MET cc_start: 0.8856 (mmp) cc_final: 0.8526 (mmp) REVERT: B 576 MET cc_start: 0.8933 (pmm) cc_final: 0.8547 (pmm) REVERT: B 582 MET cc_start: 0.9049 (ttp) cc_final: 0.8700 (tmm) REVERT: B 605 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8133 (ppp) REVERT: C 17 MET cc_start: 0.8109 (tmm) cc_final: 0.7364 (tmm) REVERT: C 32 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8608 (mmtt) REVERT: C 108 ASN cc_start: 0.9001 (m-40) cc_final: 0.8712 (m-40) REVERT: D 29 ARG cc_start: 0.7414 (mmp-170) cc_final: 0.7181 (mmp-170) REVERT: D 32 GLU cc_start: 0.8436 (tt0) cc_final: 0.7765 (tm-30) REVERT: D 42 GLN cc_start: 0.7549 (pm20) cc_final: 0.7039 (pm20) REVERT: J 201 ASP cc_start: 0.8734 (p0) cc_final: 0.8408 (p0) REVERT: J 357 ASN cc_start: 0.8780 (m-40) cc_final: 0.8387 (t0) REVERT: J 517 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8470 (tp) REVERT: A 146 MET cc_start: 0.9184 (mmp) cc_final: 0.8604 (mmm) REVERT: A 311 MET cc_start: 0.8530 (tpp) cc_final: 0.8024 (tpp) REVERT: A 480 MET cc_start: 0.7803 (mmm) cc_final: 0.7131 (mmm) REVERT: A 510 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7659 (t80) REVERT: A 539 MET cc_start: 0.7953 (tpp) cc_final: 0.7484 (tpp) REVERT: A 582 MET cc_start: 0.8165 (ptp) cc_final: 0.6621 (ttt) REVERT: A 657 MET cc_start: 0.7672 (mpp) cc_final: 0.7073 (pmm) REVERT: A 688 MET cc_start: 0.4538 (tpp) cc_final: 0.4042 (tpt) outliers start: 45 outliers final: 33 residues processed: 264 average time/residue: 0.1363 time to fit residues: 58.7168 Evaluate side-chains 262 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain J residue 517 LEU Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 537 HIS Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 510 TYR Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 238 optimal weight: 0.6980 chunk 303 optimal weight: 0.6980 chunk 271 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 304 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 229 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** J 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS A 73 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.103847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071571 restraints weight = 85796.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070724 restraints weight = 61747.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.070817 restraints weight = 47404.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071298 restraints weight = 41777.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.071650 restraints weight = 34532.887| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25670 Z= 0.135 Angle : 0.611 13.142 34688 Z= 0.310 Chirality : 0.039 0.176 3912 Planarity : 0.004 0.066 4454 Dihedral : 4.343 25.860 3413 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.48 % Allowed : 18.58 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.35 (0.15), residues: 3098 helix: 1.30 (0.12), residues: 1903 sheet: -2.23 (0.63), residues: 59 loop : -1.51 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 68 TYR 0.034 0.001 TYR C 79 PHE 0.038 0.002 PHE B 112 TRP 0.017 0.002 TRP B 14 HIS 0.006 0.001 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00306 (25670) covalent geometry : angle 0.61062 (34688) hydrogen bonds : bond 0.03901 ( 1330) hydrogen bonds : angle 4.40493 ( 3912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.34 seconds wall clock time: 82 minutes 26.64 seconds (4946.64 seconds total)