Starting phenix.real_space_refine on Tue May 27 07:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j78_61197/05_2025/9j78_61197.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j78_61197/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j78_61197/05_2025/9j78_61197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j78_61197/05_2025/9j78_61197.map" model { file = "/net/cci-nas-00/data/ceres_data/9j78_61197/05_2025/9j78_61197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j78_61197/05_2025/9j78_61197.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 5.40s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.72, per 1000 atoms: 0.78 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: 6.60 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.61 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: 8.66 Time building geometry restraints manager: 7.70 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: 30.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 60.580 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.130 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.510 ------------------------------------------------------------------------------- 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 : 8.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.020 0.002 TRP A 35 HIS 0.006 0.001 HIS J 369 PHE 0.030 0.002 PHE B 548 TYR 0.017 0.001 TYR C 79 ARG 0.008 0.000 ARG A 551 Details of bonding type rmsd hydrogen bonds : bond 0.19027 ( 1330) hydrogen bonds : angle 6.56808 ( 3912) covalent geometry : bond 0.00356 (25670) covalent geometry : angle 0.62850 (34688) *********************** 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 : 2.808 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: 0.8283 (pttm) REVERT: H 90 ILE cc_start: 0.7910 (mt) cc_final: 0.7489 (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: 0.8581 (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: 0.6987 (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: 0.8576 (p) REVERT: C 75 MET cc_start: 0.8615 (mtt) cc_final: 0.8207 (mtt) REVERT: D 2 ASP cc_start: 0.6477 (p0) cc_final: 0.5334 (p0) REVERT: D 79 PHE cc_start: 0.7535 (m-80) cc_final: 0.7202 (m-80) REVERT: J 174 LEU cc_start: 0.9209 (mt) cc_final: 0.9000 (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: 0.8832 (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: 0.8951 (tt) REVERT: A 137 MET cc_start: 0.8199 (ptp) cc_final: 0.7835 (ptp) REVERT: A 480 MET cc_start: 0.7962 (tpt) cc_final: 0.7590 (tpp) REVERT: A 657 MET cc_start: 0.7038 (mpp) cc_final: 0.6645 (pmm) REVERT: A 678 MET cc_start: 0.8152 (ppp) cc_final: 0.7779 (ppp) REVERT: A 688 MET cc_start: 0.5470 (tpp) cc_final: 0.4855 (tpt) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.3693 time to fit residues: 262.3923 Evaluate side-chains 265 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 240 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 278 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS D 10 HIS ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 427 ASN J 473 ASN ** J 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 611 ASN ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS A 274 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 508 GLN A 557 HIS ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.103998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.069357 restraints weight = 85248.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070264 restraints weight = 54789.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070639 restraints weight = 36829.171| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25670 Z= 0.186 Angle : 0.620 8.991 34688 Z= 0.329 Chirality : 0.041 0.170 3912 Planarity : 0.005 0.056 4454 Dihedral : 4.419 25.547 3413 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.12 % Allowed : 9.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3098 helix: 0.72 (0.12), residues: 1884 sheet: -2.68 (0.58), residues: 62 loop : -1.51 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 209 HIS 0.006 0.001 HIS A 88 PHE 0.039 0.002 PHE B 198 TYR 0.022 0.002 TYR G 79 ARG 0.007 0.001 ARG F 80 Details of bonding type rmsd hydrogen bonds : bond 0.05083 ( 1330) hydrogen bonds : angle 4.91086 ( 3912) covalent geometry : bond 0.00415 (25670) covalent geometry : angle 0.62027 (34688) *********************** 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: 31 poor density : 306 time to evaluate : 2.750 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 22 SER cc_start: 0.9076 (t) cc_final: 0.8825 (m) REVERT: H 36 LYS cc_start: 0.8833 (mmpt) cc_final: 0.8482 (ptpp) REVERT: H 90 ILE cc_start: 0.7949 (mt) cc_final: 0.7570 (pt) REVERT: B 449 MET cc_start: 0.8631 (ppp) cc_final: 0.8353 (tmm) REVERT: B 476 MET cc_start: 0.8811 (mtm) cc_final: 0.8575 (mtm) REVERT: B 653 ILE cc_start: 0.8812 (mp) cc_final: 0.8417 (tp) REVERT: C 17 MET cc_start: 0.8198 (tmm) cc_final: 0.7810 (tmm) REVERT: C 18 TYR cc_start: 0.8107 (m-80) cc_final: 0.7565 (m-10) REVERT: C 32 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8756 (tptp) REVERT: C 69 VAL cc_start: 0.9139 (t) cc_final: 0.8866 (p) REVERT: C 79 TYR cc_start: 0.9043 (t80) cc_final: 0.8814 (t80) REVERT: C 105 MET cc_start: 0.8496 (ttm) cc_final: 0.8217 (ttt) REVERT: D 25 PHE cc_start: 0.8023 (t80) cc_final: 0.7650 (t80) REVERT: D 32 GLU cc_start: 0.8394 (tt0) cc_final: 0.8188 (tt0) REVERT: D 79 PHE cc_start: 0.7485 (m-80) cc_final: 0.7260 (m-80) REVERT: J 201 ASP cc_start: 0.8837 (p0) cc_final: 0.8464 (p0) REVERT: J 326 MET cc_start: 0.9175 (mmt) cc_final: 0.8906 (mmp) REVERT: J 357 ASN cc_start: 0.8846 (m-40) cc_final: 0.8471 (t0) REVERT: J 398 LEU cc_start: 0.9437 (mp) cc_final: 0.9173 (tt) REVERT: J 585 SER cc_start: 0.8985 (m) cc_final: 0.8782 (p) REVERT: A 249 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8256 (ttm-80) REVERT: A 444 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8849 (mt) REVERT: A 480 MET cc_start: 0.8224 (tpt) cc_final: 0.7844 (mmm) REVERT: A 527 PHE cc_start: 0.6374 (p90) cc_final: 0.5112 (p90) REVERT: A 657 MET cc_start: 0.7608 (mpp) cc_final: 0.7118 (pmm) REVERT: A 688 MET cc_start: 0.4693 (tpp) cc_final: 0.4251 (tpt) outliers start: 31 outliers final: 19 residues processed: 325 average time/residue: 0.3578 time to fit residues: 184.8278 Evaluate side-chains 275 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 ASP 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 D residue 56 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 80 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** ** 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** 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 = 0.3935 r_free = 0.3935 target = 0.103818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.068621 restraints weight = 84323.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.069954 restraints weight = 51961.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.070468 restraints weight = 36009.340| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25670 Z= 0.185 Angle : 0.594 8.671 34688 Z= 0.314 Chirality : 0.040 0.223 3912 Planarity : 0.004 0.056 4454 Dihedral : 4.351 24.719 3413 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.12 % Allowed : 13.17 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3098 helix: 0.88 (0.12), residues: 1891 sheet: -2.56 (0.53), residues: 68 loop : -1.50 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 35 HIS 0.007 0.001 HIS A 88 PHE 0.027 0.002 PHE A 638 TYR 0.028 0.001 TYR C 76 ARG 0.009 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 1330) hydrogen bonds : angle 4.71558 ( 3912) covalent geometry : bond 0.00416 (25670) covalent geometry : angle 0.59412 (34688) *********************** 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 308 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 3.070 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: 0.8902 (t) cc_final: 0.8634 (m) REVERT: H 36 LYS cc_start: 0.8812 (mmpt) cc_final: 0.8470 (ptpp) REVERT: H 57 LEU cc_start: 0.8630 (mt) cc_final: 0.8268 (tp) REVERT: B 449 MET cc_start: 0.8656 (ppp) cc_final: 0.8362 (tmm) REVERT: B 476 MET cc_start: 0.8941 (mtm) cc_final: 0.8513 (mtm) REVERT: B 653 ILE cc_start: 0.8821 (mp) cc_final: 0.8409 (tp) REVERT: C 17 MET cc_start: 0.8127 (tmm) cc_final: 0.7820 (tmm) REVERT: C 32 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8496 (mptp) REVERT: C 69 VAL cc_start: 0.9098 (t) cc_final: 0.8803 (p) REVERT: D 25 PHE cc_start: 0.8084 (t80) cc_final: 0.7710 (t80) REVERT: D 32 GLU cc_start: 0.8314 (tt0) cc_final: 0.8053 (tt0) REVERT: J 201 ASP cc_start: 0.8842 (p0) cc_final: 0.8499 (p0) REVERT: J 202 ILE cc_start: 0.8999 (mt) cc_final: 0.8786 (mt) REVERT: J 326 MET cc_start: 0.9166 (mmt) cc_final: 0.8892 (mmp) REVERT: J 357 ASN cc_start: 0.8776 (m-40) cc_final: 0.8405 (t0) REVERT: J 398 LEU cc_start: 0.9383 (mp) cc_final: 0.9128 (tt) REVERT: A 249 ARG cc_start: 0.8637 (ttm110) cc_final: 0.7826 (ttm-80) REVERT: A 475 ARG cc_start: 0.9191 (tpt-90) cc_final: 0.8919 (tpm170) REVERT: A 527 PHE cc_start: 0.6343 (p90) cc_final: 0.5086 (p90) REVERT: A 559 LEU cc_start: 0.9125 (mt) cc_final: 0.8877 (mt) REVERT: A 688 MET cc_start: 0.4682 (tpp) cc_final: 0.4240 (tpt) REVERT: I 26 LYS cc_start: 0.8563 (tmmt) cc_final: 0.7866 (tptp) outliers start: 31 outliers final: 18 residues processed: 298 average time/residue: 0.3405 time to fit residues: 164.3497 Evaluate side-chains 262 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 ASP Chi-restraints excluded: chain B residue 137 MET 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 D residue 56 THR Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 386 LEU Chi-restraints excluded: chain J residue 499 ASP 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 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 142 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 161 optimal weight: 0.0870 chunk 257 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 219 optimal weight: 0.3980 chunk 263 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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** D 65 GLN ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3951 r_free = 0.3951 target = 0.104737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.069782 restraints weight = 85377.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071027 restraints weight = 59606.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071149 restraints weight = 38874.060| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2395 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= 0.135 Angle : 0.564 8.818 34688 Z= 0.294 Chirality : 0.039 0.200 3912 Planarity : 0.004 0.059 4454 Dihedral : 4.275 22.626 3413 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.41 % Allowed : 14.29 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3098 helix: 1.05 (0.12), residues: 1892 sheet: -2.78 (0.56), residues: 62 loop : -1.54 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 14 HIS 0.005 0.001 HIS F 565 PHE 0.028 0.002 PHE F 101 TYR 0.035 0.001 TYR C 79 ARG 0.005 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 1330) hydrogen bonds : angle 4.50172 ( 3912) covalent geometry : bond 0.00301 (25670) covalent geometry : angle 0.56432 (34688) *********************** 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 308 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 2.943 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: H 36 LYS cc_start: 0.8810 (mmpt) cc_final: 0.8260 (ptpp) REVERT: H 57 LEU cc_start: 0.8526 (mt) cc_final: 0.8095 (tp) REVERT: B 476 MET cc_start: 0.8913 (mtm) cc_final: 0.8549 (mtm) REVERT: B 605 MET cc_start: 0.8782 (ptm) cc_final: 0.8567 (ppp) REVERT: B 702 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: C 69 VAL cc_start: 0.9085 (t) cc_final: 0.8788 (p) REVERT: C 105 MET cc_start: 0.8480 (ttm) cc_final: 0.8171 (ttt) REVERT: D 25 PHE cc_start: 0.7965 (t80) cc_final: 0.7721 (t80) REVERT: D 32 GLU cc_start: 0.8399 (tt0) cc_final: 0.8095 (tt0) REVERT: J 201 ASP cc_start: 0.8790 (p0) cc_final: 0.8467 (p0) REVERT: J 326 MET cc_start: 0.9170 (mmt) cc_final: 0.8909 (mmp) REVERT: J 357 ASN cc_start: 0.8793 (m-40) cc_final: 0.8389 (t0) REVERT: J 398 LEU cc_start: 0.9412 (mp) cc_final: 0.9162 (tt) REVERT: F 395 MET cc_start: 0.8874 (mtp) cc_final: 0.8609 (mtm) REVERT: F 416 LEU cc_start: 0.9206 (mp) cc_final: 0.8823 (tp) REVERT: F 565 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.5980 (m-70) REVERT: A 249 ARG cc_start: 0.8559 (ttm110) cc_final: 0.7803 (ttm-80) REVERT: A 297 MET cc_start: 0.8216 (ttp) cc_final: 0.7947 (ttt) REVERT: A 311 MET cc_start: 0.8404 (tpp) cc_final: 0.8038 (tpp) REVERT: A 475 ARG cc_start: 0.9175 (tpt-90) cc_final: 0.8934 (tpm170) REVERT: A 480 MET cc_start: 0.7561 (mmm) cc_final: 0.6966 (mmp) REVERT: A 527 PHE cc_start: 0.6277 (p90) cc_final: 0.5470 (p90) REVERT: A 657 MET cc_start: 0.8025 (mpp) cc_final: 0.7319 (mpp) REVERT: A 688 MET cc_start: 0.4655 (tpp) cc_final: 0.4229 (tpt) outliers start: 39 outliers final: 24 residues processed: 300 average time/residue: 0.3454 time to fit residues: 166.0359 Evaluate side-chains 268 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 167 ILE 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 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 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 390 GLN Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain F residue 209 TRP 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 406 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 302 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 175 optimal weight: 0.0030 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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 65 GLN J 340 ASN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3939 r_free = 0.3939 target = 0.104067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.069312 restraints weight = 85541.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070820 restraints weight = 52609.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071424 restraints weight = 35952.360| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25670 Z= 0.157 Angle : 0.569 9.060 34688 Z= 0.296 Chirality : 0.039 0.202 3912 Planarity : 0.004 0.060 4454 Dihedral : 4.224 22.668 3413 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.84 % Allowed : 15.55 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3098 helix: 1.17 (0.12), residues: 1891 sheet: -2.71 (0.55), residues: 62 loop : -1.50 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 14 HIS 0.006 0.001 HIS J 369 PHE 0.020 0.002 PHE B 198 TYR 0.032 0.001 TYR C 79 ARG 0.006 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 1330) hydrogen bonds : angle 4.44097 ( 3912) covalent geometry : bond 0.00356 (25670) covalent geometry : angle 0.56914 (34688) *********************** 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 309 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 2.932 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: H 36 LYS cc_start: 0.8770 (mmpt) cc_final: 0.8198 (ptpp) REVERT: H 57 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8046 (tp) REVERT: B 86 MET cc_start: 0.8796 (mmp) cc_final: 0.8473 (mmp) REVERT: B 476 MET cc_start: 0.8851 (mtm) cc_final: 0.8402 (mtm) REVERT: B 605 MET cc_start: 0.8762 (ptm) cc_final: 0.8540 (ppp) REVERT: B 653 ILE cc_start: 0.8694 (mp) cc_final: 0.8202 (tp) REVERT: B 702 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: C 37 LEU cc_start: 0.8866 (tp) cc_final: 0.8641 (tp) REVERT: C 69 VAL cc_start: 0.9079 (t) cc_final: 0.8772 (p) REVERT: C 105 MET cc_start: 0.8596 (ttm) cc_final: 0.8281 (ttt) REVERT: D 32 GLU cc_start: 0.8310 (tt0) cc_final: 0.7459 (tm-30) REVERT: D 40 ASP cc_start: 0.8857 (m-30) cc_final: 0.8422 (p0) REVERT: D 42 GLN cc_start: 0.7281 (pm20) cc_final: 0.6390 (mp10) REVERT: J 201 ASP cc_start: 0.8758 (p0) cc_final: 0.8439 (p0) REVERT: J 326 MET cc_start: 0.9160 (mmt) cc_final: 0.8884 (mmp) REVERT: J 357 ASN cc_start: 0.8672 (m-40) cc_final: 0.8323 (t0) REVERT: J 390 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8735 (mp10) REVERT: J 398 LEU cc_start: 0.9365 (mp) cc_final: 0.9106 (tt) REVERT: J 627 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.4728 (m90) REVERT: F 395 MET cc_start: 0.8916 (mtp) cc_final: 0.8662 (mtm) REVERT: F 416 LEU cc_start: 0.9197 (mp) cc_final: 0.8815 (tp) REVERT: F 565 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.5884 (m-70) REVERT: A 297 MET cc_start: 0.8339 (ttp) cc_final: 0.8070 (ttm) REVERT: A 311 MET cc_start: 0.8479 (tpp) cc_final: 0.8178 (tpp) REVERT: A 475 ARG cc_start: 0.9154 (tpt-90) cc_final: 0.8922 (tpm170) REVERT: A 539 MET cc_start: 0.8071 (tpp) cc_final: 0.7538 (tpp) REVERT: A 688 MET cc_start: 0.4637 (tpp) cc_final: 0.4179 (tpt) outliers start: 51 outliers final: 29 residues processed: 295 average time/residue: 0.3480 time to fit residues: 165.8241 Evaluate side-chains 261 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 220 LYS 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 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 D residue 56 THR 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 487 LEU Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 568 MET 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 406 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain G residue 63 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 291 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 191 optimal weight: 0.0980 chunk 231 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 236 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 65 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 HIS F 394 GLN ** 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** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3943 r_free = 0.3943 target = 0.104201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.067813 restraints weight = 84885.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069597 restraints weight = 49925.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070751 restraints weight = 35319.944| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2743 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= 0.147 Angle : 0.573 9.946 34688 Z= 0.296 Chirality : 0.039 0.178 3912 Planarity : 0.004 0.062 4454 Dihedral : 4.212 23.114 3413 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.09 % Allowed : 16.49 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3098 helix: 1.22 (0.12), residues: 1901 sheet: -1.93 (0.57), residues: 69 loop : -1.55 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 14 HIS 0.006 0.001 HIS F 565 PHE 0.030 0.002 PHE A 527 TYR 0.034 0.001 TYR C 79 ARG 0.009 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 1330) hydrogen bonds : angle 4.37454 ( 3912) covalent geometry : bond 0.00330 (25670) covalent geometry : angle 0.57332 (34688) *********************** 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 303 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 2.987 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 36 LYS cc_start: 0.8659 (mmpt) cc_final: 0.8065 (ptpp) REVERT: H 57 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8204 (tp) REVERT: B 86 MET cc_start: 0.8730 (mmp) cc_final: 0.8395 (mmp) REVERT: B 476 MET cc_start: 0.8763 (mtm) cc_final: 0.8315 (mtm) REVERT: B 653 ILE cc_start: 0.8591 (mp) cc_final: 0.8197 (tp) REVERT: B 702 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: C 17 MET cc_start: 0.7994 (tmm) cc_final: 0.7371 (tmm) REVERT: C 32 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8549 (mmtt) REVERT: C 69 VAL cc_start: 0.9046 (t) cc_final: 0.8767 (p) REVERT: C 105 MET cc_start: 0.8664 (ttm) cc_final: 0.8362 (ttt) REVERT: D 32 GLU cc_start: 0.8278 (tt0) cc_final: 0.7345 (tm-30) REVERT: D 42 GLN cc_start: 0.6802 (pm20) cc_final: 0.6594 (mp10) REVERT: J 201 ASP cc_start: 0.8720 (p0) cc_final: 0.8406 (p0) REVERT: J 326 MET cc_start: 0.9162 (mmt) cc_final: 0.8878 (mmp) REVERT: J 357 ASN cc_start: 0.8614 (m-40) cc_final: 0.8281 (t0) REVERT: J 386 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8999 (mt) REVERT: J 390 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8688 (mp10) REVERT: J 395 MET cc_start: 0.8667 (ppp) cc_final: 0.8433 (ppp) REVERT: J 398 LEU cc_start: 0.9307 (mp) cc_final: 0.9025 (tt) REVERT: J 627 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.5642 (m-70) REVERT: F 395 MET cc_start: 0.8859 (mtp) cc_final: 0.8589 (mtm) REVERT: F 406 ASP cc_start: 0.8162 (m-30) cc_final: 0.7764 (m-30) REVERT: F 416 LEU cc_start: 0.9117 (mp) cc_final: 0.8730 (tp) REVERT: F 565 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.5502 (m-70) REVERT: A 297 MET cc_start: 0.8295 (ttp) cc_final: 0.8063 (ttp) REVERT: A 429 ASP cc_start: 0.7947 (m-30) cc_final: 0.7554 (t0) REVERT: A 527 PHE cc_start: 0.6571 (p90) cc_final: 0.5680 (p90) REVERT: A 657 MET cc_start: 0.7761 (mpp) cc_final: 0.7186 (mpp) REVERT: A 688 MET cc_start: 0.4737 (tpp) cc_final: 0.4250 (tpt) outliers start: 58 outliers final: 29 residues processed: 290 average time/residue: 0.3412 time to fit residues: 161.5105 Evaluate side-chains 264 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 167 ILE 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 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 396 ILE Chi-restraints excluded: chain J residue 455 THR Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain J residue 627 HIS Chi-restraints excluded: chain F residue 209 TRP 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 346 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 638 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 74 optimal weight: 2.9990 chunk 196 optimal weight: 0.1980 chunk 294 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 274 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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** B 641 ASN D 65 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 HIS ** F 565 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.102098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067152 restraints weight = 85921.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.068409 restraints weight = 54396.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.068907 restraints weight = 38325.856| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25670 Z= 0.239 Angle : 0.654 11.192 34688 Z= 0.336 Chirality : 0.041 0.212 3912 Planarity : 0.004 0.061 4454 Dihedral : 4.395 25.975 3413 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.38 % Allowed : 16.92 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3098 helix: 1.10 (0.12), residues: 1900 sheet: -2.13 (0.63), residues: 59 loop : -1.57 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 14 HIS 0.010 0.001 HIS A 88 PHE 0.034 0.002 PHE B 112 TYR 0.041 0.002 TYR A 558 ARG 0.010 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 1330) hydrogen bonds : angle 4.61939 ( 3912) covalent geometry : bond 0.00544 (25670) covalent geometry : angle 0.65406 (34688) *********************** 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 303 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 237 time to evaluate : 3.050 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: H 53 ASP cc_start: 0.7716 (m-30) cc_final: 0.6799 (t0) REVERT: H 57 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8183 (tp) REVERT: B 86 MET cc_start: 0.8860 (mmp) cc_final: 0.8532 (mmp) REVERT: B 605 MET cc_start: 0.8727 (ppp) cc_final: 0.8287 (ppp) REVERT: B 622 MET cc_start: 0.8303 (tpp) cc_final: 0.8076 (mmm) REVERT: B 702 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7717 (tp30) REVERT: C 17 MET cc_start: 0.8178 (tmm) cc_final: 0.7463 (tmm) REVERT: C 32 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8616 (mmtt) REVERT: C 69 VAL cc_start: 0.9202 (t) cc_final: 0.8919 (p) REVERT: D 32 GLU cc_start: 0.8459 (tt0) cc_final: 0.7635 (tm-30) REVERT: D 42 GLN cc_start: 0.7018 (pm20) cc_final: 0.6744 (mp10) REVERT: J 201 ASP cc_start: 0.8772 (p0) cc_final: 0.8445 (p0) REVERT: J 326 MET cc_start: 0.9181 (mmt) cc_final: 0.8858 (mmp) REVERT: J 357 ASN cc_start: 0.8780 (m-40) cc_final: 0.8406 (t0) REVERT: J 386 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9058 (mt) REVERT: J 390 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8623 (mp10) REVERT: J 395 MET cc_start: 0.8840 (ppp) cc_final: 0.8493 (ppp) REVERT: J 398 LEU cc_start: 0.9356 (mp) cc_final: 0.9122 (tt) REVERT: J 517 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8512 (tp) REVERT: F 406 ASP cc_start: 0.8450 (m-30) cc_final: 0.8187 (m-30) REVERT: F 565 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.6256 (m-70) REVERT: A 297 MET cc_start: 0.8525 (ttp) cc_final: 0.8016 (ttm) REVERT: A 311 MET cc_start: 0.8606 (tpp) cc_final: 0.8262 (tpp) REVERT: A 382 LYS cc_start: 0.7592 (mptt) cc_final: 0.7042 (mtmt) REVERT: A 480 MET cc_start: 0.7761 (mmm) cc_final: 0.6597 (mmp) REVERT: A 510 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7630 (t80) REVERT: A 657 MET cc_start: 0.7907 (mpp) cc_final: 0.7446 (mpp) REVERT: A 688 MET cc_start: 0.4596 (tpp) cc_final: 0.4271 (tpt) REVERT: G 82 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7150 (mtt180) outliers start: 66 outliers final: 41 residues processed: 284 average time/residue: 0.3575 time to fit residues: 164.4829 Evaluate side-chains 271 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 ASP 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 110 THR 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 369 ASP Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 558 TYR 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 C residue 84 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 56 THR 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 396 ILE Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain J residue 517 LEU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 475 ILE 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 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 406 MET 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 63 ARG 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 67 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 197 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 279 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 627 HIS ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.104137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071399 restraints weight = 85066.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070866 restraints weight = 57705.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.071272 restraints weight = 41213.484| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25670 Z= 0.131 Angle : 0.584 12.017 34688 Z= 0.300 Chirality : 0.039 0.202 3912 Planarity : 0.004 0.063 4454 Dihedral : 4.310 26.270 3413 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.48 % Allowed : 18.11 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3098 helix: 1.26 (0.12), residues: 1907 sheet: -1.86 (0.60), residues: 69 loop : -1.59 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 14 HIS 0.016 0.001 HIS F 166 PHE 0.033 0.002 PHE B 112 TYR 0.039 0.001 TYR C 79 ARG 0.009 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 1330) hydrogen bonds : angle 4.40347 ( 3912) covalent geometry : bond 0.00293 (25670) covalent geometry : angle 0.58425 (34688) *********************** 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 295 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 2.915 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: H 36 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8009 (pttm) REVERT: H 53 ASP cc_start: 0.7762 (m-30) cc_final: 0.6832 (t0) REVERT: H 57 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8043 (tp) REVERT: B 39 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: B 86 MET cc_start: 0.8764 (mmp) cc_final: 0.8453 (mmp) REVERT: B 605 MET cc_start: 0.8619 (ppp) cc_final: 0.8134 (ppp) REVERT: B 622 MET cc_start: 0.8298 (tpp) cc_final: 0.7999 (mmm) REVERT: B 702 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: C 17 MET cc_start: 0.8230 (tmm) cc_final: 0.7881 (tmm) REVERT: D 32 GLU cc_start: 0.8449 (tt0) cc_final: 0.7627 (tm-30) REVERT: J 201 ASP cc_start: 0.8733 (p0) cc_final: 0.8400 (p0) REVERT: J 326 MET cc_start: 0.9171 (mmt) cc_final: 0.8869 (mmp) REVERT: J 357 ASN cc_start: 0.8799 (m-40) cc_final: 0.8398 (t0) REVERT: J 368 LEU cc_start: 0.8849 (mt) cc_final: 0.8570 (tt) REVERT: J 386 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8995 (mt) REVERT: J 390 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8673 (mp10) REVERT: J 395 MET cc_start: 0.8827 (ppp) cc_final: 0.8525 (ppp) REVERT: J 398 LEU cc_start: 0.9399 (mp) cc_final: 0.9171 (tt) REVERT: F 406 ASP cc_start: 0.8439 (m-30) cc_final: 0.8175 (m-30) REVERT: F 416 LEU cc_start: 0.9159 (mp) cc_final: 0.8779 (tp) REVERT: F 565 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.6222 (m-70) REVERT: A 146 MET cc_start: 0.9034 (mmp) cc_final: 0.8559 (mmm) REVERT: A 249 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8304 (ttm-80) REVERT: A 382 LYS cc_start: 0.7573 (mptt) cc_final: 0.6956 (mtmt) REVERT: A 429 ASP cc_start: 0.8047 (m-30) cc_final: 0.7596 (t0) REVERT: A 480 MET cc_start: 0.7772 (mmm) cc_final: 0.6659 (mmp) REVERT: A 576 MET cc_start: 0.8569 (pmm) cc_final: 0.7803 (pmm) REVERT: A 582 MET cc_start: 0.7981 (ptp) cc_final: 0.6413 (tpt) REVERT: A 657 MET cc_start: 0.7936 (mpp) cc_final: 0.7446 (mpp) REVERT: A 688 MET cc_start: 0.4671 (tpp) cc_final: 0.4168 (tpt) REVERT: G 82 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7251 (mtt180) outliers start: 41 outliers final: 26 residues processed: 282 average time/residue: 0.3445 time to fit residues: 159.1668 Evaluate side-chains 262 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 39 PHE Chi-restraints excluded: chain B residue 167 ILE 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 702 GLU 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 386 LEU Chi-restraints excluded: chain J residue 390 GLN Chi-restraints excluded: chain J residue 396 ILE Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain F residue 209 TRP 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 406 MET Chi-restraints excluded: chain A residue 438 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 285 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 chunk 277 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 62 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.104163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.068215 restraints weight = 85891.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069941 restraints weight = 50526.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071123 restraints weight = 35693.729| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25670 Z= 0.139 Angle : 0.604 14.488 34688 Z= 0.306 Chirality : 0.040 0.357 3912 Planarity : 0.004 0.061 4454 Dihedral : 4.260 26.221 3413 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.48 % Allowed : 18.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3098 helix: 1.31 (0.12), residues: 1909 sheet: -1.80 (0.61), residues: 69 loop : -1.57 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 35 HIS 0.006 0.001 HIS B 547 PHE 0.038 0.002 PHE B 112 TYR 0.034 0.001 TYR C 79 ARG 0.007 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 1330) hydrogen bonds : angle 4.38359 ( 3912) covalent geometry : bond 0.00312 (25670) covalent geometry : angle 0.60358 (34688) *********************** 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 283 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 2.800 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 36 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7885 (pttm) REVERT: H 44 LEU cc_start: 0.8063 (mt) cc_final: 0.7483 (pt) REVERT: H 53 ASP cc_start: 0.7839 (m-30) cc_final: 0.6935 (t0) REVERT: H 57 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8079 (tp) REVERT: B 39 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: B 86 MET cc_start: 0.8751 (mmp) cc_final: 0.8419 (mmp) REVERT: B 582 MET cc_start: 0.8711 (ttp) cc_final: 0.8387 (tmm) REVERT: B 605 MET cc_start: 0.8569 (ppp) cc_final: 0.8126 (ppp) REVERT: C 32 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8811 (mmtt) REVERT: C 63 ARG cc_start: 0.7331 (mtm180) cc_final: 0.6792 (tmm160) REVERT: C 105 MET cc_start: 0.8525 (ttm) cc_final: 0.8115 (ttt) REVERT: D 32 GLU cc_start: 0.8362 (tt0) cc_final: 0.7503 (tm-30) REVERT: J 201 ASP cc_start: 0.8646 (p0) cc_final: 0.8330 (p0) REVERT: J 326 MET cc_start: 0.9164 (mmt) cc_final: 0.8874 (mmp) REVERT: J 357 ASN cc_start: 0.8640 (m-40) cc_final: 0.8244 (t0) REVERT: J 368 LEU cc_start: 0.8862 (mt) cc_final: 0.8576 (tt) REVERT: J 386 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8920 (mt) REVERT: J 390 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8665 (mp10) REVERT: J 395 MET cc_start: 0.8754 (ppp) cc_final: 0.8462 (ppp) REVERT: J 398 LEU cc_start: 0.9288 (mp) cc_final: 0.9033 (tt) REVERT: F 416 LEU cc_start: 0.9104 (mp) cc_final: 0.8723 (tp) REVERT: F 565 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.6368 (m-70) REVERT: A 146 MET cc_start: 0.9058 (mmp) cc_final: 0.8701 (mmm) REVERT: A 429 ASP cc_start: 0.8003 (m-30) cc_final: 0.7602 (t0) REVERT: A 510 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7494 (t80) REVERT: A 576 MET cc_start: 0.8441 (pmm) cc_final: 0.7659 (pmm) REVERT: A 657 MET cc_start: 0.7851 (mpp) cc_final: 0.7269 (mpp) REVERT: A 665 MET cc_start: 0.7374 (mtt) cc_final: 0.7138 (mpp) REVERT: A 688 MET cc_start: 0.4702 (tpp) cc_final: 0.4151 (tpt) REVERT: A 717 MET cc_start: 0.5301 (tpt) cc_final: 0.3433 (mtp) outliers start: 41 outliers final: 28 residues processed: 270 average time/residue: 0.3391 time to fit residues: 148.8779 Evaluate side-chains 264 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 39 PHE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 167 ILE 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 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 C residue 101 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 56 THR 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 499 ASP Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain F residue 396 ILE 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 510 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 116 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 chunk 128 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 191 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 627 HIS ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3928 r_free = 0.3928 target = 0.103534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068283 restraints weight = 85572.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069864 restraints weight = 52531.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070420 restraints weight = 35078.671| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25670 Z= 0.170 Angle : 0.625 12.782 34688 Z= 0.316 Chirality : 0.040 0.200 3912 Planarity : 0.004 0.079 4454 Dihedral : 4.280 26.697 3413 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.41 % Allowed : 18.61 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3098 helix: 1.30 (0.12), residues: 1910 sheet: -1.82 (0.62), residues: 69 loop : -1.57 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 14 HIS 0.006 0.001 HIS A 88 PHE 0.037 0.002 PHE B 112 TYR 0.030 0.001 TYR C 79 ARG 0.008 0.000 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 1330) hydrogen bonds : angle 4.41763 ( 3912) covalent geometry : bond 0.00389 (25670) covalent geometry : angle 0.62518 (34688) ********************** 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 271 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 2.968 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: H 36 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7954 (pttm) REVERT: H 44 LEU cc_start: 0.7960 (mt) cc_final: 0.7336 (pt) REVERT: H 53 ASP cc_start: 0.7727 (m-30) cc_final: 0.6822 (t0) REVERT: H 57 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 39 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: B 86 MET cc_start: 0.8812 (mmp) cc_final: 0.8470 (mmp) REVERT: B 582 MET cc_start: 0.8743 (ttp) cc_final: 0.8358 (tmm) REVERT: B 605 MET cc_start: 0.8570 (ppp) cc_final: 0.8094 (ppp) REVERT: C 17 MET cc_start: 0.8175 (tmm) cc_final: 0.7443 (tmm) REVERT: C 32 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8579 (mmtt) REVERT: C 55 ASN cc_start: 0.6342 (m-40) cc_final: 0.6016 (m-40) REVERT: C 63 ARG cc_start: 0.7406 (mtm180) cc_final: 0.6833 (tmm160) REVERT: D 32 GLU cc_start: 0.8387 (tt0) cc_final: 0.7658 (tm-30) REVERT: J 201 ASP cc_start: 0.8678 (p0) cc_final: 0.8368 (p0) REVERT: J 326 MET cc_start: 0.9138 (mmt) cc_final: 0.8837 (mmp) REVERT: J 357 ASN cc_start: 0.8690 (m-40) cc_final: 0.8293 (t0) REVERT: J 368 LEU cc_start: 0.8874 (mt) cc_final: 0.8565 (tt) REVERT: J 386 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8968 (mt) REVERT: J 390 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8688 (mp10) REVERT: J 395 MET cc_start: 0.8791 (ppp) cc_final: 0.8514 (ppp) REVERT: J 398 LEU cc_start: 0.9327 (mp) cc_final: 0.9074 (tt) REVERT: F 416 LEU cc_start: 0.9151 (mp) cc_final: 0.8786 (tp) REVERT: F 565 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.6574 (m-70) REVERT: A 236 MET cc_start: 0.8343 (mtt) cc_final: 0.7403 (mtp) REVERT: A 382 LYS cc_start: 0.7552 (mptt) cc_final: 0.6973 (mtmt) REVERT: A 429 ASP cc_start: 0.8111 (m-30) cc_final: 0.7663 (t0) REVERT: A 438 MET cc_start: 0.8225 (mpp) cc_final: 0.7751 (mpp) REVERT: A 480 MET cc_start: 0.7832 (mmm) cc_final: 0.7013 (mmp) REVERT: A 510 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7583 (t80) REVERT: A 582 MET cc_start: 0.8004 (ptp) cc_final: 0.6448 (ttt) REVERT: A 657 MET cc_start: 0.7938 (mpp) cc_final: 0.7638 (pmm) REVERT: A 665 MET cc_start: 0.7464 (mtt) cc_final: 0.7149 (mpp) REVERT: A 688 MET cc_start: 0.4575 (tpp) cc_final: 0.4051 (tpt) outliers start: 39 outliers final: 30 residues processed: 260 average time/residue: 0.3506 time to fit residues: 147.7491 Evaluate side-chains 260 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 39 PHE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 LEU 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 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 C residue 101 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 56 THR 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 396 ILE Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain F residue 396 ILE 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 510 TYR Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain G residue 52 PHE 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 19 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 304 optimal weight: 0.1980 chunk 285 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 302 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 177 optimal weight: 0.0020 chunk 151 optimal weight: 0.9980 chunk 296 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.104270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.068246 restraints weight = 85250.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070051 restraints weight = 49100.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.071264 restraints weight = 34467.558| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25670 Z= 0.135 Angle : 0.615 12.683 34688 Z= 0.311 Chirality : 0.039 0.296 3912 Planarity : 0.005 0.183 4454 Dihedral : 4.274 26.655 3413 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.44 % Allowed : 18.58 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3098 helix: 1.33 (0.12), residues: 1905 sheet: -1.80 (0.62), residues: 69 loop : -1.54 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 14 HIS 0.005 0.001 HIS B 547 PHE 0.038 0.002 PHE B 112 TYR 0.033 0.001 TYR C 79 ARG 0.013 0.000 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 1330) hydrogen bonds : angle 4.36176 ( 3912) covalent geometry : bond 0.00306 (25670) covalent geometry : angle 0.61486 (34688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8882.85 seconds wall clock time: 158 minutes 15.47 seconds (9495.47 seconds total)