Starting phenix.real_space_refine on Sat Jun 6 03:50:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28jm_56544/06_2026/28jm_56544.cif Found real_map, /net/cci-nas-00/data/ceres_data/28jm_56544/06_2026/28jm_56544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28jm_56544/06_2026/28jm_56544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28jm_56544/06_2026/28jm_56544.map" model { file = "/net/cci-nas-00/data/ceres_data/28jm_56544/06_2026/28jm_56544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28jm_56544/06_2026/28jm_56544.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 S 150 5.16 5 C 15989 2.51 5 N 4336 2.21 5 O 4626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25112 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5246 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6120 Classifications: {'peptide': 760} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 727} Chain: "C" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3018 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 358} Chain breaks: 5 Chain: "D" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3592 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain: "E" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2893 Classifications: {'peptide': 369} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2066 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 202} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6189 SG CYS B 116 55.111 93.425 60.490 1.00 86.33 S ATOM 6498 SG CYS B 155 56.122 98.040 55.564 1.00 74.76 S ATOM 6329 SG CYS B 134 57.064 91.623 55.086 1.00 73.43 S ATOM 6787 SG CYS B 190 60.844 95.346 58.851 1.00 64.71 S ATOM 20547 SG CYS E 345 81.818 82.633 143.707 1.00 84.13 S ATOM 20569 SG CYS E 348 80.109 79.984 145.834 1.00 94.51 S ATOM 20726 SG CYS E 368 80.281 79.551 142.047 1.00100.22 S ATOM 20747 SG CYS E 371 78.074 82.231 143.521 1.00 99.38 S ATOM 20667 SG CYS E 360 82.420 92.361 136.258 1.00100.67 S ATOM 20685 SG CYS E 363 83.846 93.245 139.637 1.00104.08 S ATOM 20834 SG CYS E 382 80.311 91.670 139.357 1.00 86.74 S ATOM 20851 SG CYS E 385 80.957 95.246 138.432 1.00 96.48 S ATOM 20111 SG CYS E 291 41.463 107.775 139.126 1.00110.01 S ATOM 20133 SG CYS E 294 37.853 108.261 137.981 1.00121.06 S ATOM 20222 SG CYS E 305 39.312 104.900 137.283 1.00108.50 S ATOM 20245 SG CYS E 308 40.759 107.683 135.502 1.00111.94 S ATOM 22756 SG CYS F 268 61.060 108.634 127.486 1.00 65.42 S ATOM 22775 SG CYS F 271 63.841 108.145 129.963 1.00 75.05 S ATOM 22860 SG CYS F 282 63.036 111.667 128.663 1.00 90.18 S ATOM 22880 SG CYS F 285 64.683 109.251 126.377 1.00 85.28 S ATOM 22648 SG CYS F 255 60.187 116.087 140.821 1.00 98.66 S ATOM 22665 SG CYS F 257 61.665 117.557 137.608 1.00 96.58 S ATOM 22814 SG CYS F 276 57.963 118.128 138.448 1.00108.15 S ATOM 23487 SG CYS H 6 33.380 49.773 33.823 1.00393.96 S ATOM 23505 SG CYS H 9 31.833 46.362 33.356 1.00394.46 S ATOM 23623 SG CYS H 31 35.607 46.630 34.088 1.00401.16 S ATOM 23639 SG CYS H 34 34.411 47.811 30.833 1.00393.30 S ATOM 23593 SG CYS H 26 41.247 53.115 22.017 1.00372.99 S ATOM 23700 SG CYS H 46 37.786 51.737 22.630 1.00392.57 S ATOM 23718 SG CYS H 49 38.116 54.742 20.620 1.00382.98 S Time building chain proxies: 5.34, per 1000 atoms: 0.21 Number of scatterers: 25112 At special positions: 0 Unit cell: (109.88, 147.4, 209.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 150 16.00 O 4626 8.00 N 4336 7.00 C 15989 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: 1.97 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" ND1 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb=" ZN H 400 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 34 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 6 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 31 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 9 " pdb=" ZN H 401 " pdb="ZN ZN H 401 " - pdb=" ND1 HIS H 28 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 49 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 26 " Number of angles added : 36 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5992 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 24 sheets defined 52.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.651A pdb=" N SER A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.744A pdb=" N VAL A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.555A pdb=" N GLN A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.530A pdb=" N LEU A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.501A pdb=" N ASN A 299 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 300 " --> pdb=" O PHE A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 300' Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.785A pdb=" N VAL A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 421 through 433 Processing helix chain 'A' and resid 447 through 458 removed outlier: 3.653A pdb=" N VAL A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.937A pdb=" N PHE A 482 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 528 through 536 removed outlier: 3.678A pdb=" N LEU A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 564 through 575 removed outlier: 3.613A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 668 through 683 removed outlier: 4.534A pdb=" N TYR A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 718 removed outlier: 3.577A pdb=" N ALA A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'B' and resid 18 through 35 removed outlier: 3.554A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.888A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.502A pdb=" N ARG B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.073A pdb=" N ARG B 227 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.781A pdb=" N VAL B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.602A pdb=" N VAL B 314 " --> pdb=" O PRO B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 325 through 344 Processing helix chain 'B' and resid 353 through 366 Processing helix chain 'B' and resid 369 through 387 removed outlier: 5.158A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 408 Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 513 through 531 removed outlier: 3.706A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 removed outlier: 3.760A pdb=" N MET B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 555 " --> pdb=" O SER B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.819A pdb=" N ASN B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 590 removed outlier: 3.929A pdb=" N VAL B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 643 Processing helix chain 'B' and resid 647 through 664 Processing helix chain 'B' and resid 681 through 685 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.662A pdb=" N GLU B 699 " --> pdb=" O ARG B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 725 Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.606A pdb=" N GLU B 745 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.871A pdb=" N ALA B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 138 through 146 removed outlier: 4.059A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.619A pdb=" N ASN C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.703A pdb=" N PHE C 225 " --> pdb=" O TRP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 261 removed outlier: 4.099A pdb=" N GLY C 261 " --> pdb=" O MET C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.667A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.543A pdb=" N ILE C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 removed outlier: 3.735A pdb=" N TYR C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 413 removed outlier: 3.541A pdb=" N ALA C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 454 through 478 Processing helix chain 'C' and resid 483 through 504 Processing helix chain 'C' and resid 504 through 516 Processing helix chain 'C' and resid 522 through 548 Processing helix chain 'D' and resid 18 through 25 removed outlier: 3.717A pdb=" N GLY D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 48 Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 144 through 164 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 207 through 222 removed outlier: 3.584A pdb=" N THR D 222 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.543A pdb=" N ILE D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.589A pdb=" N ILE D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 347 through 357 removed outlier: 3.576A pdb=" N VAL D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER D 357 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 371 removed outlier: 3.553A pdb=" N ARG D 371 " --> pdb=" O PHE D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 379 removed outlier: 4.086A pdb=" N LYS D 378 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN D 379 " --> pdb=" O MET D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 399 removed outlier: 3.614A pdb=" N THR D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 429 Processing helix chain 'D' and resid 446 through 458 removed outlier: 3.904A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS D 452 " --> pdb=" O HIS D 448 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.694A pdb=" N GLU E 20 " --> pdb=" O ARG E 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 22 " --> pdb=" O TRP E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 22' Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 79 through 99 removed outlier: 3.607A pdb=" N CYS E 83 " --> pdb=" O ASN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 removed outlier: 4.596A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 157 Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.987A pdb=" N LEU E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 3.863A pdb=" N SER E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 4.260A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 321 through 325 removed outlier: 3.505A pdb=" N LEU E 325 " --> pdb=" O TYR E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 387 removed outlier: 4.117A pdb=" N HIS E 387 " --> pdb=" O PRO E 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.171A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 121 removed outlier: 3.811A pdb=" N LYS F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 151 Processing helix chain 'F' and resid 174 through 187 Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 222 through 230 removed outlier: 3.833A pdb=" N TYR F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 49 through 64 removed outlier: 4.061A pdb=" N GLY G 58 " --> pdb=" O GLN G 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 31 through 40 Processing helix chain 'H' and resid 65 through 82 removed outlier: 4.211A pdb=" N ILE H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 111 Processing helix chain 'H' and resid 114 through 129 removed outlier: 3.804A pdb=" N THR H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN H 129 " --> pdb=" O TYR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 190 removed outlier: 3.561A pdb=" N GLN H 134 " --> pdb=" O LYS H 130 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN H 166 " --> pdb=" O ARG H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 4.567A pdb=" N LYS A 52 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS A 59 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.640A pdb=" N GLU A 115 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 167 removed outlier: 7.100A pdb=" N VAL A 166 " --> pdb=" O LEU A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 removed outlier: 3.519A pdb=" N ILE A 407 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N MET A 438 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 466 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 440 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 337 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU A 490 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 339 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 604 through 607 removed outlier: 3.613A pdb=" N ILE A 605 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 659 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 508 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 661 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE A 690 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLU A 509 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.966A pdb=" N VAL B 10 " --> pdb=" O LEU B 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.629A pdb=" N VAL B 204 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY B 38 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N SER B 458 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 40 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS B 37 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ALA B 479 " --> pdb=" O HIS B 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 39 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AB2, first strand: chain 'B' and resid 567 through 569 removed outlier: 6.951A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY B 534 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE B 619 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 536 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE B 621 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE B 538 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS B 491 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE B 679 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 188 removed outlier: 3.572A pdb=" N LEU C 188 " --> pdb=" O VAL I 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.524A pdb=" N LEU D 66 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AB6, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AB7, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.995A pdb=" N PHE D 433 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 442 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 44 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN G 36 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 113 through 121 removed outlier: 4.687A pdb=" N ALA E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS E 110 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS E 116 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 108 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU E 120 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE E 104 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG E 59 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N GLY E 105 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N HIS E 60 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU E 168 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG E 165 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N SER E 197 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 113 through 121 removed outlier: 4.687A pdb=" N ALA E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS E 110 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS E 116 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 108 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU E 120 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE E 104 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL E 63 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR E 109 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL E 65 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL E 64 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG E 165 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N SER E 197 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 303 through 304 removed outlier: 4.036A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AC3, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC4, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.757A pdb=" N VAL F 59 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER F 159 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASP F 192 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE F 161 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N CYS F 194 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL F 163 " --> pdb=" O CYS F 194 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 253 through 254 removed outlier: 4.632A pdb=" N ALA F 253 " --> pdb=" O ILE F 262 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 23 through 24 1215 hydrogen bonds defined for protein. 3504 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: 5.46 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.44: 10754 1.44 - 1.65: 14627 1.65 - 1.86: 220 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 25613 Sorted by residual: bond pdb=" CG MET C 493 " pdb=" SD MET C 493 " ideal model delta sigma weight residual 1.803 1.767 0.036 2.50e-02 1.60e+03 2.08e+00 bond pdb=" C PRO D 193 " pdb=" N PRO D 194 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.02e+00 bond pdb=" CB ARG H 155 " pdb=" CG ARG H 155 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" C VAL C 211 " pdb=" N PRO C 212 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 bond pdb=" CB LYS E 77 " pdb=" CG LYS E 77 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 25608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 34451 2.84 - 5.68: 163 5.68 - 8.51: 17 8.51 - 11.35: 2 11.35 - 14.19: 2 Bond angle restraints: 34635 Sorted by residual: angle pdb=" N MET C 493 " pdb=" CA MET C 493 " pdb=" CB MET C 493 " ideal model delta sigma weight residual 110.12 117.29 -7.17 1.47e+00 4.63e-01 2.38e+01 angle pdb=" CA LEU C 127 " pdb=" CB LEU C 127 " pdb=" CG LEU C 127 " ideal model delta sigma weight residual 116.30 130.49 -14.19 3.50e+00 8.16e-02 1.64e+01 angle pdb=" CA LEU G 23 " pdb=" CB LEU G 23 " pdb=" CG LEU G 23 " ideal model delta sigma weight residual 116.30 129.47 -13.17 3.50e+00 8.16e-02 1.42e+01 angle pdb=" CB ARG H 155 " pdb=" CG ARG H 155 " pdb=" CD ARG H 155 " ideal model delta sigma weight residual 111.30 119.39 -8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 111.62 108.87 2.75 7.90e-01 1.60e+00 1.21e+01 ... (remaining 34630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 13412 17.80 - 35.61: 1645 35.61 - 53.41: 384 53.41 - 71.22: 117 71.22 - 89.02: 37 Dihedral angle restraints: 15595 sinusoidal: 6362 harmonic: 9233 Sorted by residual: dihedral pdb=" CA PHE B 610 " pdb=" C PHE B 610 " pdb=" N VAL B 611 " pdb=" CA VAL B 611 " ideal model delta harmonic sigma weight residual 180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA THR H 11 " pdb=" C THR H 11 " pdb=" N THR H 12 " pdb=" CA THR H 12 " ideal model delta harmonic sigma weight residual -180.00 -158.27 -21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PRO D 193 " pdb=" C PRO D 193 " pdb=" N PRO D 194 " pdb=" CA PRO D 194 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 15592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3305 0.055 - 0.110: 505 0.110 - 0.165: 82 0.165 - 0.220: 5 0.220 - 0.275: 2 Chirality restraints: 3899 Sorted by residual: chirality pdb=" CG LEU C 529 " pdb=" CB LEU C 529 " pdb=" CD1 LEU C 529 " pdb=" CD2 LEU C 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA MET C 493 " pdb=" N MET C 493 " pdb=" C MET C 493 " pdb=" CB MET C 493 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB THR C 538 " pdb=" CA THR C 538 " pdb=" OG1 THR C 538 " pdb=" CG2 THR C 538 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3896 not shown) Planarity restraints: 4443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 447 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C GLY D 447 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY D 447 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS D 448 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 193 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO D 194 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 194 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 194 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 449 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C SER D 449 " 0.036 2.00e-02 2.50e+03 pdb=" O SER D 449 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP D 450 " -0.012 2.00e-02 2.50e+03 ... (remaining 4440 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 473 2.69 - 3.24: 23876 3.24 - 3.80: 37549 3.80 - 4.35: 48412 4.35 - 4.90: 81947 Nonbonded interactions: 192257 Sorted by model distance: nonbonded pdb=" OG SER A 664 " pdb=" OG1 THR A 667 " model vdw 2.138 3.040 nonbonded pdb=" O ILE A 531 " pdb=" OG1 THR A 535 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASP H 114 " pdb=" ND2 ASN H 117 " model vdw 2.184 3.120 nonbonded pdb=" O LEU D 62 " pdb=" NH1 ARG D 115 " model vdw 2.201 3.120 nonbonded pdb=" O ALA F 206 " pdb=" OG1 THR F 210 " model vdw 2.202 3.040 ... (remaining 192252 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 30.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.002 0.039 25645 Z= 0.112 Angle : 0.563 14.190 34683 Z= 0.287 Chirality : 0.041 0.275 3899 Planarity : 0.004 0.066 4443 Dihedral : 17.128 89.023 9603 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.53 % Allowed : 21.65 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 3111 helix: 1.92 (0.14), residues: 1531 sheet: -0.94 (0.28), residues: 364 loop : -1.53 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 514 TYR 0.020 0.001 TYR C 516 PHE 0.013 0.001 PHE C 475 TRP 0.015 0.001 TRP B 342 HIS 0.006 0.001 HIS D 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (25613) covalent geometry : angle 0.54205 / 0.29 (34635) hydrogen bonds : bond 0.14304 / 9.37 ( 1211) hydrogen bonds : angle 5.27012 / 3.72 ( 3504) metal coordination : bond 0.00764 / 0.33 ( 32) metal coordination : angle 4.15272 / 2.50 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 253 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6909 (mp0) REVERT: A 450 MET cc_start: 0.7663 (mtm) cc_final: 0.7376 (tpt) REVERT: A 590 MET cc_start: 0.7807 (tpt) cc_final: 0.7441 (mmt) REVERT: B 271 LEU cc_start: 0.8394 (mt) cc_final: 0.8051 (mt) REVERT: B 284 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 421 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6837 (m-80) REVERT: C 363 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7772 (mt) REVERT: C 474 HIS cc_start: 0.8175 (m170) cc_final: 0.7911 (m-70) REVERT: C 493 MET cc_start: 0.5787 (mpp) cc_final: 0.5151 (mpp) REVERT: C 545 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6534 (ppp) REVERT: D 448 HIS cc_start: 0.7183 (t-170) cc_final: 0.6511 (p-80) REVERT: D 450 ASP cc_start: 0.6862 (t0) cc_final: 0.6497 (m-30) REVERT: E 31 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8627 (mmmm) REVERT: G 16 MET cc_start: 0.7887 (mmm) cc_final: 0.7642 (mmm) REVERT: G 32 LYS cc_start: 0.3331 (OUTLIER) cc_final: 0.3085 (tptt) REVERT: G 37 ASP cc_start: 0.6679 (p0) cc_final: 0.6187 (p0) REVERT: G 61 MET cc_start: 0.8501 (mmm) cc_final: 0.8196 (mmm) REVERT: G 64 ASN cc_start: 0.6551 (m-40) cc_final: 0.5801 (m110) REVERT: H 114 ASP cc_start: 0.7061 (t0) cc_final: 0.6766 (t0) REVERT: H 142 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7213 (mmm-85) REVERT: H 146 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7260 (mm-30) outliers start: 42 outliers final: 27 residues processed: 213 average time/residue: 0.1758 time to fit residues: 59.3001 Evaluate side-chains 213 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 129 ASN Chi-restraints excluded: chain H residue 131 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 254 GLN A 281 GLN A 373 GLN A 377 GLN A 415 HIS A 539 ASN A 545 GLN A 625 GLN A 629 HIS A 714 GLN B 21 GLN B 262 ASN B 434 HIS B 613 HIS B 662 GLN C 213 HIS C 226 GLN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN C 367 ASN C 409 GLN C 496 ASN D 20 GLN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 99 GLN D 116 GLN D 117 ASN D 177 GLN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 227 HIS E 257 HIS E 376 HIS F 9 ASN ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 260 ASN G 18 GLN G 42 HIS H 96 ASN H 129 ASN H 158 ASN H 200 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.107127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.069603 restraints weight = 56953.803| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.18 r_work: 0.2846 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25645 Z= 0.269 Angle : 0.643 16.704 34683 Z= 0.327 Chirality : 0.045 0.239 3899 Planarity : 0.004 0.059 4443 Dihedral : 5.529 58.859 3474 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.31 % Allowed : 20.12 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3111 helix: 1.71 (0.13), residues: 1562 sheet: -1.00 (0.28), residues: 334 loop : -1.61 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 115 TYR 0.019 0.002 TYR A 534 PHE 0.019 0.002 PHE A 659 TRP 0.016 0.002 TRP F 229 HIS 0.008 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.27 (25613) covalent geometry : angle 0.61443 / 0.33 (34635) hydrogen bonds : bond 0.06057 / 4.02 ( 1211) hydrogen bonds : angle 4.59773 / 3.23 ( 3504) metal coordination : bond 0.01427 / 0.71 ( 32) metal coordination : angle 5.17168 / 3.10 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 190 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8500 (ptp) cc_final: 0.8175 (ptp) REVERT: A 437 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8599 (tp) REVERT: A 450 MET cc_start: 0.8003 (mtm) cc_final: 0.7697 (tpt) REVERT: A 569 LYS cc_start: 0.7866 (mttp) cc_final: 0.7604 (ptpt) REVERT: A 693 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7205 (mp) REVERT: A 717 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6964 (mm) REVERT: B 284 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7746 (tm-30) REVERT: B 286 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8075 (mmm160) REVERT: B 421 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: B 533 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7900 (t0) REVERT: B 634 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8642 (mttp) REVERT: C 215 MET cc_start: 0.8012 (ptp) cc_final: 0.7772 (ptp) REVERT: D 110 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9003 (mp) REVERT: D 185 MET cc_start: 0.8277 (mtp) cc_final: 0.7932 (mtp) REVERT: D 393 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8421 (mp) REVERT: D 448 HIS cc_start: 0.7149 (t-170) cc_final: 0.6459 (p-80) REVERT: D 450 ASP cc_start: 0.6709 (t0) cc_final: 0.6283 (m-30) REVERT: E 31 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8814 (mmmm) REVERT: G 16 MET cc_start: 0.7968 (mmm) cc_final: 0.7545 (tpt) REVERT: G 32 LYS cc_start: 0.2496 (tptt) cc_final: 0.1314 (ptmt) REVERT: G 61 MET cc_start: 0.8466 (mmm) cc_final: 0.8161 (mmm) REVERT: G 64 ASN cc_start: 0.6483 (m-40) cc_final: 0.5711 (m110) REVERT: H 114 ASP cc_start: 0.7241 (t0) cc_final: 0.7016 (t0) REVERT: H 142 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7617 (mmm-85) outliers start: 91 outliers final: 49 residues processed: 269 average time/residue: 0.1756 time to fit residues: 75.1106 Evaluate side-chains 236 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 129 ASN Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 289 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN G 42 HIS H 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.109000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071607 restraints weight = 56664.444| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.18 r_work: 0.2887 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25645 Z= 0.135 Angle : 0.534 14.055 34683 Z= 0.269 Chirality : 0.041 0.192 3899 Planarity : 0.004 0.059 4443 Dihedral : 4.586 49.208 3434 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.84 % Allowed : 20.60 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 3111 helix: 1.93 (0.13), residues: 1571 sheet: -0.99 (0.28), residues: 349 loop : -1.49 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 161 TYR 0.018 0.001 TYR A 534 PHE 0.019 0.001 PHE C 500 TRP 0.013 0.001 TRP B 342 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (25613) covalent geometry : angle 0.51062 / 0.27 (34635) hydrogen bonds : bond 0.04595 / 3.07 ( 1211) hydrogen bonds : angle 4.21055 / 2.95 ( 3504) metal coordination : bond 0.00849 / 0.40 ( 32) metal coordination : angle 4.23850 / 2.47 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 184 time to evaluate : 1.082 Fit side-chains REVERT: A 437 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 450 MET cc_start: 0.7838 (ttm) cc_final: 0.7508 (tpt) REVERT: A 569 LYS cc_start: 0.7855 (mttp) cc_final: 0.7563 (ptpt) REVERT: A 717 LEU cc_start: 0.7228 (tp) cc_final: 0.6957 (mm) REVERT: B 284 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 286 ARG cc_start: 0.8479 (mmm160) cc_final: 0.8152 (mmm160) REVERT: B 421 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: B 533 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7775 (t0) REVERT: B 634 LYS cc_start: 0.9162 (mtpt) cc_final: 0.8650 (mttt) REVERT: C 215 MET cc_start: 0.7986 (ptp) cc_final: 0.7770 (ptp) REVERT: C 528 MET cc_start: 0.7900 (mtp) cc_final: 0.7517 (mtp) REVERT: D 110 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8894 (mp) REVERT: D 185 MET cc_start: 0.8255 (mtp) cc_final: 0.7909 (mtp) REVERT: D 441 MET cc_start: 0.5937 (ttm) cc_final: 0.5585 (tpp) REVERT: D 448 HIS cc_start: 0.7334 (t-170) cc_final: 0.6548 (p-80) REVERT: D 450 ASP cc_start: 0.6792 (t0) cc_final: 0.6307 (m-30) REVERT: D 451 VAL cc_start: 0.6659 (OUTLIER) cc_final: 0.6200 (p) REVERT: E 31 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8825 (mmmm) REVERT: G 16 MET cc_start: 0.8044 (mmm) cc_final: 0.7740 (tpt) REVERT: G 32 LYS cc_start: 0.3016 (tptt) cc_final: 0.2284 (ptmt) REVERT: G 61 MET cc_start: 0.8432 (mmm) cc_final: 0.8116 (mmm) REVERT: G 64 ASN cc_start: 0.6481 (m-40) cc_final: 0.5487 (m110) REVERT: H 114 ASP cc_start: 0.7120 (t0) cc_final: 0.6747 (t0) REVERT: H 142 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7283 (mmm-85) REVERT: H 146 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7114 (mm-30) REVERT: I 167 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6671 (tt) outliers start: 78 outliers final: 47 residues processed: 249 average time/residue: 0.1769 time to fit residues: 70.2131 Evaluate side-chains 226 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 272 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 292 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS H 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.108452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070992 restraints weight = 56613.474| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.17 r_work: 0.2875 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25645 Z= 0.166 Angle : 0.546 14.458 34683 Z= 0.275 Chirality : 0.041 0.244 3899 Planarity : 0.004 0.060 4443 Dihedral : 4.368 49.644 3428 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.53 % Allowed : 20.27 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 3111 helix: 1.94 (0.13), residues: 1564 sheet: -0.98 (0.28), residues: 349 loop : -1.49 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 125 TYR 0.018 0.001 TYR A 534 PHE 0.016 0.001 PHE A 659 TRP 0.011 0.001 TRP B 342 HIS 0.006 0.001 HIS G 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (25613) covalent geometry : angle 0.52247 / 0.27 (34635) hydrogen bonds : bond 0.04766 / 3.18 ( 1211) hydrogen bonds : angle 4.19975 / 2.95 ( 3504) metal coordination : bond 0.00899 / 0.44 ( 32) metal coordination : angle 4.26234 / 2.49 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 180 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 427 MET cc_start: 0.7118 (tpp) cc_final: 0.6874 (mmt) REVERT: A 437 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8636 (tp) REVERT: A 450 MET cc_start: 0.7907 (ttm) cc_final: 0.7601 (tpt) REVERT: A 569 LYS cc_start: 0.7795 (mttp) cc_final: 0.7518 (ptpt) REVERT: A 717 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6954 (mm) REVERT: B 156 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8398 (ttp-110) REVERT: B 284 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7614 (tm-30) REVERT: B 286 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8158 (mmm160) REVERT: B 421 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: B 533 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7830 (t0) REVERT: B 634 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8663 (mttt) REVERT: C 215 MET cc_start: 0.8033 (ptp) cc_final: 0.7796 (ptp) REVERT: C 474 HIS cc_start: 0.8282 (m170) cc_final: 0.7954 (m-70) REVERT: C 528 MET cc_start: 0.7925 (mtp) cc_final: 0.7552 (mtp) REVERT: D 110 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8947 (mp) REVERT: D 185 MET cc_start: 0.8225 (mtp) cc_final: 0.7871 (mtp) REVERT: D 334 MET cc_start: 0.8400 (mmm) cc_final: 0.8198 (mmt) REVERT: D 441 MET cc_start: 0.5882 (ttm) cc_final: 0.5526 (tpp) REVERT: D 448 HIS cc_start: 0.7201 (t-170) cc_final: 0.6465 (p-80) REVERT: E 31 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8839 (mmmm) REVERT: F 68 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: G 16 MET cc_start: 0.8047 (mmm) cc_final: 0.7605 (tpt) REVERT: G 32 LYS cc_start: 0.4078 (tptt) cc_final: 0.2443 (ptmt) REVERT: G 36 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6570 (pm20) REVERT: G 61 MET cc_start: 0.8424 (mmm) cc_final: 0.8109 (mmm) REVERT: G 64 ASN cc_start: 0.6449 (m-40) cc_final: 0.5472 (m110) REVERT: H 114 ASP cc_start: 0.7144 (t0) cc_final: 0.6877 (t0) REVERT: H 142 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7313 (mmm-85) REVERT: H 146 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7116 (mm-30) outliers start: 97 outliers final: 61 residues processed: 259 average time/residue: 0.1821 time to fit residues: 74.1451 Evaluate side-chains 244 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 175 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 194 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.108046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.070576 restraints weight = 56434.369| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.18 r_work: 0.2867 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25645 Z= 0.185 Angle : 0.563 14.834 34683 Z= 0.284 Chirality : 0.042 0.212 3899 Planarity : 0.004 0.061 4443 Dihedral : 4.445 52.480 3428 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.68 % Allowed : 20.89 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 3111 helix: 1.87 (0.13), residues: 1569 sheet: -1.01 (0.28), residues: 351 loop : -1.53 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 125 TYR 0.018 0.001 TYR A 534 PHE 0.019 0.001 PHE C 500 TRP 0.011 0.001 TRP F 229 HIS 0.005 0.001 HIS B 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (25613) covalent geometry : angle 0.53871 / 0.28 (34635) hydrogen bonds : bond 0.04947 / 3.30 ( 1211) hydrogen bonds : angle 4.22190 / 2.97 ( 3504) metal coordination : bond 0.00979 / 0.49 ( 32) metal coordination : angle 4.39603 / 2.57 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 176 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8341 (pm20) REVERT: A 427 MET cc_start: 0.7194 (tpp) cc_final: 0.6863 (mmt) REVERT: A 437 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 450 MET cc_start: 0.7969 (ttm) cc_final: 0.7662 (tpt) REVERT: A 569 LYS cc_start: 0.7866 (mttp) cc_final: 0.7561 (ptpt) REVERT: A 590 MET cc_start: 0.7939 (tpt) cc_final: 0.7397 (mmt) REVERT: A 717 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7081 (mm) REVERT: B 284 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 286 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8156 (mmm160) REVERT: B 421 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: B 533 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7816 (t0) REVERT: B 634 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8648 (mttt) REVERT: C 215 MET cc_start: 0.7935 (ptp) cc_final: 0.7685 (ptp) REVERT: C 474 HIS cc_start: 0.8328 (m170) cc_final: 0.7986 (m-70) REVERT: D 393 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8372 (mp) REVERT: D 441 MET cc_start: 0.5954 (ttm) cc_final: 0.5453 (tpp) REVERT: D 448 HIS cc_start: 0.7173 (t-170) cc_final: 0.6535 (p-80) REVERT: D 450 ASP cc_start: 0.6550 (t70) cc_final: 0.6284 (p0) REVERT: F 68 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: G 16 MET cc_start: 0.8043 (mmm) cc_final: 0.7603 (tpt) REVERT: G 36 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: G 42 HIS cc_start: 0.6653 (m90) cc_final: 0.6447 (m90) REVERT: G 59 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7372 (pt0) REVERT: G 61 MET cc_start: 0.8469 (mmm) cc_final: 0.8182 (mmm) REVERT: G 64 ASN cc_start: 0.6430 (m-40) cc_final: 0.5458 (m110) REVERT: H 114 ASP cc_start: 0.7200 (t0) cc_final: 0.6898 (t0) REVERT: H 146 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7214 (mm-30) REVERT: H 208 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6552 (pp) outliers start: 101 outliers final: 73 residues processed: 258 average time/residue: 0.1730 time to fit residues: 71.5511 Evaluate side-chains 254 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 172 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain I residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 286 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 246 optimal weight: 0.0030 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN H 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.108526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.071134 restraints weight = 56528.222| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.25 r_work: 0.2878 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25645 Z= 0.152 Angle : 0.538 14.052 34683 Z= 0.271 Chirality : 0.041 0.200 3899 Planarity : 0.004 0.060 4443 Dihedral : 4.362 53.166 3428 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.53 % Allowed : 21.14 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 3111 helix: 1.95 (0.13), residues: 1570 sheet: -0.97 (0.28), residues: 351 loop : -1.52 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 161 TYR 0.018 0.001 TYR A 534 PHE 0.023 0.001 PHE E 39 TRP 0.012 0.001 TRP B 342 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (25613) covalent geometry : angle 0.51561 / 0.27 (34635) hydrogen bonds : bond 0.04570 / 3.06 ( 1211) hydrogen bonds : angle 4.11758 / 2.89 ( 3504) metal coordination : bond 0.00816 / 0.41 ( 32) metal coordination : angle 4.16668 / 2.41 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 176 time to evaluate : 1.132 Fit side-chains REVERT: A 55 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: A 427 MET cc_start: 0.7225 (tpp) cc_final: 0.7003 (mmt) REVERT: A 450 MET cc_start: 0.7930 (ttm) cc_final: 0.7632 (tpt) REVERT: A 569 LYS cc_start: 0.7901 (mttp) cc_final: 0.7593 (ptpt) REVERT: A 683 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: A 717 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7118 (mm) REVERT: B 284 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 286 ARG cc_start: 0.8524 (mmm160) cc_final: 0.8205 (mmm160) REVERT: B 421 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: B 533 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7907 (t0) REVERT: B 634 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8628 (mttt) REVERT: C 215 MET cc_start: 0.7937 (ptp) cc_final: 0.7687 (ptp) REVERT: C 474 HIS cc_start: 0.8263 (m170) cc_final: 0.7973 (m-70) REVERT: D 185 MET cc_start: 0.8185 (mtp) cc_final: 0.7859 (mtp) REVERT: D 259 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8926 (mm) REVERT: D 393 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8350 (mp) REVERT: D 441 MET cc_start: 0.5952 (ttm) cc_final: 0.5684 (tpp) REVERT: D 448 HIS cc_start: 0.7145 (t-170) cc_final: 0.6514 (p-80) REVERT: D 450 ASP cc_start: 0.6345 (t70) cc_final: 0.6049 (p0) REVERT: F 68 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7675 (ttm170) REVERT: G 16 MET cc_start: 0.8053 (mmm) cc_final: 0.7642 (tpt) REVERT: G 42 HIS cc_start: 0.6681 (m90) cc_final: 0.6450 (m90) REVERT: G 61 MET cc_start: 0.8471 (mmm) cc_final: 0.8166 (mmm) REVERT: G 64 ASN cc_start: 0.6704 (m-40) cc_final: 0.5806 (m110) REVERT: H 114 ASP cc_start: 0.7358 (t0) cc_final: 0.7055 (t0) REVERT: H 142 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7225 (mmm-85) REVERT: H 146 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7298 (mm-30) REVERT: H 208 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6555 (pp) outliers start: 97 outliers final: 72 residues processed: 256 average time/residue: 0.1700 time to fit residues: 69.5793 Evaluate side-chains 254 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 173 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain I residue 167 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 42 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 292 optimal weight: 0.0670 chunk 308 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN G 36 GLN H 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.107731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.069349 restraints weight = 55551.143| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.84 r_work: 0.2833 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25645 Z= 0.192 Angle : 0.566 14.713 34683 Z= 0.285 Chirality : 0.042 0.215 3899 Planarity : 0.004 0.061 4443 Dihedral : 4.440 54.884 3428 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.42 % Allowed : 21.87 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 3111 helix: 1.89 (0.13), residues: 1566 sheet: -1.02 (0.29), residues: 341 loop : -1.52 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 161 TYR 0.018 0.001 TYR A 534 PHE 0.026 0.001 PHE E 39 TRP 0.011 0.001 TRP F 229 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (25613) covalent geometry : angle 0.54300 / 0.28 (34635) hydrogen bonds : bond 0.04928 / 3.29 ( 1211) hydrogen bonds : angle 4.20020 / 2.95 ( 3504) metal coordination : bond 0.00985 / 0.50 ( 32) metal coordination : angle 4.34314 / 2.52 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 173 time to evaluate : 1.039 Fit side-chains REVERT: A 55 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: A 427 MET cc_start: 0.7239 (tpp) cc_final: 0.6908 (mmt) REVERT: A 437 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 450 MET cc_start: 0.7942 (ttm) cc_final: 0.7580 (tpt) REVERT: A 569 LYS cc_start: 0.7916 (mttp) cc_final: 0.7587 (ptpt) REVERT: A 590 MET cc_start: 0.8074 (tpt) cc_final: 0.7402 (mmt) REVERT: A 717 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7120 (mm) REVERT: B 284 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 286 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8156 (mmm160) REVERT: B 421 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: B 533 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8059 (t0) REVERT: B 634 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8510 (mttt) REVERT: C 215 MET cc_start: 0.7943 (ptp) cc_final: 0.7667 (ptp) REVERT: C 474 HIS cc_start: 0.8251 (m170) cc_final: 0.7947 (m-70) REVERT: D 185 MET cc_start: 0.8163 (mtp) cc_final: 0.7827 (mtp) REVERT: D 259 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8881 (mm) REVERT: D 393 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8265 (mp) REVERT: D 441 MET cc_start: 0.5957 (ttm) cc_final: 0.5446 (tpp) REVERT: D 448 HIS cc_start: 0.7186 (t-170) cc_final: 0.6556 (p-80) REVERT: D 450 ASP cc_start: 0.6232 (t70) cc_final: 0.5931 (p0) REVERT: F 68 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7754 (ttm170) REVERT: G 16 MET cc_start: 0.8036 (mmm) cc_final: 0.7638 (tpt) REVERT: G 42 HIS cc_start: 0.6654 (m90) cc_final: 0.6417 (m90) REVERT: G 59 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7198 (pt0) REVERT: G 61 MET cc_start: 0.8493 (mmm) cc_final: 0.7941 (mmm) REVERT: G 64 ASN cc_start: 0.6710 (m-40) cc_final: 0.5653 (m110) REVERT: H 114 ASP cc_start: 0.7415 (t0) cc_final: 0.7102 (t0) REVERT: H 142 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7266 (mmm160) REVERT: H 146 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7278 (mm-30) outliers start: 94 outliers final: 77 residues processed: 250 average time/residue: 0.1739 time to fit residues: 69.4035 Evaluate side-chains 259 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 174 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 167 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 294 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.107900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.071252 restraints weight = 55434.376| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.19 r_work: 0.2822 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25645 Z= 0.176 Angle : 0.560 14.465 34683 Z= 0.281 Chirality : 0.042 0.209 3899 Planarity : 0.004 0.061 4443 Dihedral : 4.427 56.059 3428 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.38 % Allowed : 22.02 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 3111 helix: 1.91 (0.13), residues: 1566 sheet: -1.00 (0.29), residues: 341 loop : -1.54 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 161 TYR 0.018 0.001 TYR A 534 PHE 0.022 0.001 PHE E 39 TRP 0.011 0.001 TRP F 229 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (25613) covalent geometry : angle 0.53672 / 0.28 (34635) hydrogen bonds : bond 0.04784 / 3.20 ( 1211) hydrogen bonds : angle 4.16395 / 2.92 ( 3504) metal coordination : bond 0.00920 / 0.46 ( 32) metal coordination : angle 4.29339 / 2.48 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 178 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: A 427 MET cc_start: 0.7080 (tpp) cc_final: 0.6754 (mmt) REVERT: A 450 MET cc_start: 0.7953 (ttm) cc_final: 0.7593 (tpt) REVERT: A 569 LYS cc_start: 0.7887 (mttp) cc_final: 0.7627 (ptpt) REVERT: A 717 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7116 (mm) REVERT: B 284 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 286 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8219 (mmm160) REVERT: B 421 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: B 533 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8049 (t0) REVERT: B 634 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8525 (mttt) REVERT: C 215 MET cc_start: 0.7961 (ptp) cc_final: 0.7682 (ptp) REVERT: C 474 HIS cc_start: 0.8269 (m170) cc_final: 0.7959 (m-70) REVERT: D 185 MET cc_start: 0.8177 (mtp) cc_final: 0.7836 (mtp) REVERT: D 259 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8889 (mm) REVERT: D 393 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8290 (mp) REVERT: D 441 MET cc_start: 0.5987 (ttm) cc_final: 0.5638 (tpp) REVERT: D 448 HIS cc_start: 0.7098 (t-170) cc_final: 0.6479 (p-80) REVERT: D 450 ASP cc_start: 0.5909 (t70) cc_final: 0.5531 (p0) REVERT: F 68 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7781 (ttm170) REVERT: G 16 MET cc_start: 0.8030 (mmm) cc_final: 0.7647 (tpt) REVERT: G 32 LYS cc_start: 0.4404 (tptt) cc_final: 0.4097 (tptp) REVERT: G 59 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7452 (pt0) REVERT: G 61 MET cc_start: 0.8438 (mmm) cc_final: 0.7934 (mmm) REVERT: G 64 ASN cc_start: 0.6749 (m-40) cc_final: 0.5739 (m110) REVERT: H 114 ASP cc_start: 0.7400 (t0) cc_final: 0.6446 (t0) REVERT: H 117 ASN cc_start: 0.9139 (m-40) cc_final: 0.8685 (p0) REVERT: H 142 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7254 (mmm160) REVERT: H 146 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7329 (mm-30) outliers start: 93 outliers final: 78 residues processed: 254 average time/residue: 0.1682 time to fit residues: 68.3606 Evaluate side-chains 259 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 174 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 194 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 167 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 295 optimal weight: 50.0000 chunk 270 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 144 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.108676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071696 restraints weight = 55985.129| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.28 r_work: 0.2834 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25645 Z= 0.145 Angle : 0.538 13.462 34683 Z= 0.269 Chirality : 0.041 0.195 3899 Planarity : 0.004 0.061 4443 Dihedral : 4.323 57.220 3428 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.28 % Allowed : 22.05 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 3111 helix: 2.05 (0.13), residues: 1561 sheet: -0.95 (0.28), residues: 351 loop : -1.48 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 161 TYR 0.018 0.001 TYR A 534 PHE 0.033 0.001 PHE E 39 TRP 0.012 0.001 TRP B 342 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (25613) covalent geometry : angle 0.51576 / 0.27 (34635) hydrogen bonds : bond 0.04369 / 2.93 ( 1211) hydrogen bonds : angle 4.05818 / 2.84 ( 3504) metal coordination : bond 0.00818 / 0.39 ( 32) metal coordination : angle 4.11258 / 2.36 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 174 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: A 427 MET cc_start: 0.7073 (tpp) cc_final: 0.6757 (mmt) REVERT: A 437 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8611 (tp) REVERT: A 450 MET cc_start: 0.7920 (ttm) cc_final: 0.7557 (tpt) REVERT: A 590 MET cc_start: 0.7948 (tpt) cc_final: 0.7362 (mmt) REVERT: A 683 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: A 717 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7114 (mm) REVERT: B 284 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 286 ARG cc_start: 0.8520 (mmm160) cc_final: 0.8194 (mmm160) REVERT: B 421 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: B 634 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8501 (mttt) REVERT: C 215 MET cc_start: 0.7950 (ptp) cc_final: 0.7675 (ptp) REVERT: C 363 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7902 (mt) REVERT: C 474 HIS cc_start: 0.8299 (m170) cc_final: 0.8099 (m-70) REVERT: D 185 MET cc_start: 0.8166 (mtp) cc_final: 0.7817 (mtp) REVERT: D 259 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8881 (mm) REVERT: D 441 MET cc_start: 0.5897 (ttm) cc_final: 0.5429 (tpp) REVERT: D 448 HIS cc_start: 0.7091 (t-170) cc_final: 0.6447 (p-80) REVERT: F 68 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7653 (ttm170) REVERT: G 16 MET cc_start: 0.8128 (mmm) cc_final: 0.7786 (tpt) REVERT: G 59 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7588 (pt0) REVERT: G 61 MET cc_start: 0.8436 (mmm) cc_final: 0.8153 (mmt) REVERT: G 64 ASN cc_start: 0.6741 (m-40) cc_final: 0.6081 (m-40) REVERT: H 114 ASP cc_start: 0.7433 (t0) cc_final: 0.6481 (t0) REVERT: H 117 ASN cc_start: 0.9131 (m-40) cc_final: 0.8665 (p0) REVERT: H 142 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7303 (mmm-85) REVERT: H 146 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7173 (mm-30) outliers start: 90 outliers final: 71 residues processed: 250 average time/residue: 0.1652 time to fit residues: 66.4875 Evaluate side-chains 250 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 171 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 289 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.108018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.071415 restraints weight = 55238.467| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.19 r_work: 0.2824 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25645 Z= 0.168 Angle : 0.560 14.099 34683 Z= 0.280 Chirality : 0.042 0.223 3899 Planarity : 0.004 0.061 4443 Dihedral : 4.379 58.200 3428 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.20 % Allowed : 22.05 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 3111 helix: 1.99 (0.13), residues: 1561 sheet: -0.98 (0.28), residues: 351 loop : -1.50 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 161 TYR 0.018 0.001 TYR A 534 PHE 0.032 0.001 PHE E 39 TRP 0.011 0.001 TRP B 342 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (25613) covalent geometry : angle 0.53782 / 0.28 (34635) hydrogen bonds : bond 0.04678 / 3.12 ( 1211) hydrogen bonds : angle 4.11807 / 2.89 ( 3504) metal coordination : bond 0.00903 / 0.44 ( 32) metal coordination : angle 4.19028 / 2.42 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 170 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: A 437 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8609 (tp) REVERT: A 450 MET cc_start: 0.7950 (ttm) cc_final: 0.7586 (tpt) REVERT: A 590 MET cc_start: 0.7958 (tpt) cc_final: 0.7348 (mmt) REVERT: A 683 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: A 717 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7121 (mm) REVERT: B 284 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 286 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8188 (mmm160) REVERT: B 421 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: B 634 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8504 (mttt) REVERT: C 215 MET cc_start: 0.7964 (ptp) cc_final: 0.7687 (ptp) REVERT: C 363 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 474 HIS cc_start: 0.8344 (m170) cc_final: 0.8140 (m-70) REVERT: D 185 MET cc_start: 0.8164 (mtp) cc_final: 0.7817 (mtp) REVERT: D 259 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8870 (mm) REVERT: D 393 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8264 (mp) REVERT: D 441 MET cc_start: 0.5967 (ttm) cc_final: 0.5608 (tpp) REVERT: D 448 HIS cc_start: 0.7124 (t-170) cc_final: 0.6482 (p-80) REVERT: F 68 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7716 (ttm170) REVERT: G 64 ASN cc_start: 0.6279 (m-40) cc_final: 0.5590 (m-40) REVERT: H 114 ASP cc_start: 0.7507 (t0) cc_final: 0.6553 (t0) REVERT: H 117 ASN cc_start: 0.9131 (m-40) cc_final: 0.8668 (p0) REVERT: H 142 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7468 (mmm-85) outliers start: 88 outliers final: 73 residues processed: 246 average time/residue: 0.1711 time to fit residues: 66.9883 Evaluate side-chains 249 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 167 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 251 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.109323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.072787 restraints weight = 55316.775| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.24 r_work: 0.2856 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25645 Z= 0.119 Angle : 0.527 12.469 34683 Z= 0.262 Chirality : 0.040 0.264 3899 Planarity : 0.004 0.061 4443 Dihedral : 4.229 58.685 3428 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.73 % Allowed : 22.67 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 3111 helix: 2.16 (0.14), residues: 1561 sheet: -0.86 (0.29), residues: 351 loop : -1.46 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 161 TYR 0.018 0.001 TYR A 534 PHE 0.035 0.001 PHE E 39 TRP 0.014 0.001 TRP B 342 HIS 0.006 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (25613) covalent geometry : angle 0.50747 / 0.26 (34635) hydrogen bonds : bond 0.04000 / 2.68 ( 1211) hydrogen bonds : angle 3.95420 / 2.77 ( 3504) metal coordination : bond 0.00670 / 0.31 ( 32) metal coordination : angle 3.86314 / 2.21 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6557.47 seconds wall clock time: 113 minutes 2.95 seconds (6782.95 seconds total)