Starting phenix.real_space_refine on Tue Jul 7 00:41:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pd4_71525/07_2026/9pd4_71525.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pd4_71525/07_2026/9pd4_71525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pd4_71525/07_2026/9pd4_71525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pd4_71525/07_2026/9pd4_71525.map" model { file = "/net/cci-nas-00/data/ceres_data/9pd4_71525/07_2026/9pd4_71525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pd4_71525/07_2026/9pd4_71525.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 101 5.49 5 S 219 5.16 5 C 25208 2.51 5 N 6894 2.21 5 O 7620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40053 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 4947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4947 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 1 Chain: "B" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5745 Classifications: {'peptide': 712} Link IDs: {'PTRANS': 30, 'TRANS': 681} Chain breaks: 1 Chain: "C" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 Chain: "D" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3483 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 1 Chain: "E" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2686 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 324} Chain breaks: 2 Chain: "F" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2001 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 1 Chain: "G" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "S" Number of atoms: 3829 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 466, 3814 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 444} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 466, 3814 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 444} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3881 Chain: "Q" Number of atoms: 5001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5001 Classifications: {'peptide': 632} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 29, 'TRANS': 602} Chain breaks: 7 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 983 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} 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: "K" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1724 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 201} Chain breaks: 3 Chain: "L" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 729 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "L" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 302 Unusual residues: {'VM6': 1} Classifications: {'DNA': 13, 'undetermined': 1} Link IDs: {'rna3p': 12, None: 1} Not linked: pdbres="VM6 L 63 " pdbres=" DC L 64 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1055 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "N" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3420 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 12, 'TRANS': 414} Chain breaks: 1 Chain: "O" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1538 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 1 Chain: "P" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 950 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} 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: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5890 SG CYS B 116 122.223 57.735 66.527 1.00162.76 S ATOM 6199 SG CYS B 155 127.250 54.174 63.543 1.00164.50 S ATOM 6030 SG CYS B 134 123.737 52.272 68.692 1.00149.78 S ATOM 6488 SG CYS B 190 127.980 57.143 69.040 1.00142.43 S ATOM 17669 SG CYS E 345 80.235 148.684 58.022 1.00180.43 S ATOM 17691 SG CYS E 348 78.146 145.527 58.596 1.00198.49 S ATOM 17848 SG CYS E 368 80.346 146.847 61.376 1.00200.05 S ATOM 17869 SG CYS E 371 81.870 145.260 58.256 1.00226.60 S ATOM 17789 SG CYS E 360 93.169 149.179 56.223 1.00211.72 S ATOM 17807 SG CYS E 363 90.960 149.911 53.216 1.00219.18 S ATOM 17956 SG CYS E 382 90.560 146.654 55.066 1.00188.36 S ATOM 17973 SG CYS E 385 93.668 147.263 52.946 1.00181.89 S ATOM 17233 SG CYS E 291 104.047 112.526 33.935 1.00257.91 S ATOM 17255 SG CYS E 294 103.918 108.683 34.016 1.00291.12 S ATOM 17344 SG CYS E 305 104.740 110.457 37.119 1.00257.12 S ATOM 17367 SG CYS E 308 107.275 110.312 34.281 1.00255.34 S ATOM 19836 SG CYS F 268 108.384 125.245 52.182 1.00190.77 S ATOM 19855 SG CYS F 271 105.717 127.880 52.719 1.00215.51 S ATOM 19940 SG CYS F 282 109.100 128.937 51.399 1.00246.15 S ATOM 19960 SG CYS F 285 108.748 127.651 55.010 1.00235.17 S ATOM 19728 SG CYS F 255 106.093 130.256 40.809 1.00218.25 S ATOM 19745 SG CYS F 257 108.386 133.190 41.555 1.00235.27 S ATOM 19894 SG CYS F 276 109.464 130.592 38.962 1.00233.19 S ATOM 30722 SG CYS K 105 115.574 107.049 159.512 1.00191.01 S ATOM 30746 SG CYS K 108 118.139 106.461 162.206 1.00195.76 S ATOM 30894 SG CYS K 126 118.323 104.508 158.905 1.00184.70 S ATOM 30916 SG CYS K 129 115.659 103.701 161.440 1.00175.77 S ATOM 36432 SG CYS N 481 129.107 77.184 162.461 1.00239.63 S ATOM 36469 SG CYS N 486 129.908 76.857 158.713 1.00221.34 S ATOM 36585 SG CYS N 500 126.189 77.268 159.636 1.00261.33 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLU S 887 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU S 887 " occ=0.46 residue: pdb=" N ASER S 893 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER S 893 " occ=0.48 Time building chain proxies: 7.52, per 1000 atoms: 0.19 Number of scatterers: 40053 At special positions: 0 Unit cell: (187.425, 172.431, 182.427, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 219 16.00 P 101 15.00 O 7620 8.00 N 6894 7.00 C 25208 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " 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 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb=" ZN E 403 " 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 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" ND1 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 108 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 129 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " pdb=" ZN N1000 " pdb="ZN ZN N1000 " - pdb=" SG CYS N 500 " pdb="ZN ZN N1000 " - pdb=" SG CYS N 481 " pdb="ZN ZN N1000 " - pdb=" SG CYS N 486 " Number of angles added : 33 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9014 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 47 sheets defined 42.3% alpha, 14.4% beta 26 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.839A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.705A pdb=" N ILE A 285 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.653A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 451 through 457 removed outlier: 4.178A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 565 through 573 removed outlier: 3.638A pdb=" N GLU A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 removed outlier: 3.710A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.920A pdb=" N VAL A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 676 Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 706 through 716 Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 140 through 148 removed outlier: 4.320A pdb=" N HIS B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.769A pdb=" N LEU B 213 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.876A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.819A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 286 Processing helix chain 'B' and resid 324 through 344 removed outlier: 4.083A pdb=" N HIS B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.919A pdb=" N PHE B 357 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 364 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 376 through 386 Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 464 through 470 Proline residue: B 468 - end of helix No H-bonds generated for 'chain 'B' and resid 464 through 470' Processing helix chain 'B' and resid 508 through 510 No H-bonds generated for 'chain 'B' and resid 508 through 510' Processing helix chain 'B' and resid 514 through 527 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 558 through 564 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 603 through 607 Processing helix chain 'B' and resid 632 through 643 Processing helix chain 'B' and resid 648 through 664 Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 692 removed outlier: 4.313A pdb=" N LYS B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 701 removed outlier: 4.414A pdb=" N HIS B 700 " --> pdb=" O TRP B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 725 Processing helix chain 'B' and resid 730 through 736 removed outlier: 4.281A pdb=" N LEU B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 413 Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 455 through 477 Processing helix chain 'C' and resid 484 through 515 removed outlier: 3.672A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 503 " --> pdb=" O ARG C 499 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 521 through 547 Processing helix chain 'D' and resid 19 through 25 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.530A pdb=" N GLY D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 50 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 112 through 123 Processing helix chain 'D' and resid 145 through 164 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 348 through 356 Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 385 through 395 Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.382A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.848A pdb=" N ARG E 320 " --> pdb=" O PRO E 316 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 103 through 120 Processing helix chain 'F' and resid 133 through 150 Processing helix chain 'F' and resid 174 through 187 Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.202A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 238 No H-bonds generated for 'chain 'F' and resid 235 through 238' Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 50 through 63 Processing helix chain 'K' and resid 23 through 44 Processing helix chain 'K' and resid 116 through 121 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 152 through 156 Processing helix chain 'K' and resid 186 through 194 Processing helix chain 'K' and resid 197 through 229 removed outlier: 3.534A pdb=" N PHE K 219 " --> pdb=" O LYS K 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 245 Processing helix chain 'N' and resid 306 through 310 removed outlier: 3.821A pdb=" N GLU N 309 " --> pdb=" O ASP N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 367 Processing helix chain 'N' and resid 406 through 421 removed outlier: 5.574A pdb=" N GLN N 420 " --> pdb=" O ASP N 416 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA N 421 " --> pdb=" O ALA N 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 451 Processing helix chain 'N' and resid 533 through 540 Processing helix chain 'N' and resid 544 through 553 Processing helix chain 'N' and resid 556 through 563 removed outlier: 3.619A pdb=" N PHE N 562 " --> pdb=" O PHE N 558 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 615 Processing helix chain 'O' and resid 51 through 55 Processing helix chain 'O' and resid 152 through 172 removed outlier: 4.099A pdb=" N SER O 170 " --> pdb=" O MET O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 218 Processing helix chain 'O' and resid 227 through 233 Processing helix chain 'O' and resid 239 through 252 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 14 through 16 No H-bonds generated for 'chain 'P' and resid 14 through 16' Processing helix chain 'P' and resid 96 through 108 Processing helix chain 'Q' and resid 17 through 28 Processing helix chain 'Q' and resid 41 through 51 Processing helix chain 'Q' and resid 66 through 79 Processing helix chain 'Q' and resid 94 through 103 removed outlier: 3.791A pdb=" N TYR Q 98 " --> pdb=" O SER Q 94 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU Q 99 " --> pdb=" O ASN Q 95 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL Q 100 " --> pdb=" O SER Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 119 Processing helix chain 'Q' and resid 136 through 138 No H-bonds generated for 'chain 'Q' and resid 136 through 138' Processing helix chain 'Q' and resid 144 through 155 Processing helix chain 'Q' and resid 168 through 170 No H-bonds generated for 'chain 'Q' and resid 168 through 170' Processing helix chain 'Q' and resid 178 through 185 Processing helix chain 'Q' and resid 198 through 205 removed outlier: 3.710A pdb=" N PHE Q 203 " --> pdb=" O ALA Q 199 " (cutoff:3.500A) Processing helix chain 'Q' and resid 220 through 243 Processing helix chain 'Q' and resid 246 through 250 Processing helix chain 'Q' and resid 254 through 258 Processing helix chain 'Q' and resid 260 through 269 removed outlier: 3.631A pdb=" N ASP Q 263 " --> pdb=" O LYS Q 260 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 275 No H-bonds generated for 'chain 'Q' and resid 273 through 275' Processing helix chain 'Q' and resid 286 through 300 Processing helix chain 'Q' and resid 303 through 308 Processing helix chain 'Q' and resid 311 through 320 Processing helix chain 'Q' and resid 333 through 341 Processing helix chain 'Q' and resid 380 through 398 Processing helix chain 'Q' and resid 414 through 426 Processing helix chain 'Q' and resid 428 through 439 removed outlier: 3.855A pdb=" N THR Q 439 " --> pdb=" O LEU Q 435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 565 through 572 Processing helix chain 'Q' and resid 585 through 597 Processing helix chain 'Q' and resid 614 through 639 removed outlier: 3.696A pdb=" N SER Q 639 " --> pdb=" O ARG Q 635 " (cutoff:3.500A) Processing helix chain 'Q' and resid 688 through 690 No H-bonds generated for 'chain 'Q' and resid 688 through 690' Processing helix chain 'Q' and resid 695 through 701 Processing helix chain 'Q' and resid 729 through 738 Processing helix chain 'Q' and resid 740 through 749 Processing helix chain 'Q' and resid 785 through 794 Processing helix chain 'Q' and resid 806 through 816 Processing helix chain 'Q' and resid 825 through 827 No H-bonds generated for 'chain 'Q' and resid 825 through 827' Processing helix chain 'R' and resid 111 through 115 removed outlier: 3.597A pdb=" N PHE R 115 " --> pdb=" O PRO R 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 111 through 115' Processing helix chain 'R' and resid 143 through 148 Processing helix chain 'R' and resid 151 through 160 Processing helix chain 'R' and resid 180 through 191 Processing helix chain 'R' and resid 202 through 214 Processing helix chain 'S' and resid 6 through 12 removed outlier: 4.632A pdb=" N CYS S 12 " --> pdb=" O LYS S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 22 Processing helix chain 'S' and resid 53 through 67 Processing helix chain 'S' and resid 83 through 89 Processing helix chain 'S' and resid 156 through 178 Processing helix chain 'S' and resid 191 through 195 Processing helix chain 'S' and resid 198 through 214 Processing helix chain 'S' and resid 226 through 269 removed outlier: 4.943A pdb=" N HIS S 258 " --> pdb=" O MET S 254 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER S 259 " --> pdb=" O ASN S 255 " (cutoff:3.500A) Processing helix chain 'S' and resid 767 through 779 Processing helix chain 'S' and resid 790 through 799 Processing helix chain 'S' and resid 811 through 816 Processing helix chain 'S' and resid 837 through 844 Processing helix chain 'S' and resid 848 through 858 Processing helix chain 'S' and resid 871 through 880 Processing helix chain 'S' and resid 887 through 901 Processing helix chain 'S' and resid 913 through 920 Processing helix chain 'S' and resid 930 through 937 Processing helix chain 'S' and resid 955 through 965 Processing helix chain 'S' and resid 970 through 985 Proline residue: S 979 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 7.083A pdb=" N LYS A 59 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARG D 337 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.503A pdb=" N PHE A 85 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 108 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.320A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.776A pdb=" N VAL A 405 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE A 392 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 407 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 438 through 441 current: chain 'A' and resid 463 through 467 removed outlier: 6.541A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 339 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU A 490 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 690 removed outlier: 3.870A pdb=" N ILE A 690 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP A 511 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.512A pdb=" N ALA B 108 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 204 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 204 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR B 72 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL B 206 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 252 removed outlier: 6.887A pdb=" N VAL B 249 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 433 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU B 251 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE B 418 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU B 352 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 479 through 481 removed outlier: 4.148A pdb=" N ALA B 479 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU B 41 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 481 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 453 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 231 " --> pdb=" O SER B 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 495 removed outlier: 4.066A pdb=" N MET B 677 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 101 Processing sheet with id=AB3, first strand: chain 'D' and resid 248 through 251 removed outlier: 7.910A pdb=" N ARG D 279 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 284 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU D 270 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 402 through 409 removed outlier: 3.807A pdb=" N MET D 441 " --> pdb=" O TYR D 409 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 184 through 186 removed outlier: 7.676A pdb=" N LEU D 184 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 197 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 118 removed outlier: 6.838A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG E 195 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 169 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER E 197 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE E 171 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE E 199 " --> pdb=" O PHE E 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 289 through 291 removed outlier: 3.941A pdb=" N TYR E 289 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N CYS E 291 " --> pdb=" O ALA E 296 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA E 296 " --> pdb=" O CYS E 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 332 through 335 removed outlier: 3.712A pdb=" N VAL E 359 " --> pdb=" O GLN E 332 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN E 365 " --> pdb=" O CYS E 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 303 through 305 removed outlier: 4.265A pdb=" N LEU E 310 " --> pdb=" O CYS E 305 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 343 through 345 removed outlier: 7.353A pdb=" N ARG E 343 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU E 352 " --> pdb=" O ARG E 343 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY E 350 " --> pdb=" O CYS E 345 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.580A pdb=" N ARG F 68 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA F 61 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 253 through 255 removed outlier: 4.896A pdb=" N ALA F 253 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN F 260 " --> pdb=" O CYS F 255 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 273 through 275 removed outlier: 4.357A pdb=" N SER F 273 " --> pdb=" O CYS F 268 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLY F 265 " --> pdb=" O MET E 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 5 through 11 removed outlier: 3.817A pdb=" N HIS G 42 " --> pdb=" O ASP G 39 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE G 44 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP G 37 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 103 through 105 removed outlier: 4.366A pdb=" N LYS K 110 " --> pdb=" O CYS K 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 138 through 140 removed outlier: 3.562A pdb=" N LYS K 167 " --> pdb=" O MET K 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 248 through 252 removed outlier: 4.427A pdb=" N THR K 260 " --> pdb=" O PRO K 248 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU K 252 " --> pdb=" O MET K 256 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR K 257 " --> pdb=" O TYR K 270 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR K 270 " --> pdb=" O TYR K 257 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU K 268 " --> pdb=" O LYS K 259 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 254 through 258 current: chain 'N' and resid 198 through 206 removed outlier: 6.904A pdb=" N GLU N 225 " --> pdb=" O THR N 204 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS N 206 " --> pdb=" O SER N 223 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER N 223 " --> pdb=" O LYS N 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE N 222 " --> pdb=" O ALA N 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 261 through 264 Processing sheet with id=AD2, first strand: chain 'N' and resid 398 through 401 removed outlier: 7.118A pdb=" N TYR N 347 " --> pdb=" O LYS N 324 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR N 326 " --> pdb=" O ASN N 345 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASN N 345 " --> pdb=" O TYR N 326 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL N 356 " --> pdb=" O LEU N 348 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 382 through 384 Processing sheet with id=AD4, first strand: chain 'N' and resid 526 through 531 removed outlier: 3.507A pdb=" N ASN N 519 " --> pdb=" O TYR N 470 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR N 470 " --> pdb=" O ASN N 519 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA N 521 " --> pdb=" O VAL N 468 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL N 468 " --> pdb=" O ALA N 521 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG N 575 " --> pdb=" O VAL N 591 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL N 591 " --> pdb=" O ARG N 575 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LYS N 577 " --> pdb=" O ALA N 589 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA N 589 " --> pdb=" O LYS N 577 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU N 579 " --> pdb=" O ILE N 587 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE N 587 " --> pdb=" O GLU N 579 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR N 581 " --> pdb=" O SER N 585 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER N 585 " --> pdb=" O TYR N 581 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 477 through 480 Processing sheet with id=AD6, first strand: chain 'N' and resid 490 through 492 Processing sheet with id=AD7, first strand: chain 'O' and resid 58 through 60 Processing sheet with id=AD8, first strand: chain 'O' and resid 74 through 79 removed outlier: 7.802A pdb=" N HIS O 131 " --> pdb=" O ALA O 143 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA O 143 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG O 133 " --> pdb=" O LEU O 141 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU O 141 " --> pdb=" O ARG O 133 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE O 135 " --> pdb=" O LYS O 139 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS O 139 " --> pdb=" O PHE O 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 83 through 85 Processing sheet with id=AE1, first strand: chain 'P' and resid 50 through 54 removed outlier: 5.738A pdb=" N SER P 44 " --> pdb=" O LEU P 31 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU P 31 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG P 72 " --> pdb=" O CYS P 81 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N CYS P 81 " --> pdb=" O ARG P 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 190 through 192 removed outlier: 6.196A pdb=" N LEU Q 32 " --> pdb=" O TYR Q 191 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL Q 33 " --> pdb=" O ILE Q 161 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA Q 163 " --> pdb=" O VAL Q 33 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU Q 58 " --> pdb=" O THR Q 129 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE Q 131 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU Q 60 " --> pdb=" O ILE Q 131 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL Q 133 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 86 through 88 Processing sheet with id=AE4, first strand: chain 'Q' and resid 210 through 217 removed outlier: 6.483A pdb=" N VAL Q 605 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE Q 214 " --> pdb=" O VAL Q 605 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE Q 607 " --> pdb=" O ILE Q 214 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL Q 216 " --> pdb=" O PHE Q 607 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE Q 609 " --> pdb=" O VAL Q 216 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU Q 608 " --> pdb=" O LEU Q 580 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE Q 553 " --> pdb=" O VAL Q 407 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS Q 555 " --> pdb=" O ILE Q 409 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Q 411 " --> pdb=" O HIS Q 555 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 552 through 556 current: chain 'S' and resid 356 through 360 Processing sheet with id=AE5, first strand: chain 'Q' and resid 705 through 709 removed outlier: 3.721A pdb=" N VAL Q 686 " --> pdb=" O GLU Q 707 " (cutoff:3.500A) removed outlier: 12.660A pdb=" N ASP Q 715 " --> pdb=" O SER Q 683 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL Q 685 " --> pdb=" O ASP Q 715 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ASP Q 687 " --> pdb=" O ILE Q 717 " (cutoff:3.500A) removed outlier: 15.267A pdb=" N THR Q 719 " --> pdb=" O ASP Q 687 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS Q 723 " --> pdb=" O ARG Q 754 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU Q 760 " --> pdb=" O LYS Q 727 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG Q 799 " --> pdb=" O PRO Q 755 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 101 through 104 Processing sheet with id=AE7, first strand: chain 'R' and resid 130 through 132 removed outlier: 4.919A pdb=" N THR R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR R 195 " --> pdb=" O LEU R 169 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL R 171 " --> pdb=" O THR R 195 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE R 197 " --> pdb=" O VAL R 171 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 15 through 17 removed outlier: 3.902A pdb=" N VAL S 17 " --> pdb=" O VAL S 832 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL S 832 " --> pdb=" O VAL S 17 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 806 through 807 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 806 through 807 current: chain 'S' and resid 26 through 30 removed outlier: 6.222A pdb=" N ARG S 71 " --> pdb=" O LEU S 27 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL S 29 " --> pdb=" O ARG S 71 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE S 73 " --> pdb=" O VAL S 29 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 275 through 280 Processing sheet with id=AF2, first strand: chain 'O' and resid 263 through 266 1548 hydrogen bonds defined for protein. 4375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 10.58 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 17308 1.43 - 1.64: 23426 1.64 - 1.86: 326 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 41072 Sorted by residual: bond pdb=" C8 VM6 L 63 " pdb=" C9 VM6 L 63 " ideal model delta sigma weight residual 1.504 1.324 0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C6 VM6 L 63 " pdb=" C7 VM6 L 63 " ideal model delta sigma weight residual 1.343 1.522 -0.179 2.00e-02 2.50e+03 8.01e+01 bond pdb=" C10 VM6 L 63 " pdb=" C9 VM6 L 63 " ideal model delta sigma weight residual 1.340 1.503 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" O1 VM6 L 63 " pdb=" P VM6 L 63 " ideal model delta sigma weight residual 1.721 1.614 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C10 VM6 L 63 " pdb=" N1 VM6 L 63 " ideal model delta sigma weight residual 1.397 1.462 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 41067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 55822 2.90 - 5.81: 152 5.81 - 8.71: 5 8.71 - 11.62: 0 11.62 - 14.52: 3 Bond angle restraints: 55982 Sorted by residual: angle pdb=" C ARG S 91 " pdb=" CA ARG S 91 " pdb=" CB ARG S 91 " ideal model delta sigma weight residual 116.54 110.89 5.65 1.15e+00 7.56e-01 2.42e+01 angle pdb=" C6 VM6 L 63 " pdb=" C7 VM6 L 63 " pdb=" C8 VM6 L 63 " ideal model delta sigma weight residual 127.15 112.63 14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" N ILE B 117 " pdb=" CA ILE B 117 " pdb=" C ILE B 117 " ideal model delta sigma weight residual 113.71 109.34 4.37 9.50e-01 1.11e+00 2.12e+01 angle pdb=" C5 VM6 L 63 " pdb=" C6 VM6 L 63 " pdb=" C7 VM6 L 63 " ideal model delta sigma weight residual 126.06 112.27 13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C7 VM6 L 63 " pdb=" C8 VM6 L 63 " pdb=" C9 VM6 L 63 " ideal model delta sigma weight residual 112.55 126.22 -13.67 3.00e+00 1.11e-01 2.08e+01 ... (remaining 55977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 23395 27.64 - 55.28: 1144 55.28 - 82.92: 125 82.92 - 110.56: 16 110.56 - 138.20: 2 Dihedral angle restraints: 24682 sinusoidal: 10800 harmonic: 13882 Sorted by residual: dihedral pdb=" C13 VM6 L 63 " pdb=" C11 VM6 L 63 " pdb=" C12 VM6 L 63 " pdb=" N1 VM6 L 63 " ideal model delta sinusoidal sigma weight residual 181.09 48.14 132.95 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" C23 VM6 L 63 " pdb=" C24 VM6 L 63 " pdb=" C25 VM6 L 63 " pdb=" O2 VM6 L 63 " ideal model delta sinusoidal sigma weight residual -62.16 -169.62 107.46 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C4' DG L 35 " pdb=" C3' DG L 35 " pdb=" O3' DG L 35 " pdb=" P DC L 36 " ideal model delta sinusoidal sigma weight residual 220.00 81.80 138.20 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 24679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4023 0.028 - 0.055: 1400 0.055 - 0.083: 404 0.083 - 0.111: 375 0.111 - 0.139: 84 Chirality restraints: 6286 Sorted by residual: chirality pdb=" CA VAL O 120 " pdb=" N VAL O 120 " pdb=" C VAL O 120 " pdb=" CB VAL O 120 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" C3' DT L 40 " pdb=" C4' DT L 40 " pdb=" O3' DT L 40 " pdb=" C2' DT L 40 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE S 866 " pdb=" N ILE S 866 " pdb=" C ILE S 866 " pdb=" CB ILE S 866 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 6283 not shown) Planarity restraints: 6825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 VM6 L 63 " -0.087 2.00e-02 2.50e+03 2.32e-01 6.75e+02 pdb=" C20 VM6 L 63 " -0.000 2.00e-02 2.50e+03 pdb=" C8 VM6 L 63 " 0.294 2.00e-02 2.50e+03 pdb=" C9 VM6 L 63 " -0.382 2.00e-02 2.50e+03 pdb=" N1 VM6 L 63 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 VM6 L 63 " 0.009 2.00e-02 2.50e+03 4.64e-02 2.69e+01 pdb=" C4 VM6 L 63 " 0.017 2.00e-02 2.50e+03 pdb=" C5 VM6 L 63 " 0.074 2.00e-02 2.50e+03 pdb=" C6 VM6 L 63 " -0.054 2.00e-02 2.50e+03 pdb=" N2 VM6 L 63 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 VM6 L 63 " -0.050 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C6 VM6 L 63 " 0.049 2.00e-02 2.50e+03 pdb=" C7 VM6 L 63 " 0.050 2.00e-02 2.50e+03 pdb=" C8 VM6 L 63 " -0.050 2.00e-02 2.50e+03 ... (remaining 6822 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5187 2.76 - 3.29: 39371 3.29 - 3.83: 67455 3.83 - 4.36: 75771 4.36 - 4.90: 129969 Nonbonded interactions: 317753 Sorted by model distance: nonbonded pdb=" OG1 THR A 705 " pdb=" OE1 GLU A 708 " model vdw 2.222 3.040 nonbonded pdb=" O GLY A 500 " pdb=" NZ LYS A 648 " model vdw 2.227 3.120 nonbonded pdb=" NE ARG Q 153 " pdb=" O GLU Q 647 " model vdw 2.238 3.120 nonbonded pdb=" OE2 GLU S 189 " pdb=" OH TYR S 242 " model vdw 2.241 3.040 nonbonded pdb=" O CYS B 134 " pdb=" OG1 THR B 138 " model vdw 2.277 3.040 ... (remaining 317748 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=0.46 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: 2.030 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 47.690 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.100 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:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 0.003 0.180 41105 Z= 0.204 Angle : 0.482 14.522 56027 Z= 0.303 Chirality : 0.039 0.139 6286 Planarity : 0.004 0.232 6825 Dihedral : 14.799 138.202 15668 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.82 % Allowed : 6.99 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.13), residues: 4664 helix: 2.55 (0.12), residues: 2145 sheet: 0.40 (0.20), residues: 761 loop : -0.73 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 589 TYR 0.010 0.001 TYR E 95 PHE 0.014 0.001 PHE S 840 TRP 0.007 0.001 TRP A 511 HIS 0.002 0.000 HIS A 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.20 (41072) covalent geometry : angle 0.47297 / 0.30 (55982) hydrogen bonds : bond 0.11878 / 7.78 ( 1612) hydrogen bonds : angle 4.62439 / 3.24 ( 4503) metal coordination : bond 0.00498 / 0.26 ( 31) metal coordination : angle 3.31515 / 1.71 ( 45) Misc. bond : bond 0.04128 / 2.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 341 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8382 (pp) REVERT: A 71 HIS cc_start: 0.8231 (p-80) cc_final: 0.8027 (p-80) REVERT: A 275 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8616 (mp0) REVERT: A 380 MET cc_start: 0.8153 (ppp) cc_final: 0.7713 (ppp) REVERT: A 381 TRP cc_start: 0.8575 (m-10) cc_final: 0.8342 (m-10) REVERT: A 433 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: B 357 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: B 422 ASP cc_start: 0.7938 (m-30) cc_final: 0.7410 (m-30) REVERT: B 571 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7701 (p) REVERT: C 493 MET cc_start: 0.9451 (mmp) cc_final: 0.9112 (tpp) REVERT: C 526 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9181 (mm-30) REVERT: D 271 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8590 (p) REVERT: E 98 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8063 (tm-30) REVERT: E 103 GLN cc_start: 0.7994 (mt0) cc_final: 0.7762 (mt0) REVERT: E 166 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8085 (mt-10) REVERT: E 356 HIS cc_start: 0.9148 (OUTLIER) cc_final: 0.8934 (t-90) REVERT: F 51 MET cc_start: 0.8897 (mmm) cc_final: 0.8655 (mmm) REVERT: F 146 ARG cc_start: 0.9449 (ttt180) cc_final: 0.9204 (tmm-80) REVERT: F 175 MET cc_start: 0.8937 (pmm) cc_final: 0.8697 (pmm) REVERT: G 27 ASN cc_start: 0.8669 (p0) cc_final: 0.8459 (p0) REVERT: G 37 ASP cc_start: 0.9193 (p0) cc_final: 0.8917 (t0) REVERT: G 56 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8379 (tpp-160) REVERT: S 801 ASP cc_start: 0.9022 (t0) cc_final: 0.8772 (m-30) REVERT: S 871 CYS cc_start: 0.9178 (m) cc_final: 0.8710 (p) REVERT: Q 12 MET cc_start: 0.7638 (ppp) cc_final: 0.6872 (ppp) REVERT: N 287 MET cc_start: 0.9615 (ppp) cc_final: 0.9352 (ppp) REVERT: N 611 ARG cc_start: 0.9478 (OUTLIER) cc_final: 0.9077 (mmm160) REVERT: O 102 MET cc_start: 0.8567 (mmt) cc_final: 0.8112 (mmt) REVERT: O 152 MET cc_start: 0.8407 (mmp) cc_final: 0.7978 (mmp) REVERT: O 264 PHE cc_start: 0.9427 (m-80) cc_final: 0.9172 (m-80) REVERT: P 1 MET cc_start: 0.0031 (tpt) cc_final: -0.1183 (tpt) REVERT: P 5 MET cc_start: 0.8967 (mmt) cc_final: 0.8619 (mmt) REVERT: P 25 VAL cc_start: 0.8443 (m) cc_final: 0.7715 (m) REVERT: P 30 ARG cc_start: 0.9486 (ttm170) cc_final: 0.9280 (ttm-80) REVERT: P 88 LYS cc_start: 0.8756 (ptmm) cc_final: 0.8108 (ptmm) REVERT: P 91 SER cc_start: 0.9484 (t) cc_final: 0.9121 (p) outliers start: 76 outliers final: 19 residues processed: 407 average time/residue: 0.2684 time to fit residues: 175.7807 Evaluate side-chains 274 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain S residue 941 VAL Chi-restraints excluded: chain Q residue 579 VAL Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain N residue 611 ARG Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 ASN A 307 ASN A 677 GLN B 114 ASN B 402 ASN B 649 ASN B 662 GLN C 402 ASN C 420 GLN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 530 GLN D 20 GLN D 181 GLN ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 HIS F 25 GLN F 185 GLN G 36 GLN S 37 GLN S 182 ASN S 793 GLN S 802 GLN S 812 ASN Q 286 GLN Q 296 GLN Q 395 ASN Q 571 HIS Q 744 GLN N 294 HIS N 420 GLN N 524 GLN O 106 GLN O 211 GLN O 244 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.071674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.048785 restraints weight = 380553.766| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 5.51 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 41105 Z= 0.183 Angle : 0.586 18.230 56027 Z= 0.295 Chirality : 0.041 0.198 6286 Planarity : 0.005 0.212 6825 Dihedral : 14.239 155.072 6334 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.96 % Allowed : 9.77 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.13), residues: 4664 helix: 2.28 (0.12), residues: 2145 sheet: 0.08 (0.19), residues: 762 loop : -0.70 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 473 TYR 0.016 0.001 TYR N 478 PHE 0.029 0.001 PHE A 615 TRP 0.012 0.001 TRP R 200 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (41072) covalent geometry : angle 0.56509 / 0.29 (55982) hydrogen bonds : bond 0.03371 / 2.27 ( 1612) hydrogen bonds : angle 4.05370 / 2.83 ( 4503) metal coordination : bond 0.01357 / 0.77 ( 31) metal coordination : angle 5.49715 / 3.53 ( 45) Misc. bond : bond 0.01122 / 0.59 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 252 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8334 (ptp) cc_final: 0.7990 (ptp) REVERT: A 71 HIS cc_start: 0.8353 (p-80) cc_final: 0.8145 (p-80) REVERT: A 275 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8587 (mp0) REVERT: A 292 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7679 (pp) REVERT: A 380 MET cc_start: 0.8209 (ppp) cc_final: 0.7892 (ppp) REVERT: A 433 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: A 692 LYS cc_start: 0.8431 (tppt) cc_final: 0.7522 (tmtt) REVERT: B 422 ASP cc_start: 0.7015 (m-30) cc_final: 0.6688 (m-30) REVERT: B 571 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8088 (p) REVERT: B 724 MET cc_start: 0.9126 (mmp) cc_final: 0.8915 (mmm) REVERT: C 417 LYS cc_start: 0.7436 (pttm) cc_final: 0.7149 (pttm) REVERT: C 493 MET cc_start: 0.9468 (mmp) cc_final: 0.9100 (tpp) REVERT: C 526 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9137 (mm-30) REVERT: D 54 ASN cc_start: 0.9502 (m-40) cc_final: 0.9068 (m110) REVERT: D 55 TRP cc_start: 0.8239 (m-10) cc_final: 0.8028 (m-10) REVERT: E 98 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8090 (tm-30) REVERT: E 166 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8340 (mt-10) REVERT: E 356 HIS cc_start: 0.9228 (OUTLIER) cc_final: 0.8970 (t-90) REVERT: F 69 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7886 (t80) REVERT: F 146 ARG cc_start: 0.9466 (ttt180) cc_final: 0.9154 (tmm-80) REVERT: F 175 MET cc_start: 0.8987 (pmm) cc_final: 0.8710 (pmm) REVERT: F 256 PHE cc_start: 0.9119 (m-80) cc_final: 0.8808 (m-80) REVERT: G 27 ASN cc_start: 0.8630 (p0) cc_final: 0.8420 (p0) REVERT: G 37 ASP cc_start: 0.9203 (p0) cc_final: 0.8978 (t0) REVERT: S 871 CYS cc_start: 0.9280 (m) cc_final: 0.8916 (p) REVERT: Q 12 MET cc_start: 0.7665 (ppp) cc_final: 0.7001 (ppp) REVERT: Q 326 TRP cc_start: 0.6629 (m100) cc_final: 0.6396 (m100) REVERT: K 178 MET cc_start: 0.7118 (ptp) cc_final: 0.6681 (mpp) REVERT: N 576 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8355 (p) REVERT: N 611 ARG cc_start: 0.9472 (OUTLIER) cc_final: 0.9092 (mmm160) REVERT: O 102 MET cc_start: 0.8755 (mmt) cc_final: 0.8281 (mmt) REVERT: O 152 MET cc_start: 0.8894 (mmp) cc_final: 0.8264 (mmp) REVERT: O 154 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: O 264 PHE cc_start: 0.9404 (m-80) cc_final: 0.9163 (m-80) REVERT: P 1 MET cc_start: 0.0096 (tpt) cc_final: -0.0997 (tpt) REVERT: P 30 ARG cc_start: 0.9451 (ttm170) cc_final: 0.9189 (mmm-85) REVERT: P 88 LYS cc_start: 0.8800 (ptmm) cc_final: 0.8174 (ptmm) outliers start: 82 outliers final: 44 residues processed: 315 average time/residue: 0.2492 time to fit residues: 130.0304 Evaluate side-chains 277 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 941 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain N residue 294 HIS Chi-restraints excluded: chain N residue 465 VAL Chi-restraints excluded: chain N residue 576 VAL Chi-restraints excluded: chain N residue 611 ARG Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 125 TYR Chi-restraints excluded: chain O residue 154 GLU Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain P residue 109 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 286 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 462 optimal weight: 8.9990 chunk 396 optimal weight: 30.0000 chunk 280 optimal weight: 0.0370 chunk 178 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 356 optimal weight: 8.9990 chunk 460 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 chunk 140 optimal weight: 30.0000 overall best weight: 4.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN S 202 HIS Q 226 GLN R 107 GLN N 294 HIS N 524 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.071052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.047927 restraints weight = 349366.605| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 5.28 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 41105 Z= 0.169 Angle : 0.547 16.346 56027 Z= 0.276 Chirality : 0.040 0.203 6286 Planarity : 0.004 0.133 6825 Dihedral : 14.266 156.530 6323 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.25 % Allowed : 10.30 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 4664 helix: 2.12 (0.12), residues: 2161 sheet: -0.05 (0.19), residues: 785 loop : -0.69 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 453 TYR 0.016 0.001 TYR B 207 PHE 0.018 0.001 PHE F 177 TRP 0.013 0.001 TRP A 511 HIS 0.015 0.001 HIS N 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (41072) covalent geometry : angle 0.52655 / 0.28 (55982) hydrogen bonds : bond 0.03090 / 2.08 ( 1612) hydrogen bonds : angle 3.92936 / 2.74 ( 4503) metal coordination : bond 0.01033 / 0.53 ( 31) metal coordination : angle 5.27604 / 3.26 ( 45) Misc. bond : bond 0.00362 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 228 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8387 (pp) REVERT: A 275 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8598 (mp0) REVERT: A 292 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7628 (pp) REVERT: A 692 LYS cc_start: 0.8536 (tppt) cc_final: 0.8254 (tppt) REVERT: B 81 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8427 (mm-30) REVERT: B 659 HIS cc_start: 0.8265 (OUTLIER) cc_final: 0.7744 (t-90) REVERT: C 493 MET cc_start: 0.9450 (mmp) cc_final: 0.9041 (tpp) REVERT: C 526 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9164 (mm-30) REVERT: D 55 TRP cc_start: 0.8339 (m-10) cc_final: 0.8083 (m-10) REVERT: D 59 MET cc_start: 0.9059 (ttm) cc_final: 0.8616 (ptm) REVERT: D 185 MET cc_start: 0.8866 (pmm) cc_final: 0.8647 (pmm) REVERT: E 98 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8118 (tm-30) REVERT: E 356 HIS cc_start: 0.9169 (OUTLIER) cc_final: 0.8929 (t-90) REVERT: F 69 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7882 (t80) REVERT: F 146 ARG cc_start: 0.9455 (ttt180) cc_final: 0.9144 (tmm-80) REVERT: F 175 MET cc_start: 0.8973 (pmm) cc_final: 0.8761 (pmm) REVERT: F 256 PHE cc_start: 0.9148 (m-80) cc_final: 0.8733 (m-80) REVERT: G 11 GLU cc_start: 0.8409 (tp30) cc_final: 0.7988 (tp30) REVERT: G 37 ASP cc_start: 0.9215 (p0) cc_final: 0.8914 (t0) REVERT: G 54 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8001 (mm-40) REVERT: S 871 CYS cc_start: 0.9286 (m) cc_final: 0.9054 (p) REVERT: S 875 MET cc_start: 0.9132 (ptt) cc_final: 0.8859 (ppp) REVERT: Q 12 MET cc_start: 0.7782 (ppp) cc_final: 0.7131 (ppp) REVERT: Q 748 MET cc_start: 0.8934 (ttp) cc_final: 0.8655 (ttp) REVERT: K 178 MET cc_start: 0.7228 (ptp) cc_final: 0.6806 (mpp) REVERT: N 611 ARG cc_start: 0.9471 (OUTLIER) cc_final: 0.9073 (mmm160) REVERT: O 70 GLU cc_start: 0.9067 (mp0) cc_final: 0.8710 (mm-30) REVERT: O 102 MET cc_start: 0.8733 (mmt) cc_final: 0.8320 (mmt) REVERT: O 152 MET cc_start: 0.8923 (mmp) cc_final: 0.8542 (mmp) REVERT: O 264 PHE cc_start: 0.9384 (m-80) cc_final: 0.9180 (m-80) REVERT: P 1 MET cc_start: 0.0068 (tpt) cc_final: -0.1115 (tpt) REVERT: P 88 LYS cc_start: 0.8734 (ptmm) cc_final: 0.8227 (ptmm) REVERT: P 115 LEU cc_start: 0.9195 (mt) cc_final: 0.8657 (tt) outliers start: 94 outliers final: 48 residues processed: 306 average time/residue: 0.2382 time to fit residues: 121.9796 Evaluate side-chains 275 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 485 PHE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 941 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 641 VAL Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain Q residue 758 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain N residue 611 ARG Chi-restraints excluded: chain O residue 82 HIS Chi-restraints excluded: chain O residue 125 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 370 optimal weight: 0.7980 chunk 271 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 90 optimal weight: 20.0000 chunk 470 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 431 optimal weight: 20.0000 chunk 256 optimal weight: 30.0000 chunk 366 optimal weight: 6.9990 chunk 357 optimal weight: 0.6980 chunk 188 optimal weight: 20.0000 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 HIS A 635 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN E 324 HIS S 922 GLN Q 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.070989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047973 restraints weight = 339794.088| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 5.15 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41105 Z= 0.136 Angle : 0.534 15.071 56027 Z= 0.269 Chirality : 0.040 0.198 6286 Planarity : 0.003 0.076 6825 Dihedral : 14.279 161.135 6317 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.23 % Allowed : 10.97 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4664 helix: 2.09 (0.12), residues: 2159 sheet: -0.08 (0.19), residues: 788 loop : -0.72 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.018 0.001 TYR B 197 PHE 0.039 0.001 PHE F 32 TRP 0.011 0.001 TRP A 511 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (41072) covalent geometry : angle 0.51474 / 0.27 (55982) hydrogen bonds : bond 0.02928 / 1.97 ( 1612) hydrogen bonds : angle 3.87757 / 2.71 ( 4503) metal coordination : bond 0.00827 / 0.45 ( 31) metal coordination : angle 5.08416 / 3.08 ( 45) Misc. bond : bond 0.00114 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 229 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8421 (pp) REVERT: A 65 MET cc_start: 0.8259 (ptp) cc_final: 0.7998 (ptp) REVERT: A 275 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8584 (mp0) REVERT: A 292 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7640 (pp) REVERT: A 381 TRP cc_start: 0.8648 (m-10) cc_final: 0.8315 (m-10) REVERT: A 692 LYS cc_start: 0.8571 (tppt) cc_final: 0.7822 (tmtt) REVERT: B 81 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8425 (mm-30) REVERT: B 659 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7707 (t-90) REVERT: C 493 MET cc_start: 0.9454 (mmp) cc_final: 0.9065 (tpp) REVERT: C 526 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9141 (mm-30) REVERT: D 55 TRP cc_start: 0.8327 (m-10) cc_final: 0.8021 (m-10) REVERT: D 185 MET cc_start: 0.8855 (pmm) cc_final: 0.8641 (pmm) REVERT: E 98 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8110 (tm-30) REVERT: E 356 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8925 (t-90) REVERT: F 69 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7949 (t80) REVERT: F 175 MET cc_start: 0.8964 (pmm) cc_final: 0.8711 (pmm) REVERT: F 256 PHE cc_start: 0.9102 (m-80) cc_final: 0.8660 (m-80) REVERT: G 11 GLU cc_start: 0.8388 (tp30) cc_final: 0.7944 (tp30) REVERT: G 37 ASP cc_start: 0.9256 (p0) cc_final: 0.8925 (t0) REVERT: G 59 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8664 (pp20) REVERT: S 871 CYS cc_start: 0.9270 (m) cc_final: 0.8914 (p) REVERT: Q 12 MET cc_start: 0.7859 (ppp) cc_final: 0.7247 (ppp) REVERT: Q 748 MET cc_start: 0.8907 (ttp) cc_final: 0.8610 (ttp) REVERT: K 178 MET cc_start: 0.7311 (ptp) cc_final: 0.6814 (mpp) REVERT: N 349 MET cc_start: 0.5841 (mmm) cc_final: 0.5115 (mmp) REVERT: N 576 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8573 (p) REVERT: N 611 ARG cc_start: 0.9483 (OUTLIER) cc_final: 0.9111 (mmm160) REVERT: O 70 GLU cc_start: 0.9025 (mp0) cc_final: 0.8655 (mm-30) REVERT: O 102 MET cc_start: 0.8721 (mmt) cc_final: 0.8317 (mmt) REVERT: O 152 MET cc_start: 0.8933 (mmp) cc_final: 0.8603 (mmp) REVERT: O 264 PHE cc_start: 0.9385 (m-80) cc_final: 0.9174 (m-80) REVERT: P 1 MET cc_start: -0.0016 (tpt) cc_final: -0.1238 (tpt) REVERT: P 88 LYS cc_start: 0.8766 (ptmm) cc_final: 0.8268 (ptmm) REVERT: P 115 LEU cc_start: 0.9208 (mt) cc_final: 0.8670 (tt) outliers start: 93 outliers final: 58 residues processed: 305 average time/residue: 0.2414 time to fit residues: 123.4236 Evaluate side-chains 286 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 220 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 729 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 485 PHE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 941 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 641 VAL Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain Q residue 758 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain N residue 294 HIS Chi-restraints excluded: chain N residue 465 VAL Chi-restraints excluded: chain N residue 576 VAL Chi-restraints excluded: chain N residue 611 ARG Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 125 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 278 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 269 optimal weight: 0.4980 chunk 231 optimal weight: 40.0000 chunk 364 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 393 optimal weight: 50.0000 chunk 339 optimal weight: 4.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 HIS A 459 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN S 824 ASN ** N 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.070562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047475 restraints weight = 324982.296| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 5.08 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41105 Z= 0.152 Angle : 0.535 13.870 56027 Z= 0.269 Chirality : 0.040 0.224 6286 Planarity : 0.003 0.049 6825 Dihedral : 14.317 164.314 6317 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.32 % Allowed : 11.21 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.13), residues: 4664 helix: 2.09 (0.12), residues: 2162 sheet: -0.13 (0.19), residues: 773 loop : -0.71 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.017 0.001 TYR B 197 PHE 0.028 0.001 PHE F 32 TRP 0.014 0.001 TRP A 511 HIS 0.022 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (41072) covalent geometry : angle 0.51443 / 0.27 (55982) hydrogen bonds : bond 0.02941 / 1.98 ( 1612) hydrogen bonds : angle 3.83526 / 2.68 ( 4503) metal coordination : bond 0.00871 / 0.47 ( 31) metal coordination : angle 5.18799 / 3.12 ( 45) Misc. bond : bond 0.00037 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 224 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8415 (pp) REVERT: A 65 MET cc_start: 0.8260 (ptp) cc_final: 0.7792 (ptp) REVERT: A 275 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8570 (mp0) REVERT: A 292 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7655 (pp) REVERT: A 381 TRP cc_start: 0.8659 (m-10) cc_final: 0.8397 (m-10) REVERT: A 419 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7314 (ttm-80) REVERT: A 510 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7398 (m) REVERT: A 692 LYS cc_start: 0.8614 (tppt) cc_final: 0.8243 (tppt) REVERT: B 81 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8424 (mm-30) REVERT: B 659 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7735 (t-90) REVERT: C 417 LYS cc_start: 0.7675 (pttm) cc_final: 0.7375 (pttm) REVERT: C 526 GLU cc_start: 0.9531 (mm-30) cc_final: 0.9150 (mm-30) REVERT: D 55 TRP cc_start: 0.8406 (m-10) cc_final: 0.8095 (m-10) REVERT: D 185 MET cc_start: 0.8874 (pmm) cc_final: 0.8642 (pmm) REVERT: E 98 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8133 (tm-30) REVERT: E 356 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8949 (t-90) REVERT: F 69 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7922 (t80) REVERT: F 175 MET cc_start: 0.8965 (pmm) cc_final: 0.8744 (pmm) REVERT: F 256 PHE cc_start: 0.9095 (m-80) cc_final: 0.8667 (m-80) REVERT: G 11 GLU cc_start: 0.8424 (tp30) cc_final: 0.8153 (tp30) REVERT: G 37 ASP cc_start: 0.9299 (p0) cc_final: 0.8934 (t0) REVERT: S 801 ASP cc_start: 0.9152 (t0) cc_final: 0.8882 (m-30) REVERT: S 871 CYS cc_start: 0.9266 (m) cc_final: 0.8915 (p) REVERT: Q 12 MET cc_start: 0.7929 (ppp) cc_final: 0.7341 (ppp) REVERT: Q 748 MET cc_start: 0.8946 (ttp) cc_final: 0.8642 (ttp) REVERT: N 349 MET cc_start: 0.5936 (mmm) cc_final: 0.5693 (mmp) REVERT: N 576 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8583 (p) REVERT: N 611 ARG cc_start: 0.9492 (OUTLIER) cc_final: 0.9106 (mmm160) REVERT: N 616 MET cc_start: 0.7412 (ppp) cc_final: 0.6222 (pmm) REVERT: O 70 GLU cc_start: 0.9002 (mp0) cc_final: 0.8606 (mm-30) REVERT: O 102 MET cc_start: 0.8757 (mmt) cc_final: 0.8353 (mmt) REVERT: O 152 MET cc_start: 0.8972 (mmp) cc_final: 0.8690 (mmp) REVERT: P 1 MET cc_start: 0.0113 (tpt) cc_final: -0.1184 (tpt) REVERT: P 88 LYS cc_start: 0.8784 (ptmm) cc_final: 0.8288 (ptmm) REVERT: P 115 LEU cc_start: 0.9186 (mt) cc_final: 0.8670 (tt) outliers start: 97 outliers final: 68 residues processed: 303 average time/residue: 0.2317 time to fit residues: 118.3933 Evaluate side-chains 292 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 214 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 729 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 485 PHE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 941 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 641 VAL Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain Q residue 758 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain N residue 294 HIS Chi-restraints excluded: chain N residue 465 VAL Chi-restraints excluded: chain N residue 574 VAL Chi-restraints excluded: chain N residue 576 VAL Chi-restraints excluded: chain N residue 611 ARG Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 109 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 131 optimal weight: 20.0000 chunk 299 optimal weight: 0.1980 chunk 305 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 335 optimal weight: 40.0000 chunk 345 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** N 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.070182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.046671 restraints weight = 384928.065| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 5.63 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41105 Z= 0.160 Angle : 0.548 12.937 56027 Z= 0.274 Chirality : 0.040 0.282 6286 Planarity : 0.003 0.053 6825 Dihedral : 14.364 167.951 6317 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.61 % Allowed : 11.71 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4664 helix: 2.03 (0.12), residues: 2172 sheet: -0.20 (0.19), residues: 783 loop : -0.72 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.019 0.001 TYR B 197 PHE 0.023 0.001 PHE F 32 TRP 0.018 0.001 TRP A 511 HIS 0.011 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (41072) covalent geometry : angle 0.52764 / 0.27 (55982) hydrogen bonds : bond 0.02964 / 1.98 ( 1612) hydrogen bonds : angle 3.80715 / 2.67 ( 4503) metal coordination : bond 0.01129 / 0.60 ( 31) metal coordination : angle 5.25125 / 3.10 ( 45) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 219 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8392 (pp) REVERT: A 275 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8576 (mp0) REVERT: A 276 MET cc_start: 0.8599 (ttp) cc_final: 0.8080 (tmm) REVERT: A 292 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 381 TRP cc_start: 0.8638 (m-10) cc_final: 0.8431 (m-10) REVERT: A 510 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7598 (m) REVERT: A 692 LYS cc_start: 0.8609 (tppt) cc_final: 0.8219 (tppt) REVERT: B 81 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8397 (mm-30) REVERT: B 659 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7783 (t-90) REVERT: B 724 MET cc_start: 0.8957 (mmt) cc_final: 0.8393 (mmt) REVERT: C 417 LYS cc_start: 0.7742 (pttm) cc_final: 0.7434 (pttm) REVERT: C 526 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9130 (mm-30) REVERT: D 185 MET cc_start: 0.8825 (pmm) cc_final: 0.8575 (pmm) REVERT: D 254 MET cc_start: 0.8448 (mpp) cc_final: 0.7840 (ptp) REVERT: E 98 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8152 (tm-30) REVERT: E 117 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8857 (mp) REVERT: E 356 HIS cc_start: 0.9147 (OUTLIER) cc_final: 0.8943 (t-90) REVERT: F 69 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7968 (t80) REVERT: F 256 PHE cc_start: 0.9111 (m-80) cc_final: 0.8710 (m-80) REVERT: G 11 GLU cc_start: 0.8447 (tp30) cc_final: 0.8165 (tp30) REVERT: G 37 ASP cc_start: 0.9289 (p0) cc_final: 0.8892 (t0) REVERT: S 801 ASP cc_start: 0.9183 (t0) cc_final: 0.8927 (m-30) REVERT: S 871 CYS cc_start: 0.9284 (m) cc_final: 0.8975 (p) REVERT: Q 12 MET cc_start: 0.8008 (ppp) cc_final: 0.7477 (ppp) REVERT: Q 748 MET cc_start: 0.9003 (ttp) cc_final: 0.8691 (ttp) REVERT: N 576 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8660 (p) REVERT: N 611 ARG cc_start: 0.9505 (OUTLIER) cc_final: 0.9134 (mmm160) REVERT: O 70 GLU cc_start: 0.8997 (mp0) cc_final: 0.8623 (mm-30) REVERT: O 102 MET cc_start: 0.8772 (mmt) cc_final: 0.8382 (mmt) REVERT: O 152 MET cc_start: 0.8953 (mmp) cc_final: 0.8710 (mmp) REVERT: O 221 ARG cc_start: 0.6883 (mtp-110) cc_final: 0.6681 (mtp-110) REVERT: P 1 MET cc_start: 0.0553 (tpt) cc_final: -0.0668 (tpt) REVERT: P 88 LYS cc_start: 0.8772 (ptmm) cc_final: 0.8283 (ptmm) REVERT: P 115 LEU cc_start: 0.9172 (mt) cc_final: 0.8679 (tt) outliers start: 109 outliers final: 77 residues processed: 311 average time/residue: 0.2345 time to fit residues: 123.2287 Evaluate side-chains 298 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 211 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 729 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 807 ILE Chi-restraints excluded: chain S residue 941 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain Q residue 641 VAL Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain Q residue 758 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain N residue 294 HIS Chi-restraints excluded: chain N residue 465 VAL Chi-restraints excluded: chain N residue 512 TYR Chi-restraints excluded: chain N residue 514 MET Chi-restraints excluded: chain N residue 574 VAL Chi-restraints excluded: chain N residue 576 VAL Chi-restraints excluded: chain N residue 611 ARG Chi-restraints excluded: chain O residue 82 HIS Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 131 HIS Chi-restraints excluded: chain O residue 264 PHE Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 109 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 105 optimal weight: 0.6980 chunk 165 optimal weight: 20.0000 chunk 195 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 308 optimal weight: 0.8980 chunk 293 optimal weight: 40.0000 chunk 96 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 360 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 HIS B 154 HIS ** N 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.070429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.047663 restraints weight = 374441.670| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 5.88 r_work: 0.2961 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41105 Z= 0.115 Angle : 0.537 12.526 56027 Z= 0.266 Chirality : 0.040 0.278 6286 Planarity : 0.003 0.050 6825 Dihedral : 14.344 170.930 6317 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.11 % Allowed : 12.40 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4664 helix: 2.00 (0.11), residues: 2169 sheet: -0.17 (0.20), residues: 776 loop : -0.72 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 30 TYR 0.025 0.001 TYR B 146 PHE 0.025 0.001 PHE F 177 TRP 0.016 0.001 TRP A 511 HIS 0.024 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (41072) covalent geometry : angle 0.51786 / 0.27 (55982) hydrogen bonds : bond 0.02813 / 1.88 ( 1612) hydrogen bonds : angle 3.76838 / 2.64 ( 4503) metal coordination : bond 0.00711 / 0.38 ( 31) metal coordination : angle 5.01751 / 2.94 ( 45) Misc. bond : bond 0.00038 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 215 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8500 (pp) REVERT: A 172 HIS cc_start: 0.8024 (t-90) cc_final: 0.7791 (t70) REVERT: A 275 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8777 (mp0) REVERT: A 276 MET cc_start: 0.8830 (ttp) cc_final: 0.7991 (tmm) REVERT: A 292 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7608 (pp) REVERT: A 380 MET cc_start: 0.8357 (ppp) cc_final: 0.7955 (ppp) REVERT: A 510 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7912 (m) REVERT: A 692 LYS cc_start: 0.8785 (tppt) cc_final: 0.8425 (tppt) REVERT: B 81 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8880 (mm-30) REVERT: B 659 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.8260 (t-90) REVERT: B 724 MET cc_start: 0.9042 (mmt) cc_final: 0.8651 (mmt) REVERT: C 417 LYS cc_start: 0.8157 (pttm) cc_final: 0.7768 (pttm) REVERT: C 526 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9139 (mm-30) REVERT: D 185 MET cc_start: 0.8962 (pmm) cc_final: 0.8643 (pmm) REVERT: D 254 MET cc_start: 0.8607 (mpp) cc_final: 0.7892 (ptp) REVERT: E 98 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8441 (tm-30) REVERT: E 356 HIS cc_start: 0.9319 (OUTLIER) cc_final: 0.9077 (t-90) REVERT: F 147 MET cc_start: 0.9390 (mmm) cc_final: 0.9138 (mmm) REVERT: F 256 PHE cc_start: 0.9143 (m-80) cc_final: 0.8724 (m-80) REVERT: G 11 GLU cc_start: 0.8509 (tp30) cc_final: 0.8230 (tp30) REVERT: G 37 ASP cc_start: 0.9336 (p0) cc_final: 0.8872 (t0) REVERT: S 801 ASP cc_start: 0.9184 (t0) cc_final: 0.8919 (m-30) REVERT: S 871 CYS cc_start: 0.9238 (m) cc_final: 0.8907 (p) REVERT: Q 12 MET cc_start: 0.8095 (ppp) cc_final: 0.7530 (ppp) REVERT: Q 748 MET cc_start: 0.8961 (ttp) cc_final: 0.8666 (ttp) REVERT: N 349 MET cc_start: 0.6205 (mmm) cc_final: 0.5655 (mmp) REVERT: N 576 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8754 (p) REVERT: N 616 MET cc_start: 0.7773 (ppp) cc_final: 0.7109 (pmm) REVERT: O 70 GLU cc_start: 0.9137 (mp0) cc_final: 0.8718 (mm-30) REVERT: O 102 MET cc_start: 0.8904 (mmt) cc_final: 0.8542 (mmt) REVERT: O 152 MET cc_start: 0.9521 (mmp) cc_final: 0.9299 (mmp) REVERT: P 1 MET cc_start: 0.0441 (tpt) cc_final: -0.0965 (tpt) REVERT: P 30 ARG cc_start: 0.9314 (mmm-85) cc_final: 0.8858 (mmm-85) REVERT: P 41 PHE cc_start: 0.8981 (p90) cc_final: 0.8383 (p90) REVERT: P 88 LYS cc_start: 0.8635 (ptmm) cc_final: 0.8100 (ptmm) REVERT: P 115 LEU cc_start: 0.9111 (mt) cc_final: 0.8686 (tt) outliers start: 88 outliers final: 69 residues processed: 291 average time/residue: 0.2259 time to fit residues: 111.0707 Evaluate side-chains 283 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 207 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 729 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 807 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 641 VAL Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain Q residue 758 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain N residue 294 HIS Chi-restraints excluded: chain N residue 514 MET Chi-restraints excluded: chain N residue 574 VAL Chi-restraints excluded: chain N residue 576 VAL Chi-restraints excluded: chain O residue 131 HIS Chi-restraints excluded: chain O residue 264 PHE Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 361 optimal weight: 4.9990 chunk 432 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 384 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 446 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 455 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS C 530 GLN E 349 GLN ** N 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.070102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.047232 restraints weight = 380820.958| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.62 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41105 Z= 0.134 Angle : 0.544 12.215 56027 Z= 0.272 Chirality : 0.040 0.281 6286 Planarity : 0.003 0.053 6825 Dihedral : 14.350 172.774 6311 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.27 % Allowed : 12.40 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4664 helix: 2.00 (0.11), residues: 2167 sheet: -0.16 (0.19), residues: 790 loop : -0.73 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 221 TYR 0.019 0.001 TYR B 197 PHE 0.020 0.001 PHE F 177 TRP 0.018 0.001 TRP A 511 HIS 0.005 0.001 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (41072) covalent geometry : angle 0.52658 / 0.27 (55982) hydrogen bonds : bond 0.02877 / 1.92 ( 1612) hydrogen bonds : angle 3.78943 / 2.66 ( 4503) metal coordination : bond 0.00784 / 0.43 ( 31) metal coordination : angle 4.90223 / 2.86 ( 45) Misc. bond : bond 0.00035 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 211 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8366 (pp) REVERT: A 276 MET cc_start: 0.8808 (ttp) cc_final: 0.7370 (tmm) REVERT: A 292 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7677 (pp) REVERT: A 510 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7622 (m) REVERT: A 692 LYS cc_start: 0.8598 (tppt) cc_final: 0.8215 (tppt) REVERT: B 81 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: B 659 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7769 (t-90) REVERT: B 724 MET cc_start: 0.8963 (mmt) cc_final: 0.8526 (mmt) REVERT: C 417 LYS cc_start: 0.7796 (pttm) cc_final: 0.7493 (pttm) REVERT: C 526 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9035 (mm-30) REVERT: D 185 MET cc_start: 0.8930 (pmm) cc_final: 0.8640 (pmm) REVERT: D 254 MET cc_start: 0.8525 (mpp) cc_final: 0.7957 (ptp) REVERT: E 98 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8142 (tm-30) REVERT: E 117 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8832 (mp) REVERT: E 356 HIS cc_start: 0.9328 (OUTLIER) cc_final: 0.9082 (t-90) REVERT: F 256 PHE cc_start: 0.9113 (m-80) cc_final: 0.8714 (m-80) REVERT: G 11 GLU cc_start: 0.8437 (tp30) cc_final: 0.8111 (tp30) REVERT: G 37 ASP cc_start: 0.9330 (p0) cc_final: 0.8924 (t0) REVERT: S 169 MET cc_start: 0.9038 (tmm) cc_final: 0.8697 (ppp) REVERT: S 788 MET cc_start: 0.7469 (tmm) cc_final: 0.7242 (tmm) REVERT: S 801 ASP cc_start: 0.9041 (t0) cc_final: 0.8717 (m-30) REVERT: S 871 CYS cc_start: 0.9193 (m) cc_final: 0.8841 (p) REVERT: Q 12 MET cc_start: 0.7960 (ppp) cc_final: 0.7551 (ppp) REVERT: Q 748 MET cc_start: 0.8884 (ttp) cc_final: 0.8584 (ttp) REVERT: N 349 MET cc_start: 0.6223 (mmm) cc_final: 0.5764 (mmp) REVERT: N 576 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8678 (p) REVERT: N 616 MET cc_start: 0.7651 (ppp) cc_final: 0.6610 (pmm) REVERT: O 70 GLU cc_start: 0.9040 (mp0) cc_final: 0.8647 (mm-30) REVERT: O 102 MET cc_start: 0.8776 (mmt) cc_final: 0.8411 (mmt) REVERT: O 152 MET cc_start: 0.9122 (mmp) cc_final: 0.8905 (mmp) REVERT: P 1 MET cc_start: 0.0236 (tpt) cc_final: -0.0801 (tpt) REVERT: P 30 ARG cc_start: 0.9334 (mmm-85) cc_final: 0.8884 (mmm-85) REVERT: P 41 PHE cc_start: 0.8985 (p90) cc_final: 0.8404 (p90) REVERT: P 88 LYS cc_start: 0.8862 (ptmm) cc_final: 0.8359 (ptmm) REVERT: P 115 LEU cc_start: 0.9184 (mt) cc_final: 0.8636 (tt) outliers start: 95 outliers final: 77 residues processed: 293 average time/residue: 0.2316 time to fit residues: 115.0647 Evaluate side-chains 293 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 208 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 729 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 807 ILE Chi-restraints excluded: chain S residue 941 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 641 VAL Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain Q residue 758 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain N residue 294 HIS Chi-restraints excluded: chain N residue 512 TYR Chi-restraints excluded: chain N residue 514 MET Chi-restraints excluded: chain N residue 574 VAL Chi-restraints excluded: chain N residue 576 VAL Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 125 TYR Chi-restraints excluded: chain O residue 131 HIS Chi-restraints excluded: chain O residue 264 PHE Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 373 optimal weight: 7.9990 chunk 364 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 360 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 446 optimal weight: 30.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 349 GLN ** N 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.070801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047827 restraints weight = 364168.822| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 5.31 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41105 Z= 0.096 Angle : 0.536 11.622 56027 Z= 0.267 Chirality : 0.040 0.284 6286 Planarity : 0.003 0.051 6825 Dihedral : 14.300 174.918 6311 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.94 % Allowed : 13.03 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.13), residues: 4664 helix: 1.94 (0.11), residues: 2159 sheet: -0.11 (0.20), residues: 786 loop : -0.74 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 259 TYR 0.021 0.001 TYR B 197 PHE 0.020 0.001 PHE F 177 TRP 0.014 0.001 TRP A 511 HIS 0.004 0.000 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (41072) covalent geometry : angle 0.51978 / 0.27 (55982) hydrogen bonds : bond 0.02714 / 1.81 ( 1612) hydrogen bonds : angle 3.70636 / 2.60 ( 4503) metal coordination : bond 0.00423 / 0.23 ( 31) metal coordination : angle 4.64485 / 2.72 ( 45) Misc. bond : bond 0.00030 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 218 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8378 (pp) REVERT: A 65 MET cc_start: 0.8286 (ptp) cc_final: 0.8041 (ptp) REVERT: A 276 MET cc_start: 0.8828 (ttp) cc_final: 0.7334 (tmm) REVERT: A 292 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7613 (pp) REVERT: A 510 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7652 (m) REVERT: A 692 LYS cc_start: 0.8610 (tppt) cc_final: 0.8230 (tppt) REVERT: B 81 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8334 (mm-30) REVERT: B 724 MET cc_start: 0.8863 (mmt) cc_final: 0.8494 (mmt) REVERT: C 417 LYS cc_start: 0.7706 (pttm) cc_final: 0.7413 (pttm) REVERT: C 526 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9058 (mm-30) REVERT: D 185 MET cc_start: 0.8745 (pmm) cc_final: 0.8506 (pmm) REVERT: D 254 MET cc_start: 0.8186 (mpp) cc_final: 0.7850 (ptp) REVERT: E 98 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8057 (tm-30) REVERT: F 119 MET cc_start: 0.8673 (mmm) cc_final: 0.8231 (mmp) REVERT: F 146 ARG cc_start: 0.9351 (ttt180) cc_final: 0.9134 (tmm-80) REVERT: F 256 PHE cc_start: 0.9000 (m-80) cc_final: 0.8664 (m-80) REVERT: G 11 GLU cc_start: 0.8383 (tp30) cc_final: 0.8024 (tp30) REVERT: G 37 ASP cc_start: 0.9316 (p0) cc_final: 0.8915 (t0) REVERT: S 169 MET cc_start: 0.8965 (tmm) cc_final: 0.8693 (ppp) REVERT: S 788 MET cc_start: 0.7492 (tmm) cc_final: 0.7267 (tmm) REVERT: S 801 ASP cc_start: 0.9131 (t0) cc_final: 0.8857 (m-30) REVERT: S 871 CYS cc_start: 0.9221 (m) cc_final: 0.8836 (p) REVERT: Q 12 MET cc_start: 0.7992 (ppp) cc_final: 0.7561 (ppp) REVERT: Q 748 MET cc_start: 0.8866 (ttp) cc_final: 0.8534 (ttp) REVERT: N 349 MET cc_start: 0.6241 (mmm) cc_final: 0.5765 (mmp) REVERT: N 576 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8725 (p) REVERT: N 616 MET cc_start: 0.7408 (ppp) cc_final: 0.6246 (pmm) REVERT: O 70 GLU cc_start: 0.8991 (mp0) cc_final: 0.8632 (mm-30) REVERT: O 102 MET cc_start: 0.8714 (mmt) cc_final: 0.8350 (mmt) REVERT: O 152 MET cc_start: 0.8975 (mmp) cc_final: 0.8631 (mmp) REVERT: P 1 MET cc_start: 0.0532 (tpt) cc_final: -0.0799 (tpt) REVERT: P 16 MET cc_start: 0.9024 (pmm) cc_final: 0.8819 (pmm) REVERT: P 41 PHE cc_start: 0.9071 (p90) cc_final: 0.8589 (p90) REVERT: P 88 LYS cc_start: 0.8888 (ptmm) cc_final: 0.8312 (ptmm) REVERT: P 115 LEU cc_start: 0.9178 (mt) cc_final: 0.8640 (tt) outliers start: 81 outliers final: 64 residues processed: 289 average time/residue: 0.2369 time to fit residues: 115.7094 Evaluate side-chains 276 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 729 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 807 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain Q residue 758 LEU Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain N residue 512 TYR Chi-restraints excluded: chain N residue 514 MET Chi-restraints excluded: chain N residue 574 VAL Chi-restraints excluded: chain N residue 576 VAL Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 125 TYR Chi-restraints excluded: chain O residue 131 HIS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 463 optimal weight: 40.0000 chunk 258 optimal weight: 9.9990 chunk 273 optimal weight: 0.0870 chunk 11 optimal weight: 20.0000 chunk 427 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 356 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 288 optimal weight: 50.0000 chunk 383 optimal weight: 7.9990 overall best weight: 6.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS C 530 GLN E 349 GLN ** N 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.069539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046295 restraints weight = 335056.461| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.96 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 41105 Z= 0.211 Angle : 0.604 13.329 56027 Z= 0.302 Chirality : 0.041 0.273 6286 Planarity : 0.003 0.052 6825 Dihedral : 14.381 177.117 6309 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.77 % Allowed : 13.29 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.13), residues: 4664 helix: 1.98 (0.12), residues: 2166 sheet: -0.19 (0.19), residues: 800 loop : -0.75 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.018 0.001 TYR B 197 PHE 0.023 0.001 PHE B 473 TRP 0.022 0.001 TRP A 511 HIS 0.007 0.001 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (41072) covalent geometry : angle 0.58697 / 0.30 (55982) hydrogen bonds : bond 0.03176 / 2.10 ( 1612) hydrogen bonds : angle 3.88661 / 2.71 ( 4503) metal coordination : bond 0.01162 / 0.63 ( 31) metal coordination : angle 4.99837 / 2.95 ( 45) Misc. bond : bond 0.00051 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9328 Ramachandran restraints generated. 4664 Oldfield, 0 Emsley, 4664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 211 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8437 (pp) REVERT: A 65 MET cc_start: 0.8314 (ptp) cc_final: 0.8013 (ptp) REVERT: A 276 MET cc_start: 0.8848 (ttp) cc_final: 0.7320 (tmm) REVERT: A 292 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7730 (pp) REVERT: A 510 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7732 (m) REVERT: A 692 LYS cc_start: 0.8664 (tppt) cc_final: 0.8269 (tppt) REVERT: B 81 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8374 (mm-30) REVERT: B 724 MET cc_start: 0.9000 (mmt) cc_final: 0.8630 (mmm) REVERT: C 526 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9099 (mm-30) REVERT: D 185 MET cc_start: 0.8834 (pmm) cc_final: 0.8567 (pmm) REVERT: D 254 MET cc_start: 0.8206 (mpp) cc_final: 0.7821 (ptp) REVERT: E 98 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8188 (tm-30) REVERT: F 256 PHE cc_start: 0.9058 (m-80) cc_final: 0.8723 (m-80) REVERT: G 11 GLU cc_start: 0.8407 (tp30) cc_final: 0.8040 (tp30) REVERT: S 169 MET cc_start: 0.8984 (tmm) cc_final: 0.8680 (ppp) REVERT: S 788 MET cc_start: 0.7534 (tmm) cc_final: 0.7294 (tmm) REVERT: S 801 ASP cc_start: 0.9126 (t0) cc_final: 0.8858 (m-30) REVERT: S 875 MET cc_start: 0.9091 (ptt) cc_final: 0.8820 (ppp) REVERT: Q 12 MET cc_start: 0.8116 (ppp) cc_final: 0.7637 (ppp) REVERT: Q 748 MET cc_start: 0.9026 (ttp) cc_final: 0.8704 (ttp) REVERT: N 349 MET cc_start: 0.6466 (mmm) cc_final: 0.5992 (mmp) REVERT: O 70 GLU cc_start: 0.8995 (mp0) cc_final: 0.8643 (mm-30) REVERT: O 102 MET cc_start: 0.8737 (mmt) cc_final: 0.8382 (mmt) REVERT: O 152 MET cc_start: 0.9030 (mmp) cc_final: 0.8712 (mmp) REVERT: P 1 MET cc_start: 0.0441 (tpt) cc_final: -0.0607 (tpt) REVERT: P 30 ARG cc_start: 0.9451 (mmm-85) cc_final: 0.8999 (mmm-85) REVERT: P 41 PHE cc_start: 0.9080 (p90) cc_final: 0.8597 (p90) REVERT: P 88 LYS cc_start: 0.8862 (ptmm) cc_final: 0.8302 (ptmm) REVERT: P 115 LEU cc_start: 0.9166 (mt) cc_final: 0.8652 (tt) outliers start: 74 outliers final: 64 residues processed: 275 average time/residue: 0.2327 time to fit residues: 108.6489 Evaluate side-chains 275 residues out of total 4209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 729 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain S residue 273 LEU Chi-restraints excluded: chain S residue 807 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 304 VAL Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 579 VAL Chi-restraints excluded: chain Q residue 642 VAL Chi-restraints excluded: chain Q residue 758 LEU Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain N residue 514 MET Chi-restraints excluded: chain N residue 574 VAL Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 125 TYR Chi-restraints excluded: chain O residue 131 HIS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 356 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 337 optimal weight: 6.9990 chunk 430 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 217 optimal weight: 0.4980 chunk 312 optimal weight: 0.0970 chunk 405 optimal weight: 8.9990 chunk 333 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS ** N 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.070202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.047045 restraints weight = 367584.053| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 5.27 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 41105 Z= 0.106 Angle : 0.565 13.082 56027 Z= 0.279 Chirality : 0.040 0.279 6286 Planarity : 0.003 0.052 6825 Dihedral : 14.362 177.324 6309 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.75 % Allowed : 13.41 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.13), residues: 4664 helix: 1.91 (0.11), residues: 2161 sheet: -0.16 (0.20), residues: 799 loop : -0.77 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 221 TYR 0.021 0.001 TYR B 197 PHE 0.021 0.001 PHE F 32 TRP 0.017 0.001 TRP A 511 HIS 0.005 0.001 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (41072) covalent geometry : angle 0.54742 / 0.28 (55982) hydrogen bonds : bond 0.02817 / 1.86 ( 1612) hydrogen bonds : angle 3.79894 / 2.65 ( 4503) metal coordination : bond 0.00608 / 0.33 ( 31) metal coordination : angle 4.94397 / 2.88 ( 45) Misc. bond : bond 0.00010 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11071.21 seconds wall clock time: 190 minutes 25.62 seconds (11425.62 seconds total)