Starting phenix.real_space_refine on Mon Jul 6 17:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pcp_71512/07_2026/9pcp_71512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pcp_71512/07_2026/9pcp_71512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pcp_71512/07_2026/9pcp_71512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pcp_71512/07_2026/9pcp_71512.map" model { file = "/net/cci-nas-00/data/ceres_data/9pcp_71512/07_2026/9pcp_71512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pcp_71512/07_2026/9pcp_71512.cif" } resolution = 4.3 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= 0.004 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 Zn 6 6.06 5 P 98 5.49 5 S 196 5.16 5 C 22886 2.51 5 N 6308 2.21 5 O 6856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 36356 Number of models: 1 Model: "" Number of chains: 21 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: 5913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5913 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 32, 'TRANS': 701} Chain: "C" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1076 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain breaks: 2 Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3430 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 405} Chain breaks: 2 Chain: "E" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2668 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2013 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 4123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4123 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 22, 'TRANS': 480} Chain breaks: 2 Chain: "I" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "J" Number of atoms: 573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 558 Chain: "K" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1701 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain breaks: 3 Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "L" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 323 Unusual residues: {'VM6': 1} Classifications: {'DNA': 14, 'undetermined': 1} Link IDs: {'rna3p': 13, 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: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "Q" Number of atoms: 5451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5451 Classifications: {'peptide': 713} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 76} Link IDs: {'PTRANS': 34, 'TRANS': 678} Chain breaks: 5 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 22, 'ARG:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 178 Chain: "R" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1400 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 93 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: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "K" 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 94.319 50.633 136.893 1.00133.71 S ATOM 6199 SG CYS B 155 94.142 48.785 143.247 1.00165.98 S ATOM 6488 SG CYS B 190 96.899 50.411 141.566 1.00132.45 S ATOM 6030 SG CYS B 134 91.108 52.702 142.361 1.00146.79 S ATOM 6488 SG CYS B 190 96.899 50.411 141.566 1.00132.45 S ATOM 17276 SG CYS E 291 112.493 44.537 74.669 1.00480.69 S ATOM 17298 SG CYS E 294 112.474 41.043 76.728 1.00538.40 S ATOM 17387 SG CYS E 305 110.033 43.841 77.666 1.00506.73 S ATOM 17410 SG CYS E 308 113.620 44.270 77.928 1.00570.44 S ATOM 17712 SG CYS E 345 116.884 81.183 43.732 1.00439.16 S ATOM 17734 SG CYS E 348 114.553 80.924 43.001 1.00453.14 S ATOM 17891 SG CYS E 368 114.477 83.289 46.274 1.00464.01 S ATOM 17912 SG CYS E 371 114.703 79.638 46.774 1.00469.25 S ATOM 17832 SG CYS E 360 125.638 76.217 51.024 1.00321.41 S ATOM 17850 SG CYS E 363 125.232 73.915 48.123 1.00314.04 S ATOM 17999 SG CYS E 382 122.419 74.536 50.581 1.00350.60 S ATOM 18016 SG CYS E 385 125.498 72.482 51.686 1.00348.46 S ATOM 19891 SG CYS F 268 124.225 62.385 74.611 1.00363.71 S ATOM 19910 SG CYS F 271 124.434 64.238 71.229 1.00402.19 S ATOM 19995 SG CYS F 282 126.976 61.445 72.108 1.00495.33 S ATOM 20015 SG CYS F 285 126.731 64.796 74.076 1.00528.72 S ATOM 19783 SG CYS F 255 124.543 53.108 65.007 1.00462.64 S ATOM 19800 SG CYS F 257 128.307 52.679 65.025 1.00499.59 S ATOM 19949 SG CYS F 276 126.143 49.713 66.230 1.00465.09 S ATOM 26104 SG CYS K 105 90.671 155.560 137.608 1.00271.54 S ATOM 26128 SG CYS K 108 91.246 157.060 141.025 1.00303.28 S ATOM 26276 SG CYS K 126 90.404 153.502 140.798 1.00283.40 S ATOM 26298 SG CYS K 129 87.660 155.736 140.147 1.00291.67 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 127 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS J 127 " occ=0.50 Time building chain proxies: 7.85, per 1000 atoms: 0.22 Number of scatterers: 36356 At special positions: 0 Unit cell: (144.42, 174.3, 245.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 Ca 2 19.99 S 196 16.00 P 98 15.00 O 6856 8.00 N 6308 7.00 C 22886 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE2 SF4 B1000 " - pdb=" ND1 HIS B 118 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 291 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 368 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 385 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" NE2 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 300 " pdb="ZN ZN K 300 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 300 " - pdb=" SG CYS K 108 " pdb="ZN ZN K 300 " - pdb=" SG CYS K 105 " pdb="ZN ZN K 300 " - pdb=" SG CYS K 129 " Number of angles added : 33 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8226 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 32 sheets defined 51.9% alpha, 9.9% beta 37 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.501A pdb=" N VAL A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 181 through 189 removed outlier: 3.894A pdb=" N ILE A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.634A pdb=" N CYS A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.641A pdb=" N VAL A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.289A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.610A pdb=" N LEU A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 525 removed outlier: 4.146A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 536 removed outlier: 3.553A pdb=" N LEU A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 632 through 640 Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 677 through 684 Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.837A pdb=" N GLU A 698 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 699 " --> pdb=" O MET A 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 695 through 699' Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.923A pdb=" N GLN A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 34 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 76 through 99 removed outlier: 3.574A pdb=" N ILE B 80 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 removed outlier: 4.159A pdb=" N VAL B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.680A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 296 removed outlier: 3.529A pdb=" N GLY B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.516A pdb=" N ALA B 303 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 320 through 344 removed outlier: 3.744A pdb=" N ALA B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 374 through 386 removed outlier: 4.098A pdb=" N LEU B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 Processing helix chain 'B' and resid 439 through 444 removed outlier: 4.228A pdb=" N ALA B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 444' Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.814A pdb=" N PHE B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.915A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 531 removed outlier: 3.637A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 557 through 565 Processing helix chain 'B' and resid 573 through 590 Processing helix chain 'B' and resid 631 through 645 Processing helix chain 'B' and resid 647 through 665 Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 702 through 707 removed outlier: 3.954A pdb=" N LEU B 706 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN B 707 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 725 removed outlier: 3.694A pdb=" N GLY B 713 " --> pdb=" O THR B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.758A pdb=" N ASP B 732 " --> pdb=" O HIS B 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 removed outlier: 3.885A pdb=" N ILE C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 454 through 478 Processing helix chain 'C' and resid 483 through 516 removed outlier: 4.290A 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 520 through 542 removed outlier: 4.428A pdb=" N HIS C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.919A pdb=" N CYS D 41 " --> pdb=" O HIS D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 113 through 120 removed outlier: 3.726A pdb=" N ARG D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 172 through 183 removed outlier: 3.749A pdb=" N GLY D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 207 through 222 Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.657A pdb=" N GLY D 227 " --> pdb=" O GLN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.646A pdb=" N ILE D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 332 removed outlier: 3.546A pdb=" N ILE D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 358 removed outlier: 3.564A pdb=" N VAL D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 371 through 372 No H-bonds generated for 'chain 'D' and resid 371 through 372' Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'D' and resid 384 through 397 Processing helix chain 'D' and resid 414 through 429 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.815A pdb=" N VAL D 451 " --> pdb=" O GLY D 447 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.859A pdb=" N LYS E 23 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 24 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP E 25 " --> pdb=" O LEU E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 20 through 25' Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 79 through 99 removed outlier: 3.550A pdb=" N CYS E 83 " --> pdb=" O ASN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 removed outlier: 3.706A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 144 through 156 removed outlier: 3.746A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 193 removed outlier: 3.653A pdb=" N THR E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 224 through 235 Processing helix chain 'E' and resid 272 through 278 removed outlier: 4.154A pdb=" N GLY E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 324 Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 387 removed outlier: 3.547A pdb=" N HIS E 387 " --> pdb=" O PRO E 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 28 removed outlier: 4.188A pdb=" N TRP F 22 " --> pdb=" O ASN F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.055A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 121 removed outlier: 3.647A pdb=" N LYS F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 151 removed outlier: 3.842A pdb=" N SER F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 49 through 64 Processing helix chain 'H' and resid 172 through 225 Processing helix chain 'H' and resid 226 through 237 Processing helix chain 'H' and resid 238 through 243 removed outlier: 3.836A pdb=" N THR H 242 " --> pdb=" O PRO H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 265 removed outlier: 3.651A pdb=" N LEU H 254 " --> pdb=" O ASP H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 290 Processing helix chain 'H' and resid 294 through 307 Processing helix chain 'H' and resid 554 through 561 removed outlier: 4.017A pdb=" N CYS H 558 " --> pdb=" O GLN H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 585 Processing helix chain 'H' and resid 599 through 607 Processing helix chain 'H' and resid 614 through 628 removed outlier: 3.969A pdb=" N GLU H 618 " --> pdb=" O PHE H 614 " (cutoff:3.500A) Processing helix chain 'H' and resid 686 through 693 Processing helix chain 'H' and resid 713 through 721 removed outlier: 3.987A pdb=" N LEU H 719 " --> pdb=" O ARG H 715 " (cutoff:3.500A) Processing helix chain 'H' and resid 723 through 728 removed outlier: 3.869A pdb=" N GLU H 727 " --> pdb=" O GLN H 723 " (cutoff:3.500A) Processing helix chain 'H' and resid 763 through 767 Processing helix chain 'H' and resid 778 through 787 Processing helix chain 'H' and resid 799 through 803 removed outlier: 3.612A pdb=" N TYR H 803 " --> pdb=" O HIS H 800 " (cutoff:3.500A) Processing helix chain 'H' and resid 818 through 859 removed outlier: 3.932A pdb=" N GLU H 826 " --> pdb=" O LEU H 822 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASN H 827 " --> pdb=" O THR H 823 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU H 833 " --> pdb=" O GLN H 829 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 902 Processing helix chain 'H' and resid 903 through 908 removed outlier: 3.504A pdb=" N ASN H 907 " --> pdb=" O SER H 903 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG H 908 " --> pdb=" O TRP H 904 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 903 through 908' Processing helix chain 'I' and resid 274 through 281 removed outlier: 3.723A pdb=" N GLU I 277 " --> pdb=" O HIS I 274 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE I 278 " --> pdb=" O PRO I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 295 removed outlier: 3.554A pdb=" N GLN I 294 " --> pdb=" O GLN I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 299 through 309 removed outlier: 4.123A pdb=" N LEU I 303 " --> pdb=" O LEU I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 316 Processing helix chain 'I' and resid 321 through 329 Processing helix chain 'J' and resid 104 through 114 Processing helix chain 'J' and resid 122 through 134 Processing helix chain 'J' and resid 138 through 150 Processing helix chain 'J' and resid 158 through 168 removed outlier: 3.680A pdb=" N LYS J 168 " --> pdb=" O ARG J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 39 removed outlier: 4.059A pdb=" N ARG K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ARG K 34 " --> pdb=" O ARG K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 121 removed outlier: 3.717A pdb=" N HIS K 120 " --> pdb=" O TYR K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 130 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 151 through 156 Processing helix chain 'K' and resid 183 through 195 Processing helix chain 'K' and resid 197 through 232 removed outlier: 3.999A pdb=" N GLU K 201 " --> pdb=" O GLN K 197 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 28 removed outlier: 4.244A pdb=" N ASP Q 28 " --> pdb=" O LEU Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 52 Processing helix chain 'Q' and resid 65 through 80 Processing helix chain 'Q' and resid 93 through 104 removed outlier: 3.559A pdb=" N GLY Q 104 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 120 Processing helix chain 'Q' and resid 136 through 141 removed outlier: 3.624A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 153 removed outlier: 4.039A pdb=" N PHE Q 147 " --> pdb=" O CYS Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 186 removed outlier: 3.942A pdb=" N VAL Q 181 " --> pdb=" O HIS Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 200 through 207 removed outlier: 3.522A pdb=" N HIS Q 207 " --> pdb=" O PHE Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 219 through 243 removed outlier: 4.016A pdb=" N ILE Q 225 " --> pdb=" O THR Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 253 through 258 Processing helix chain 'Q' and resid 260 through 267 removed outlier: 3.802A pdb=" N LYS Q 264 " --> pdb=" O LYS Q 260 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 277 removed outlier: 3.682A pdb=" N LEU Q 277 " --> pdb=" O TRP Q 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 301 removed outlier: 3.799A pdb=" N GLN Q 286 " --> pdb=" O LYS Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 320 removed outlier: 3.679A pdb=" N PHE Q 320 " --> pdb=" O THR Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 326 through 331 Processing helix chain 'Q' and resid 333 through 341 removed outlier: 3.533A pdb=" N ILE Q 337 " --> pdb=" O THR Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 378 through 398 removed outlier: 3.634A pdb=" N GLU Q 382 " --> pdb=" O ASN Q 378 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 426 Processing helix chain 'Q' and resid 427 through 439 Processing helix chain 'Q' and resid 564 through 573 Processing helix chain 'Q' and resid 584 through 596 removed outlier: 3.782A pdb=" N VAL Q 588 " --> pdb=" O GLU Q 584 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG Q 589 " --> pdb=" O LEU Q 585 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN Q 590 " --> pdb=" O THR Q 586 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA Q 596 " --> pdb=" O GLU Q 592 " (cutoff:3.500A) Processing helix chain 'Q' and resid 613 through 640 removed outlier: 3.539A pdb=" N TYR Q 619 " --> pdb=" O GLU Q 615 " (cutoff:3.500A) Processing helix chain 'Q' and resid 688 through 693 removed outlier: 3.679A pdb=" N ARG Q 692 " --> pdb=" O ARG Q 689 " (cutoff:3.500A) Processing helix chain 'Q' and resid 694 through 703 Processing helix chain 'Q' and resid 729 through 738 Processing helix chain 'Q' and resid 739 through 752 removed outlier: 3.591A pdb=" N TYR Q 752 " --> pdb=" O MET Q 748 " (cutoff:3.500A) Processing helix chain 'Q' and resid 783 through 795 Processing helix chain 'Q' and resid 805 through 817 removed outlier: 3.517A pdb=" N LYS Q 817 " --> pdb=" O PHE Q 813 " (cutoff:3.500A) Processing helix chain 'Q' and resid 847 through 853 removed outlier: 3.783A pdb=" N LEU Q 853 " --> pdb=" O ASP Q 850 " (cutoff:3.500A) Processing helix chain 'Q' and resid 865 through 870 Processing helix chain 'Q' and resid 872 through 878 Processing helix chain 'Q' and resid 880 through 889 Processing helix chain 'Q' and resid 890 through 902 removed outlier: 3.787A pdb=" N ALA Q 894 " --> pdb=" O ASN Q 890 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 108 Processing helix chain 'R' and resid 143 through 149 Processing helix chain 'R' and resid 151 through 161 Processing helix chain 'R' and resid 178 through 192 removed outlier: 3.822A pdb=" N LEU R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 215 Processing helix chain 'R' and resid 230 through 239 Processing helix chain 'R' and resid 246 through 257 Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 278 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.702A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.674A pdb=" N GLU A 115 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 206 removed outlier: 4.521A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 166 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 392 removed outlier: 4.325A pdb=" N THR A 409 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASP A 441 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 364 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY A 436 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU A 464 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N MET A 438 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU A 466 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 440 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 337 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU A 490 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 339 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.518A pdb=" N LYS A 557 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN A 621 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N TYR A 660 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 661 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 510 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS A 507 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A 690 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU A 509 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 40 removed outlier: 7.967A pdb=" N ILE B 455 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 231 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR B 457 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 233 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 234 " --> pdb=" O CYS B 73 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 70 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 107 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 252 Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 495 removed outlier: 6.320A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA B 680 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N MET B 620 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AB3, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AB4, first strand: chain 'D' and resid 431 through 435 removed outlier: 6.548A pdb=" N VAL D 442 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU D 434 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 440 " --> pdb=" O GLU D 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 113 through 121 removed outlier: 6.686A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU E 119 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 104 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N HIS E 60 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU E 168 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR E 62 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE E 170 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL E 64 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG E 165 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER E 197 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 289 through 291 Processing sheet with id=AB7, first strand: chain 'E' and resid 358 through 360 removed outlier: 3.713A pdb=" N ASN E 365 " --> pdb=" O CYS E 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.071A pdb=" N SER F 67 " --> pdb=" O HIS F 63 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS F 63 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE F 69 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA F 61 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LYS F 56 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 8 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ARG F 160 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N LEU F 190 " --> pdb=" O MET F 157 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N SER F 159 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASP F 192 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE F 161 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N CYS F 194 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL F 163 " --> pdb=" O CYS F 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 266 through 267 removed outlier: 6.564A pdb=" N THR H 266 " --> pdb=" O ALA H 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 541 through 545 removed outlier: 4.290A pdb=" N TYR H 568 " --> pdb=" O LEU H 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 657 through 659 removed outlier: 3.554A pdb=" N ALA H 658 " --> pdb=" O HIS H 682 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 695 through 697 Processing sheet with id=AC4, first strand: chain 'H' and resid 705 through 707 Processing sheet with id=AC5, first strand: chain 'H' and resid 759 through 760 removed outlier: 6.526A pdb=" N VAL H 759 " --> pdb=" O ILE H 794 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLY H 796 " --> pdb=" O VAL H 759 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 771 through 774 Processing sheet with id=AC7, first strand: chain 'K' and resid 103 through 104 Processing sheet with id=AC8, first strand: chain 'K' and resid 138 through 139 Processing sheet with id=AC9, first strand: chain 'K' and resid 246 through 252 removed outlier: 5.315A pdb=" N THR K 260 " --> pdb=" O GLY K 247 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU K 249 " --> pdb=" O ARG K 258 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ARG K 258 " --> pdb=" O GLU K 249 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN K 251 " --> pdb=" O MET K 256 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET K 256 " --> pdb=" O ASN K 251 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 86 through 87 removed outlier: 3.582A pdb=" N VAL Q 59 " --> pdb=" O GLY Q 105 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE Q 107 " --> pdb=" O VAL Q 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL Q 61 " --> pdb=" O ILE Q 107 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU Q 58 " --> pdb=" O GLY Q 130 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LEU Q 132 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU Q 60 " --> pdb=" O LEU Q 132 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR Q 134 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU Q 62 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR Q 129 " --> pdb=" O PHE Q 160 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LYS Q 162 " --> pdb=" O THR Q 129 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE Q 131 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N PHE Q 164 " --> pdb=" O ILE Q 131 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL Q 133 " --> pdb=" O PHE Q 164 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY Q 31 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N THR Q 165 " --> pdb=" O GLY Q 31 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL Q 33 " --> pdb=" O THR Q 165 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU Q 32 " --> pdb=" O TYR Q 191 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 210 through 217 removed outlier: 6.459A pdb=" N GLU Q 210 " --> pdb=" O VAL Q 605 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE Q 607 " --> pdb=" O GLU Q 210 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL Q 212 " --> pdb=" O PHE Q 607 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE Q 609 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE Q 214 " --> pdb=" O ILE Q 609 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY Q 611 " --> pdb=" O ILE Q 214 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL Q 216 " --> pdb=" O GLY Q 611 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU Q 608 " --> pdb=" O LEU Q 580 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLN Q 406 " --> pdb=" O ARG Q 576 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL Q 578 " --> pdb=" O GLN Q 406 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU Q 408 " --> pdb=" O VAL Q 578 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU Q 580 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS Q 410 " --> pdb=" O LEU Q 580 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N HIS Q 555 " --> pdb=" O VAL Q 407 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE Q 409 " --> pdb=" O HIS Q 555 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 705 through 706 removed outlier: 10.386A pdb=" N SER Q 683 " --> pdb=" O THR Q 719 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR Q 719 " --> pdb=" O SER Q 683 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU Q 718 " --> pdb=" O MET Q 722 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET Q 722 " --> pdb=" O LEU Q 718 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS Q 723 " --> pdb=" O VAL Q 756 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU Q 758 " --> pdb=" O CYS Q 723 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU Q 725 " --> pdb=" O LEU Q 758 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLU Q 760 " --> pdb=" O GLU Q 725 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS Q 727 " --> pdb=" O GLU Q 760 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU Q 801 " --> pdb=" O PRO Q 755 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU Q 757 " --> pdb=" O LEU Q 801 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 102 through 103 Processing sheet with id=AD5, first strand: chain 'R' and resid 130 through 131 removed outlier: 6.775A pdb=" N CYS R 137 " --> pdb=" O VAL R 168 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU R 170 " --> pdb=" O CYS R 137 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU R 139 " --> pdb=" O LEU R 170 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLN R 172 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU R 141 " --> pdb=" O GLN R 172 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG R 167 " --> pdb=" O THR R 195 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE R 197 " --> pdb=" O ARG R 167 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU R 169 " --> pdb=" O ILE R 197 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA R 199 " --> pdb=" O LEU R 169 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL R 171 " --> pdb=" O ALA R 199 " (cutoff:3.500A) 1598 hydrogen bonds defined for protein. 4585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 8.39 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 2.01: 37286 2.01 - 2.82: 12 2.82 - 3.62: 0 3.62 - 4.42: 0 4.42 - 5.23: 1 Warning: very large bond lengths. Bond restraints: 37299 Sorted by residual: bond pdb=" CG LEU C 434 " pdb=" CD2 LEU C 434 " ideal model delta sigma weight residual 1.521 5.225 -3.704 3.30e-02 9.18e+02 1.26e+04 bond pdb=" CE3 TRP F 229 " pdb=" CZ3 TRP F 229 " ideal model delta sigma weight residual 1.382 1.984 -0.602 3.00e-02 1.11e+03 4.03e+02 bond pdb=" CE2 TRP F 229 " pdb=" CZ2 TRP F 229 " ideal model delta sigma weight residual 1.394 1.759 -0.365 2.10e-02 2.27e+03 3.02e+02 bond pdb=" CZ3 TRP F 229 " pdb=" CH2 TRP F 229 " ideal model delta sigma weight residual 1.400 1.781 -0.381 2.50e-02 1.60e+03 2.32e+02 bond pdb=" CD2 TRP F 229 " pdb=" CE2 TRP F 229 " ideal model delta sigma weight residual 1.409 1.634 -0.225 1.70e-02 3.46e+03 1.74e+02 ... (remaining 37294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 50102 3.83 - 7.66: 712 7.66 - 11.50: 88 11.50 - 15.33: 15 15.33 - 19.16: 3 Bond angle restraints: 50920 Sorted by residual: angle pdb=" N HIS E 324 " pdb=" CA HIS E 324 " pdb=" C HIS E 324 " ideal model delta sigma weight residual 111.30 100.09 11.21 1.43e+00 4.89e-01 6.15e+01 angle pdb=" N ILE A 484 " pdb=" CA ILE A 484 " pdb=" C ILE A 484 " ideal model delta sigma weight residual 112.12 106.07 6.05 8.40e-01 1.42e+00 5.18e+01 angle pdb=" O4' DT M 31 " pdb=" C1' DT M 31 " pdb=" N1 DT M 31 " ideal model delta sigma weight residual 108.00 112.73 -4.73 7.00e-01 2.04e+00 4.57e+01 angle pdb=" O4' DA M 21 " pdb=" C4' DA M 21 " pdb=" C3' DA M 21 " ideal model delta sigma weight residual 106.00 101.96 4.04 6.00e-01 2.78e+00 4.53e+01 angle pdb=" CB MET B 724 " pdb=" CG MET B 724 " pdb=" SD MET B 724 " ideal model delta sigma weight residual 112.70 93.54 19.16 3.00e+00 1.11e-01 4.08e+01 ... (remaining 50915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 21442 34.62 - 69.24: 872 69.24 - 103.86: 45 103.86 - 138.48: 2 138.48 - 173.10: 1 Dihedral angle restraints: 22362 sinusoidal: 9688 harmonic: 12674 Sorted by residual: dihedral pdb=" CA LEU E 301 " pdb=" C LEU E 301 " pdb=" N PRO E 302 " pdb=" CA PRO E 302 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA MET Q 867 " pdb=" C MET Q 867 " pdb=" N HIS Q 868 " pdb=" CA HIS Q 868 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LYS K 31 " pdb=" C LYS K 31 " pdb=" N ARG K 32 " pdb=" CA ARG K 32 " ideal model delta harmonic sigma weight residual 180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 22359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 5077 0.096 - 0.193: 625 0.193 - 0.289: 45 0.289 - 0.386: 9 0.386 - 0.482: 2 Chirality restraints: 5758 Sorted by residual: chirality pdb=" CB THR B 425 " pdb=" CA THR B 425 " pdb=" OG1 THR B 425 " pdb=" CG2 THR B 425 " both_signs ideal model delta sigma weight residual False 2.55 2.07 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CB ILE R 127 " pdb=" CA ILE R 127 " pdb=" CG1 ILE R 127 " pdb=" CG2 ILE R 127 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB ILE B 619 " pdb=" CA ILE B 619 " pdb=" CG1 ILE B 619 " pdb=" CG2 ILE B 619 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 5755 not shown) Planarity restraints: 6177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 VM6 L 63 " 0.055 2.00e-02 2.50e+03 2.78e-01 9.63e+02 pdb=" C4 VM6 L 63 " -0.107 2.00e-02 2.50e+03 pdb=" C5 VM6 L 63 " -0.473 2.00e-02 2.50e+03 pdb=" C6 VM6 L 63 " 0.327 2.00e-02 2.50e+03 pdb=" N2 VM6 L 63 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 VM6 L 63 " -0.295 2.00e-02 2.50e+03 2.06e-01 5.28e+02 pdb=" C20 VM6 L 63 " 0.103 2.00e-02 2.50e+03 pdb=" C8 VM6 L 63 " -0.134 2.00e-02 2.50e+03 pdb=" C9 VM6 L 63 " 0.309 2.00e-02 2.50e+03 pdb=" N1 VM6 L 63 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 VM6 L 63 " -0.129 2.00e-02 2.50e+03 2.12e-01 4.50e+02 pdb=" C6 VM6 L 63 " 0.272 2.00e-02 2.50e+03 pdb=" C7 VM6 L 63 " -0.270 2.00e-02 2.50e+03 pdb=" C8 VM6 L 63 " 0.127 2.00e-02 2.50e+03 ... (remaining 6174 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 9178 2.80 - 3.32: 33991 3.32 - 3.85: 66181 3.85 - 4.37: 74145 4.37 - 4.90: 119549 Nonbonded interactions: 303044 Sorted by model distance: nonbonded pdb=" O ILE B 504 " pdb=" OH TYR B 520 " model vdw 2.269 3.040 nonbonded pdb=" O ILE K 186 " pdb=" OG SER K 190 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP A 309 " pdb=" OG1 THR A 383 " model vdw 2.274 3.040 nonbonded pdb=" OH TYR D 35 " pdb=" O LEU D 93 " model vdw 2.275 3.040 nonbonded pdb=" O LEU F 133 " pdb=" OG SER F 136 " model vdw 2.282 3.040 ... (remaining 303039 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 45.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.021 3.704 37331 Z= 0.737 Angle : 1.317 58.957 50965 Z= 0.702 Chirality : 0.063 0.482 5758 Planarity : 0.009 0.278 6177 Dihedral : 17.346 173.098 14136 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.28 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -2.89 (0.11), residues: 4260 helix: -1.90 (0.09), residues: 2105 sheet: -0.66 (0.24), residues: 500 loop : -2.16 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG H 196 TYR 0.033 0.003 TYR E 62 PHE 0.061 0.003 PHE B 720 TRP 0.057 0.003 TRP A 511 HIS 0.016 0.002 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.02097 / 0.73 (37299) covalent geometry : angle 1.21003 / 0.70 (50920) hydrogen bonds : bond 0.15640 / 10.53 ( 1689) hydrogen bonds : angle 7.64049 / 5.39 ( 4767) metal coordination : bond 0.13665 / 6.53 ( 29) metal coordination : angle 17.51126 / 11.07 ( 45) Misc. bond : bond 0.00082 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 MET cc_start: 0.8322 (mtm) cc_final: 0.7463 (ptt) REVERT: B 545 MET cc_start: 0.9373 (tmm) cc_final: 0.9000 (tmm) REVERT: B 620 MET cc_start: 0.8845 (ppp) cc_final: 0.8488 (ppp) REVERT: B 677 MET cc_start: 0.8536 (mpp) cc_final: 0.8304 (mpp) REVERT: B 724 MET cc_start: 0.8729 (mtm) cc_final: 0.8460 (mpp) REVERT: C 411 MET cc_start: -0.5147 (mmt) cc_final: -0.5579 (mtt) REVERT: D 254 MET cc_start: 0.8395 (pmm) cc_final: 0.8008 (pmm) REVERT: D 376 MET cc_start: 0.8809 (ptp) cc_final: 0.8553 (mtm) REVERT: E 153 MET cc_start: 0.8925 (mmt) cc_final: 0.8476 (mmp) REVERT: F 51 MET cc_start: 0.9643 (mpp) cc_final: 0.9213 (mpp) REVERT: F 157 MET cc_start: 0.8287 (tpt) cc_final: 0.8061 (tpt) REVERT: G 16 MET cc_start: 0.8343 (mmt) cc_final: 0.8119 (mmm) REVERT: H 566 MET cc_start: 0.5430 (mmm) cc_final: 0.5192 (mmm) REVERT: H 766 MET cc_start: 0.1300 (mpp) cc_final: 0.0351 (mtp) REVERT: H 898 ARG cc_start: 0.8292 (ttt-90) cc_final: 0.7923 (tmt-80) REVERT: J 103 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7392 (mmmt) REVERT: K 178 MET cc_start: 0.5776 (mmm) cc_final: 0.5530 (mmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2266 time to fit residues: 51.2519 Evaluate side-chains 116 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 GLN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN B 649 ASN B 733 GLN D 106 GLN D 211 GLN D 218 GLN D 424 HIS D 460 HIS E 154 GLN F 145 HIS H 712 ASN H 728 ASN H 847 ASN ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 HIS Q 849 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.043366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.032587 restraints weight = 454963.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.032648 restraints weight = 337552.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.032716 restraints weight = 243812.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.032830 restraints weight = 224612.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.032844 restraints weight = 208749.828| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 2.124 37331 Z= 0.398 Angle : 0.817 53.829 50965 Z= 0.359 Chirality : 0.043 0.281 5758 Planarity : 0.005 0.077 6177 Dihedral : 16.772 160.348 5820 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.39 % Rotamer: Outliers : 0.11 % Allowed : 5.18 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.80 (0.12), residues: 4260 helix: -0.70 (0.10), residues: 2138 sheet: -0.73 (0.24), residues: 506 loop : -1.87 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG D 400 TYR 0.028 0.001 TYR A 534 PHE 0.035 0.002 PHE B 720 TRP 0.050 0.002 TRP H 904 HIS 0.005 0.001 HIS E 376 Details of bonding type rmsd/Z covalent geometry : bond 0.01200 / 0.40 (37299) covalent geometry : angle 0.66600 / 0.36 (50920) hydrogen bonds : bond 0.04689 / 3.05 ( 1689) hydrogen bonds : angle 5.66331 / 4.00 ( 4767) metal coordination : bond 0.01120 / 0.68 ( 29) metal coordination : angle 15.95578 / 9.53 ( 45) Misc. bond : bond 0.00322 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8546 (ppp) cc_final: 0.8172 (ppp) REVERT: A 536 MET cc_start: 0.8715 (mmp) cc_final: 0.8435 (mmm) REVERT: A 650 MET cc_start: 0.8908 (mpp) cc_final: 0.8167 (mpp) REVERT: B 545 MET cc_start: 0.9294 (tmm) cc_final: 0.8932 (tmm) REVERT: B 620 MET cc_start: 0.8643 (ppp) cc_final: 0.8383 (ppp) REVERT: B 677 MET cc_start: 0.8509 (mpp) cc_final: 0.8248 (mpp) REVERT: C 441 MET cc_start: 0.3251 (mpp) cc_final: 0.2586 (mpp) REVERT: C 528 MET cc_start: 0.8188 (mmt) cc_final: 0.7763 (mmt) REVERT: D 185 MET cc_start: 0.8361 (tpp) cc_final: 0.7897 (tpp) REVERT: D 254 MET cc_start: 0.8600 (pmm) cc_final: 0.8192 (pmm) REVERT: D 341 MET cc_start: 0.8715 (ppp) cc_final: 0.8341 (ppp) REVERT: D 376 MET cc_start: 0.9454 (ptp) cc_final: 0.9240 (ptp) REVERT: E 137 MET cc_start: 0.8412 (tmm) cc_final: 0.8196 (tmm) REVERT: F 51 MET cc_start: 0.9584 (mpp) cc_final: 0.9355 (mpp) REVERT: G 16 MET cc_start: 0.8787 (mmt) cc_final: 0.8304 (mmm) REVERT: H 766 MET cc_start: 0.1524 (mpp) cc_final: 0.0811 (mtp) REVERT: J 160 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8033 (tm-30) REVERT: K 37 MET cc_start: 0.8883 (mmm) cc_final: 0.8682 (mmm) REVERT: K 113 MET cc_start: 0.8178 (mmp) cc_final: 0.7863 (mmp) REVERT: K 178 MET cc_start: 0.5710 (mmm) cc_final: 0.5507 (mmm) REVERT: Q 182 MET cc_start: 0.8824 (pmm) cc_final: 0.8550 (pmm) REVERT: Q 722 MET cc_start: 0.7706 (tmm) cc_final: 0.7345 (tmm) outliers start: 4 outliers final: 1 residues processed: 138 average time/residue: 0.2115 time to fit residues: 51.2042 Evaluate side-chains 119 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 404 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 400 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 323 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN C 496 ASN C 530 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 211 GLN D 460 HIS E 60 HIS E 154 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 HIS H 728 ASN ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 HIS ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 700 HIS Q 849 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.042405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.033119 restraints weight = 468107.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.032418 restraints weight = 336008.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.032551 restraints weight = 283044.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.032780 restraints weight = 239096.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.032749 restraints weight = 209038.477| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 37331 Z= 0.262 Angle : 0.844 54.241 50965 Z= 0.381 Chirality : 0.044 0.266 5758 Planarity : 0.005 0.074 6177 Dihedral : 16.662 159.425 5820 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.93 % Favored : 93.02 % Rotamer: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.47 (0.13), residues: 4260 helix: -0.30 (0.11), residues: 2141 sheet: -0.88 (0.24), residues: 506 loop : -1.81 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 676 TYR 0.021 0.002 TYR A 534 PHE 0.027 0.002 PHE B 720 TRP 0.037 0.002 TRP F 229 HIS 0.008 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (37299) covalent geometry : angle 0.70564 / 0.38 (50920) hydrogen bonds : bond 0.05180 / 3.35 ( 1689) hydrogen bonds : angle 5.52032 / 3.89 ( 4767) metal coordination : bond 0.01587 / 1.15 ( 29) metal coordination : angle 15.57402 / 9.13 ( 45) Misc. bond : bond 0.00239 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8702 (ppp) cc_final: 0.8309 (ppp) REVERT: A 412 MET cc_start: 0.6664 (ttm) cc_final: 0.6416 (ttm) REVERT: A 650 MET cc_start: 0.8853 (mpp) cc_final: 0.8179 (mpp) REVERT: B 545 MET cc_start: 0.9270 (tmm) cc_final: 0.8926 (tmm) REVERT: B 620 MET cc_start: 0.8675 (ppp) cc_final: 0.8453 (ppp) REVERT: B 677 MET cc_start: 0.8513 (mpp) cc_final: 0.8272 (mpp) REVERT: C 528 MET cc_start: 0.7885 (mmt) cc_final: 0.7364 (mmt) REVERT: D 185 MET cc_start: 0.8330 (tpp) cc_final: 0.7837 (tpp) REVERT: D 254 MET cc_start: 0.8545 (pmm) cc_final: 0.7999 (pmm) REVERT: D 341 MET cc_start: 0.8490 (ppp) cc_final: 0.8058 (ppp) REVERT: G 16 MET cc_start: 0.8750 (mmt) cc_final: 0.8035 (mmm) REVERT: H 766 MET cc_start: 0.1186 (mpp) cc_final: 0.0626 (mtp) REVERT: K 37 MET cc_start: 0.8832 (mmm) cc_final: 0.8499 (mmp) REVERT: K 113 MET cc_start: 0.7972 (mmp) cc_final: 0.7709 (mmp) REVERT: K 178 MET cc_start: 0.5996 (tpt) cc_final: 0.5232 (tpt) REVERT: Q 182 MET cc_start: 0.8851 (pmm) cc_final: 0.8554 (pmm) outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.2129 time to fit residues: 46.8394 Evaluate side-chains 115 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 237 optimal weight: 20.0000 chunk 312 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 167 optimal weight: 0.3980 chunk 177 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 411 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN B 705 ASN C 405 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 211 GLN D 460 HIS ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN H 206 HIS H 728 ASN ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.043123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.033268 restraints weight = 463430.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.032530 restraints weight = 366718.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.032598 restraints weight = 310357.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.032749 restraints weight = 263062.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.032738 restraints weight = 247885.089| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37331 Z= 0.145 Angle : 0.774 54.361 50965 Z= 0.332 Chirality : 0.043 0.248 5758 Planarity : 0.004 0.069 6177 Dihedral : 16.509 151.345 5820 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.06 % Favored : 93.89 % Rotamer: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.17 (0.13), residues: 4260 helix: 0.03 (0.11), residues: 2147 sheet: -0.86 (0.24), residues: 516 loop : -1.77 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 146 TYR 0.026 0.001 TYR A 534 PHE 0.040 0.001 PHE D 114 TRP 0.045 0.002 TRP A 511 HIS 0.007 0.001 HIS R 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (37299) covalent geometry : angle 0.62110 / 0.33 (50920) hydrogen bonds : bond 0.04112 / 2.67 ( 1689) hydrogen bonds : angle 5.16965 / 3.65 ( 4767) metal coordination : bond 0.01459 / 0.95 ( 29) metal coordination : angle 15.56907 / 9.27 ( 45) Misc. bond : bond 0.00154 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8522 (ppp) cc_final: 0.8120 (ppp) REVERT: A 536 MET cc_start: 0.9000 (mmp) cc_final: 0.8309 (mmm) REVERT: A 650 MET cc_start: 0.8968 (mpp) cc_final: 0.8123 (mpp) REVERT: B 438 MET cc_start: 0.6717 (mmm) cc_final: 0.5067 (tpp) REVERT: B 527 MET cc_start: 0.9634 (mmp) cc_final: 0.9374 (mmm) REVERT: B 545 MET cc_start: 0.9303 (tmm) cc_final: 0.9057 (ppp) REVERT: B 620 MET cc_start: 0.8633 (ppp) cc_final: 0.8416 (ppp) REVERT: B 677 MET cc_start: 0.8355 (mpp) cc_final: 0.8110 (mpp) REVERT: B 724 MET cc_start: 0.8369 (mpp) cc_final: 0.8032 (mpp) REVERT: C 528 MET cc_start: 0.7978 (mmt) cc_final: 0.7458 (mmt) REVERT: D 185 MET cc_start: 0.8386 (tpp) cc_final: 0.7824 (tpp) REVERT: D 254 MET cc_start: 0.8554 (pmm) cc_final: 0.8131 (pmm) REVERT: D 341 MET cc_start: 0.8367 (ppp) cc_final: 0.8017 (ppp) REVERT: D 376 MET cc_start: 0.9349 (ptp) cc_final: 0.9106 (ptp) REVERT: F 51 MET cc_start: 0.9642 (mpp) cc_final: 0.9408 (mpp) REVERT: G 16 MET cc_start: 0.8650 (mmt) cc_final: 0.7905 (mmm) REVERT: G 40 ASP cc_start: 0.8769 (p0) cc_final: 0.8563 (p0) REVERT: H 194 MET cc_start: 0.8743 (ptt) cc_final: 0.8531 (ppp) REVERT: H 766 MET cc_start: 0.1179 (mpp) cc_final: 0.0555 (mtp) REVERT: K 113 MET cc_start: 0.8038 (mmp) cc_final: 0.7723 (mmp) REVERT: K 178 MET cc_start: 0.5919 (tpt) cc_final: 0.5286 (tpt) REVERT: Q 182 MET cc_start: 0.8884 (pmm) cc_final: 0.8565 (pmm) outliers start: 3 outliers final: 1 residues processed: 135 average time/residue: 0.2169 time to fit residues: 51.2634 Evaluate side-chains 122 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 89 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 231 optimal weight: 40.0000 chunk 431 optimal weight: 40.0000 chunk 222 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 386 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 460 HIS ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN H 206 HIS H 728 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 617 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.043572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.033328 restraints weight = 473120.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.033252 restraints weight = 314906.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.033516 restraints weight = 231389.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.033527 restraints weight = 198257.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.033543 restraints weight = 190071.739| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37331 Z= 0.159 Angle : 0.767 54.870 50965 Z= 0.330 Chirality : 0.043 0.223 5758 Planarity : 0.004 0.067 6177 Dihedral : 16.398 146.314 5820 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.54 % Rotamer: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 4260 helix: 0.22 (0.11), residues: 2154 sheet: -0.86 (0.24), residues: 516 loop : -1.71 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 146 TYR 0.023 0.001 TYR A 534 PHE 0.030 0.002 PHE C 404 TRP 0.020 0.001 TRP A 511 HIS 0.012 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (37299) covalent geometry : angle 0.61734 / 0.33 (50920) hydrogen bonds : bond 0.04146 / 2.69 ( 1689) hydrogen bonds : angle 5.04921 / 3.55 ( 4767) metal coordination : bond 0.01123 / 0.75 ( 29) metal coordination : angle 15.33752 / 9.11 ( 45) Misc. bond : bond 0.00084 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8640 (ppp) cc_final: 0.8219 (ppp) REVERT: A 514 MET cc_start: 0.8108 (ppp) cc_final: 0.7622 (ppp) REVERT: A 536 MET cc_start: 0.8639 (mmp) cc_final: 0.8365 (mmm) REVERT: A 650 MET cc_start: 0.8902 (mpp) cc_final: 0.8095 (mpp) REVERT: B 1 MET cc_start: 0.8018 (pmm) cc_final: 0.7805 (pmm) REVERT: B 438 MET cc_start: 0.6978 (mmm) cc_final: 0.5363 (tpp) REVERT: B 527 MET cc_start: 0.9606 (mmp) cc_final: 0.9361 (mmm) REVERT: B 545 MET cc_start: 0.9316 (tmm) cc_final: 0.9066 (ppp) REVERT: B 620 MET cc_start: 0.8635 (ppp) cc_final: 0.8424 (ppp) REVERT: C 528 MET cc_start: 0.7993 (mmt) cc_final: 0.7492 (mmt) REVERT: D 185 MET cc_start: 0.8262 (tpp) cc_final: 0.7754 (tpp) REVERT: D 254 MET cc_start: 0.8608 (pmm) cc_final: 0.8244 (pmm) REVERT: D 376 MET cc_start: 0.9408 (ptp) cc_final: 0.9171 (ptp) REVERT: E 137 MET cc_start: 0.8638 (tmm) cc_final: 0.8213 (tmm) REVERT: G 16 MET cc_start: 0.8719 (mmt) cc_final: 0.7960 (mmm) REVERT: H 766 MET cc_start: 0.1666 (mpp) cc_final: 0.0885 (mtp) REVERT: K 37 MET cc_start: 0.8771 (mmm) cc_final: 0.8539 (mmp) REVERT: K 113 MET cc_start: 0.8116 (mmp) cc_final: 0.7797 (mmp) REVERT: K 178 MET cc_start: 0.5689 (tpt) cc_final: 0.5077 (tpt) REVERT: Q 182 MET cc_start: 0.8912 (pmm) cc_final: 0.8635 (pmm) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2199 time to fit residues: 50.8973 Evaluate side-chains 119 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 332 optimal weight: 10.0000 chunk 423 optimal weight: 40.0000 chunk 420 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 413 optimal weight: 30.0000 chunk 410 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 362 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN C 509 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 460 HIS E 220 HIS H 206 HIS H 728 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.043004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.032573 restraints weight = 459064.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.032276 restraints weight = 392536.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.032492 restraints weight = 266213.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.032793 restraints weight = 236097.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.032792 restraints weight = 205289.828| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37331 Z= 0.140 Angle : 0.751 54.638 50965 Z= 0.320 Chirality : 0.042 0.197 5758 Planarity : 0.004 0.068 6177 Dihedral : 16.313 141.178 5820 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.81 (0.13), residues: 4260 helix: 0.38 (0.11), residues: 2161 sheet: -0.84 (0.24), residues: 512 loop : -1.65 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 601 TYR 0.020 0.001 TYR D 316 PHE 0.028 0.001 PHE C 404 TRP 0.019 0.001 TRP D 96 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (37299) covalent geometry : angle 0.59974 / 0.32 (50920) hydrogen bonds : bond 0.03891 / 2.53 ( 1689) hydrogen bonds : angle 4.91420 / 3.47 ( 4767) metal coordination : bond 0.01023 / 0.71 ( 29) metal coordination : angle 15.19730 / 8.96 ( 45) Misc. bond : bond 0.00075 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8678 (ppp) cc_final: 0.8251 (ppp) REVERT: A 514 MET cc_start: 0.8170 (ppp) cc_final: 0.7710 (ppp) REVERT: A 650 MET cc_start: 0.8908 (mpp) cc_final: 0.8091 (mpp) REVERT: A 696 MET cc_start: 0.8184 (tpt) cc_final: 0.7742 (tpt) REVERT: B 1 MET cc_start: 0.7889 (pmm) cc_final: 0.7683 (pmm) REVERT: B 438 MET cc_start: 0.6917 (mmm) cc_final: 0.5302 (tpp) REVERT: B 527 MET cc_start: 0.9613 (mmp) cc_final: 0.9363 (mmm) REVERT: B 545 MET cc_start: 0.9318 (tmm) cc_final: 0.9063 (ppp) REVERT: B 620 MET cc_start: 0.8642 (ppp) cc_final: 0.8422 (ppp) REVERT: B 677 MET cc_start: 0.8451 (mpp) cc_final: 0.8231 (mpp) REVERT: B 724 MET cc_start: 0.8309 (mpp) cc_final: 0.8061 (mpp) REVERT: C 528 MET cc_start: 0.7903 (mmt) cc_final: 0.7431 (mmt) REVERT: D 185 MET cc_start: 0.8259 (tpp) cc_final: 0.7820 (tpt) REVERT: D 254 MET cc_start: 0.8448 (pmm) cc_final: 0.7953 (pmm) REVERT: D 341 MET cc_start: 0.8504 (ppp) cc_final: 0.8272 (ppp) REVERT: D 376 MET cc_start: 0.9475 (ptp) cc_final: 0.9232 (ptp) REVERT: E 71 MET cc_start: 0.8730 (tpp) cc_final: 0.8462 (mmm) REVERT: G 16 MET cc_start: 0.8706 (mmt) cc_final: 0.7954 (mmm) REVERT: H 766 MET cc_start: 0.1698 (mpp) cc_final: 0.0908 (mtp) REVERT: K 37 MET cc_start: 0.8785 (mmm) cc_final: 0.8550 (mmp) REVERT: K 113 MET cc_start: 0.8075 (mmp) cc_final: 0.7757 (mmp) REVERT: K 178 MET cc_start: 0.5662 (tpt) cc_final: 0.5317 (tpt) REVERT: Q 182 MET cc_start: 0.8778 (pmm) cc_final: 0.8338 (pmm) REVERT: Q 722 MET cc_start: 0.7219 (tmm) cc_final: 0.6761 (tmm) REVERT: Q 748 MET cc_start: 0.8199 (tpt) cc_final: 0.7911 (tpt) REVERT: R 184 GLU cc_start: 0.8550 (pm20) cc_final: 0.7612 (pm20) REVERT: R 203 GLU cc_start: 0.8912 (pm20) cc_final: 0.8501 (tp30) REVERT: R 215 TYR cc_start: 0.6200 (m-80) cc_final: 0.5850 (m-80) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2128 time to fit residues: 51.4271 Evaluate side-chains 124 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 367 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 373 optimal weight: 6.9990 chunk 406 optimal weight: 1.9990 chunk 400 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 460 HIS E 60 HIS E 356 HIS H 728 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 185 GLN ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 872 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.042634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.032274 restraints weight = 463800.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.031960 restraints weight = 376753.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.032103 restraints weight = 274894.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.032203 restraints weight = 235076.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.032234 restraints weight = 222526.581| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37331 Z= 0.178 Angle : 0.767 56.242 50965 Z= 0.333 Chirality : 0.043 0.185 5758 Planarity : 0.004 0.100 6177 Dihedral : 16.279 138.813 5820 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.33 % Rotamer: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.77 (0.13), residues: 4260 helix: 0.43 (0.11), residues: 2164 sheet: -0.88 (0.24), residues: 514 loop : -1.63 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 146 TYR 0.015 0.001 TYR B 24 PHE 0.022 0.002 PHE C 404 TRP 0.016 0.001 TRP A 511 HIS 0.005 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (37299) covalent geometry : angle 0.62631 / 0.33 (50920) hydrogen bonds : bond 0.04161 / 2.70 ( 1689) hydrogen bonds : angle 4.90679 / 3.46 ( 4767) metal coordination : bond 0.01162 / 0.77 ( 29) metal coordination : angle 14.92163 / 8.71 ( 45) Misc. bond : bond 0.00084 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8715 (ppp) cc_final: 0.8294 (ppp) REVERT: A 514 MET cc_start: 0.8395 (ppp) cc_final: 0.7986 (ppp) REVERT: A 536 MET cc_start: 0.8659 (mmp) cc_final: 0.8122 (mmm) REVERT: A 650 MET cc_start: 0.8900 (mpp) cc_final: 0.8081 (mpp) REVERT: B 1 MET cc_start: 0.8029 (pmm) cc_final: 0.7799 (pmm) REVERT: B 438 MET cc_start: 0.6998 (mmm) cc_final: 0.5349 (tpp) REVERT: B 527 MET cc_start: 0.9618 (mmp) cc_final: 0.9367 (mmm) REVERT: B 545 MET cc_start: 0.9325 (tmm) cc_final: 0.9065 (ppp) REVERT: B 620 MET cc_start: 0.8683 (ppp) cc_final: 0.8444 (ppp) REVERT: B 677 MET cc_start: 0.8357 (mpp) cc_final: 0.8127 (mpp) REVERT: B 724 MET cc_start: 0.8615 (mpp) cc_final: 0.8357 (mpp) REVERT: C 441 MET cc_start: 0.3952 (mpp) cc_final: 0.3607 (mpp) REVERT: C 528 MET cc_start: 0.7938 (mmt) cc_final: 0.7460 (mmt) REVERT: D 185 MET cc_start: 0.8333 (tpp) cc_final: 0.7941 (tpt) REVERT: D 254 MET cc_start: 0.8402 (pmm) cc_final: 0.7794 (pmm) REVERT: D 341 MET cc_start: 0.8549 (ppp) cc_final: 0.8265 (ppp) REVERT: D 376 MET cc_start: 0.9506 (ptp) cc_final: 0.9261 (ptp) REVERT: F 51 MET cc_start: 0.9639 (mpp) cc_final: 0.9188 (mpp) REVERT: G 16 MET cc_start: 0.8731 (mmt) cc_final: 0.8270 (mmm) REVERT: H 766 MET cc_start: 0.1811 (mpp) cc_final: 0.0955 (mtp) REVERT: K 113 MET cc_start: 0.7986 (mmp) cc_final: 0.7699 (mmp) REVERT: K 178 MET cc_start: 0.5722 (tpt) cc_final: 0.4759 (tpt) REVERT: Q 182 MET cc_start: 0.8789 (pmm) cc_final: 0.8310 (pmm) REVERT: Q 722 MET cc_start: 0.7305 (tmm) cc_final: 0.6838 (tmm) REVERT: R 215 TYR cc_start: 0.6390 (m-80) cc_final: 0.6075 (m-80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2188 time to fit residues: 50.2783 Evaluate side-chains 118 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 313 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 377 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 67 optimal weight: 0.0010 chunk 340 optimal weight: 40.0000 chunk 417 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 433 optimal weight: 50.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 177 GLN D 211 GLN D 273 GLN D 324 GLN D 410 ASN D 435 ASN D 460 HIS E 98 GLN E 154 GLN ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS H 728 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 315 GLN ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 215 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.041885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.031530 restraints weight = 465132.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.031357 restraints weight = 340706.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.031623 restraints weight = 265000.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.031533 restraints weight = 243507.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.031571 restraints weight = 223916.749| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 37331 Z= 0.267 Angle : 0.863 55.153 50965 Z= 0.384 Chirality : 0.045 0.207 5758 Planarity : 0.005 0.068 6177 Dihedral : 16.388 139.813 5820 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.47 % Favored : 92.48 % Rotamer: Outliers : 0.05 % Allowed : 1.21 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.06 (0.13), residues: 4260 helix: 0.17 (0.11), residues: 2172 sheet: -1.06 (0.24), residues: 511 loop : -1.73 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 196 TYR 0.022 0.002 TYR B 24 PHE 0.026 0.002 PHE A 659 TRP 0.017 0.002 TRP D 96 HIS 0.007 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.27 (37299) covalent geometry : angle 0.72719 / 0.38 (50920) hydrogen bonds : bond 0.05024 / 3.24 ( 1689) hydrogen bonds : angle 5.17279 / 3.63 ( 4767) metal coordination : bond 0.01946 / 1.12 ( 29) metal coordination : angle 15.64969 / 9.31 ( 45) Misc. bond : bond 0.00095 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8772 (ppp) cc_final: 0.8325 (ppp) REVERT: A 514 MET cc_start: 0.8295 (ppp) cc_final: 0.7642 (ppp) REVERT: A 536 MET cc_start: 0.8786 (mmp) cc_final: 0.8337 (mmm) REVERT: A 650 MET cc_start: 0.8911 (mpp) cc_final: 0.8191 (mpp) REVERT: B 1 MET cc_start: 0.8253 (pmm) cc_final: 0.7926 (pmm) REVERT: B 438 MET cc_start: 0.7293 (mmm) cc_final: 0.5779 (tpp) REVERT: B 527 MET cc_start: 0.9667 (mmp) cc_final: 0.9390 (mmm) REVERT: B 545 MET cc_start: 0.9328 (tmm) cc_final: 0.9062 (ppp) REVERT: B 677 MET cc_start: 0.8295 (mpp) cc_final: 0.8087 (mpp) REVERT: B 724 MET cc_start: 0.8740 (mpp) cc_final: 0.8461 (mpp) REVERT: C 441 MET cc_start: 0.3895 (mpp) cc_final: 0.2585 (mpp) REVERT: C 528 MET cc_start: 0.7456 (mmt) cc_final: 0.7135 (mmt) REVERT: D 185 MET cc_start: 0.8303 (tpp) cc_final: 0.7954 (tpp) REVERT: D 254 MET cc_start: 0.8678 (pmm) cc_final: 0.8048 (pmm) REVERT: D 341 MET cc_start: 0.8627 (ppp) cc_final: 0.8301 (ppp) REVERT: F 51 MET cc_start: 0.9625 (mpp) cc_final: 0.9422 (mpp) REVERT: G 16 MET cc_start: 0.8692 (mmt) cc_final: 0.8161 (mmm) REVERT: H 766 MET cc_start: 0.2140 (mpp) cc_final: 0.0872 (mtt) REVERT: K 113 MET cc_start: 0.8074 (mmp) cc_final: 0.7749 (mmp) REVERT: K 178 MET cc_start: 0.5594 (tpt) cc_final: 0.5330 (tpt) REVERT: Q 182 MET cc_start: 0.8940 (pmm) cc_final: 0.8693 (pmm) REVERT: Q 722 MET cc_start: 0.7554 (tmm) cc_final: 0.7074 (tmm) REVERT: R 215 TYR cc_start: 0.6586 (m-80) cc_final: 0.6268 (m-80) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.2162 time to fit residues: 48.1421 Evaluate side-chains 117 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 79 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 376 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 397 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 235 optimal weight: 30.0000 chunk 335 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 211 GLN D 460 HIS ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 728 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.042655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.032444 restraints weight = 460237.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.031934 restraints weight = 348510.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.032201 restraints weight = 274972.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.032126 restraints weight = 238044.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.032185 restraints weight = 232751.932| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37331 Z= 0.154 Angle : 0.778 54.218 50965 Z= 0.333 Chirality : 0.043 0.184 5758 Planarity : 0.004 0.066 6177 Dihedral : 16.264 136.199 5820 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.53 % Favored : 93.42 % Rotamer: Outliers : 0.03 % Allowed : 0.84 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.82 (0.13), residues: 4260 helix: 0.41 (0.11), residues: 2165 sheet: -1.02 (0.24), residues: 509 loop : -1.64 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 146 TYR 0.018 0.002 TYR A 139 PHE 0.027 0.002 PHE B 448 TRP 0.020 0.001 TRP A 511 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (37299) covalent geometry : angle 0.62994 / 0.33 (50920) hydrogen bonds : bond 0.03971 / 2.57 ( 1689) hydrogen bonds : angle 4.95696 / 3.49 ( 4767) metal coordination : bond 0.01115 / 0.75 ( 29) metal coordination : angle 15.40641 / 9.15 ( 45) Misc. bond : bond 0.00081 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8695 (ppp) cc_final: 0.8340 (ppp) REVERT: A 514 MET cc_start: 0.8325 (ppp) cc_final: 0.8073 (ppp) REVERT: A 536 MET cc_start: 0.8563 (mmp) cc_final: 0.8190 (mmm) REVERT: A 650 MET cc_start: 0.8917 (mpp) cc_final: 0.8089 (mpp) REVERT: B 1 MET cc_start: 0.8084 (pmm) cc_final: 0.7766 (pmm) REVERT: B 438 MET cc_start: 0.7461 (mmm) cc_final: 0.5848 (tpp) REVERT: B 527 MET cc_start: 0.9624 (mmp) cc_final: 0.9354 (mmm) REVERT: B 545 MET cc_start: 0.9324 (tmm) cc_final: 0.9040 (ppp) REVERT: C 441 MET cc_start: 0.3936 (mpp) cc_final: 0.2656 (mpp) REVERT: C 528 MET cc_start: 0.7413 (mmt) cc_final: 0.7051 (mmt) REVERT: D 185 MET cc_start: 0.8221 (tpp) cc_final: 0.7966 (tpp) REVERT: D 254 MET cc_start: 0.8611 (pmm) cc_final: 0.7964 (pmm) REVERT: D 341 MET cc_start: 0.8526 (ppp) cc_final: 0.8223 (ppp) REVERT: E 137 MET cc_start: 0.8662 (tmm) cc_final: 0.8260 (tmm) REVERT: F 51 MET cc_start: 0.9648 (mpp) cc_final: 0.9385 (mpp) REVERT: G 16 MET cc_start: 0.8650 (mmt) cc_final: 0.7942 (mmm) REVERT: H 766 MET cc_start: 0.1975 (mpp) cc_final: 0.1161 (mtp) REVERT: K 113 MET cc_start: 0.7931 (mmp) cc_final: 0.7658 (mmp) REVERT: K 178 MET cc_start: 0.5600 (tpt) cc_final: 0.5345 (tpt) REVERT: Q 722 MET cc_start: 0.7603 (tmm) cc_final: 0.7277 (tmm) REVERT: R 215 TYR cc_start: 0.6453 (m-80) cc_final: 0.6138 (m-80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2153 time to fit residues: 49.3799 Evaluate side-chains 119 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 252 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 279 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN B 402 ASN B 564 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 460 HIS E 279 ASN ** H 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 728 ASN ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.042843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.032430 restraints weight = 460396.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.032228 restraints weight = 309312.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.032464 restraints weight = 252644.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.032421 restraints weight = 210480.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.032408 restraints weight = 214377.826| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37331 Z= 0.138 Angle : 0.764 55.549 50965 Z= 0.326 Chirality : 0.043 0.241 5758 Planarity : 0.004 0.066 6177 Dihedral : 16.131 133.523 5820 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.33 % Rotamer: Outliers : 0.03 % Allowed : 0.40 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.65 (0.13), residues: 4260 helix: 0.59 (0.11), residues: 2149 sheet: -0.97 (0.24), residues: 505 loop : -1.60 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 676 TYR 0.017 0.001 TYR A 139 PHE 0.029 0.001 PHE B 720 TRP 0.020 0.001 TRP D 96 HIS 0.006 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (37299) covalent geometry : angle 0.61795 / 0.32 (50920) hydrogen bonds : bond 0.03757 / 2.46 ( 1689) hydrogen bonds : angle 4.83723 / 3.41 ( 4767) metal coordination : bond 0.00944 / 0.65 ( 29) metal coordination : angle 15.14756 / 9.00 ( 45) Misc. bond : bond 0.00064 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8695 (ppp) cc_final: 0.8314 (ppp) REVERT: A 514 MET cc_start: 0.8242 (ppp) cc_final: 0.7998 (ppp) REVERT: A 536 MET cc_start: 0.8456 (mmp) cc_final: 0.8134 (mmm) REVERT: A 650 MET cc_start: 0.8899 (mpp) cc_final: 0.8098 (mpp) REVERT: A 696 MET cc_start: 0.8100 (tpt) cc_final: 0.7735 (tpt) REVERT: B 1 MET cc_start: 0.8063 (pmm) cc_final: 0.7840 (pmm) REVERT: B 438 MET cc_start: 0.7430 (mmm) cc_final: 0.5607 (tpp) REVERT: B 527 MET cc_start: 0.9627 (mmp) cc_final: 0.9335 (mmm) REVERT: B 545 MET cc_start: 0.9331 (tmm) cc_final: 0.9049 (ppp) REVERT: C 441 MET cc_start: 0.4099 (mpp) cc_final: 0.2800 (mpp) REVERT: C 528 MET cc_start: 0.7100 (mmt) cc_final: 0.6820 (mmt) REVERT: D 185 MET cc_start: 0.8278 (tpp) cc_final: 0.8042 (tpp) REVERT: D 254 MET cc_start: 0.8566 (pmm) cc_final: 0.7957 (pmm) REVERT: D 341 MET cc_start: 0.8500 (ppp) cc_final: 0.8293 (ppp) REVERT: E 137 MET cc_start: 0.8636 (tmm) cc_final: 0.8222 (tmm) REVERT: F 51 MET cc_start: 0.9616 (mpp) cc_final: 0.9303 (mpp) REVERT: G 16 MET cc_start: 0.8644 (mmt) cc_final: 0.7923 (mmm) REVERT: H 766 MET cc_start: 0.1928 (mpp) cc_final: 0.1090 (mtp) REVERT: K 113 MET cc_start: 0.8011 (mmp) cc_final: 0.7729 (mmp) REVERT: K 178 MET cc_start: 0.5515 (tpt) cc_final: 0.5284 (tpt) REVERT: Q 722 MET cc_start: 0.7370 (tmm) cc_final: 0.7054 (tmm) REVERT: R 215 TYR cc_start: 0.6387 (m-80) cc_final: 0.6053 (m-80) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2171 time to fit residues: 50.6324 Evaluate side-chains 118 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 433 optimal weight: 30.0000 chunk 424 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 316 optimal weight: 50.0000 chunk 209 optimal weight: 0.0570 chunk 146 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 564 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 460 HIS ** H 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 728 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 GLN ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.042363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.031991 restraints weight = 456241.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.031785 restraints weight = 321946.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.031950 restraints weight = 243470.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.031910 restraints weight = 232520.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.031909 restraints weight = 210718.308| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37331 Z= 0.184 Angle : 0.788 55.912 50965 Z= 0.340 Chirality : 0.043 0.181 5758 Planarity : 0.004 0.064 6177 Dihedral : 16.133 133.745 5820 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.05 % Rotamer: Outliers : 0.03 % Allowed : 0.49 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.67 (0.13), residues: 4260 helix: 0.55 (0.11), residues: 2155 sheet: -1.06 (0.24), residues: 512 loop : -1.56 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 289 TYR 0.015 0.001 TYR A 139 PHE 0.027 0.002 PHE B 720 TRP 0.020 0.001 TRP D 96 HIS 0.007 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (37299) covalent geometry : angle 0.64441 / 0.34 (50920) hydrogen bonds : bond 0.04136 / 2.70 ( 1689) hydrogen bonds : angle 4.91104 / 3.45 ( 4767) metal coordination : bond 0.01124 / 0.75 ( 29) metal coordination : angle 15.25537 / 9.06 ( 45) Misc. bond : bond 0.00057 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6566.37 seconds wall clock time: 114 minutes 54.24 seconds (6894.24 seconds total)