Starting phenix.real_space_refine on Mon May 4 14:39:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpl_37718/05_2026/8wpl_37718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpl_37718/05_2026/8wpl_37718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wpl_37718/05_2026/8wpl_37718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpl_37718/05_2026/8wpl_37718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wpl_37718/05_2026/8wpl_37718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpl_37718/05_2026/8wpl_37718.map" } resolution = 3.04 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 Zn 4 6.06 5 P 4 5.49 5 S 116 5.16 5 C 14416 2.51 5 N 3624 2.21 5 O 3936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22103 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5427 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 15, 'TRANS': 654} Chain breaks: 4 Chain: "B" Number of atoms: 5425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5425 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 23, 'TRANS': 640} Chain breaks: 6 Chain: "C" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5470 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 24, 'TRANS': 644} Chain breaks: 6 Chain: "D" Number of atoms: 5493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5493 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 24, 'TRANS': 648} Chain breaks: 5 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' ZN': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' CA': 1, ' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 125 Unusual residues: {' CA': 1, ' ZN': 1, 'LPP': 2, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1081 SG CYS A 193 11.983 79.981 59.538 1.00141.71 S ATOM 1096 SG CYS A 195 9.191 78.444 61.701 1.00132.99 S ATOM 1117 SG CYS A 198 12.792 77.076 61.944 1.00135.95 S ATOM 6586 SG CYS B 176 56.156 54.583 94.962 1.00134.51 S ATOM 6600 SG CYS B 178 55.703 52.111 97.857 1.00127.75 S ATOM 6622 SG CYS B 181 57.285 50.921 94.560 1.00126.86 S ATOM 12011 SG CYS C 176 94.422 55.819 49.639 1.00118.52 S ATOM 12025 SG CYS C 178 96.484 53.466 47.409 1.00120.54 S ATOM 12047 SG CYS C 181 92.929 54.367 46.411 1.00124.67 S ATOM 17470 SG CYS D 176 52.017 81.227 15.265 1.00127.05 S ATOM 17484 SG CYS D 178 51.362 80.495 11.522 1.00121.78 S ATOM 17506 SG CYS D 181 49.574 78.480 14.197 1.00121.60 S Time building chain proxies: 5.27, per 1000 atoms: 0.24 Number of scatterers: 22103 At special positions: 0 Unit cell: (117.26, 149.24, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 3 19.99 S 116 16.00 P 4 15.00 O 3936 8.00 N 3624 7.00 C 14416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS D 549 " - pdb=" SG CYS D 554 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 900.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 189 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 195 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 193 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 198 " pdb=" ZN B1003 " pdb="ZN ZN B1003 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 178 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 176 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 181 " pdb=" ZN C1003 " pdb="ZN ZN C1003 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 181 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 178 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 176 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 181 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 178 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 176 " Number of angles added : 12 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5154 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 4 sheets defined 77.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.071A pdb=" N LYS A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 73 Processing helix chain 'A' and resid 86 through 94 Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.587A pdb=" N LEU A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.659A pdb=" N VAL A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.755A pdb=" N VAL A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 197 through 221 removed outlier: 3.617A pdb=" N LYS A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ARG A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 232 through 251 Processing helix chain 'A' and resid 254 through 274 Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.740A pdb=" N ARG A 343 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.675A pdb=" N PHE A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 382 through 408 removed outlier: 4.300A pdb=" N SER A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 445 Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.734A pdb=" N GLU A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 480 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.514A pdb=" N TRP A 489 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.520A pdb=" N MET A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 560 removed outlier: 4.828A pdb=" N GLN A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP A 536 " --> pdb=" O GLN A 532 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 537 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.608A pdb=" N THR A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.591A pdb=" N VAL A 608 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 635 Processing helix chain 'A' and resid 636 through 653 Processing helix chain 'A' and resid 655 through 673 removed outlier: 3.558A pdb=" N TYR A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 754 removed outlier: 3.814A pdb=" N ASP A 754 " --> pdb=" O MET A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 779 removed outlier: 3.581A pdb=" N LEU A 761 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.799A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.576A pdb=" N PHE B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 165 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 257 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 303 through 315 Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.606A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.905A pdb=" N ILE B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 385 Processing helix chain 'B' and resid 406 through 423 Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 432 through 458 Processing helix chain 'B' and resid 472 through 491 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.827A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 498 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 539 removed outlier: 3.578A pdb=" N GLN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.786A pdb=" N VAL B 583 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 584 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 611 through 628 Processing helix chain 'B' and resid 630 through 648 removed outlier: 3.610A pdb=" N TYR B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU B 648 " --> pdb=" O MET B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.610A pdb=" N ASN B 658 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 726 Processing helix chain 'B' and resid 732 through 754 removed outlier: 4.509A pdb=" N PHE B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 57 removed outlier: 3.812A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.552A pdb=" N PHE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 110 through 117 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 165 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 257 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 303 through 315 Processing helix chain 'C' and resid 325 through 339 Processing helix chain 'C' and resid 339 through 350 removed outlier: 3.555A pdb=" N PHE C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 359 removed outlier: 3.891A pdb=" N ILE C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 385 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 405 through 423 removed outlier: 4.288A pdb=" N TRP C 409 " --> pdb=" O MET C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 459 Processing helix chain 'C' and resid 464 through 468 removed outlier: 3.624A pdb=" N SER C 467 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 Processing helix chain 'C' and resid 492 through 498 removed outlier: 3.749A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 498 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 512 removed outlier: 4.543A pdb=" N LEU C 505 " --> pdb=" O HIS C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 539 Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 563 through 573 Processing helix chain 'C' and resid 580 through 585 removed outlier: 3.788A pdb=" N VAL C 583 " --> pdb=" O ASN C 580 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 584 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 611 Processing helix chain 'C' and resid 611 through 628 Processing helix chain 'C' and resid 630 through 648 removed outlier: 3.582A pdb=" N TYR C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU C 648 " --> pdb=" O MET C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 726 Processing helix chain 'C' and resid 732 through 754 removed outlier: 4.009A pdb=" N PHE C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 165 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.568A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 339 through 350 Processing helix chain 'D' and resid 353 through 359 removed outlier: 4.142A pdb=" N ILE D 359 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 385 removed outlier: 3.859A pdb=" N SER D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 405 removed outlier: 3.569A pdb=" N MET D 405 " --> pdb=" O VAL D 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 406 through 423 Processing helix chain 'D' and resid 426 through 432 Processing helix chain 'D' and resid 432 through 458 Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 472 through 491 Processing helix chain 'D' and resid 492 through 498 removed outlier: 3.681A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 498 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 539 removed outlier: 4.433A pdb=" N LEU D 505 " --> pdb=" O HIS D 501 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 573 Processing helix chain 'D' and resid 580 through 585 removed outlier: 3.682A pdb=" N VAL D 583 " --> pdb=" O ASN D 580 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 584 " --> pdb=" O LEU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 611 through 628 Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.642A pdb=" N GLU D 634 " --> pdb=" O HIS D 630 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 659 removed outlier: 3.957A pdb=" N VAL D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 727 Processing helix chain 'D' and resid 733 through 754 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.519A pdb=" N MET A 32 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 168 " --> pdb=" O MET A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 186 removed outlier: 4.300A pdb=" N VAL A 183 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.522A pdb=" N LEU C 20 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1449 hydrogen bonds defined for protein. 4275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3542 1.32 - 1.44: 6088 1.44 - 1.57: 12778 1.57 - 1.69: 4 1.69 - 1.81: 179 Bond restraints: 22591 Sorted by residual: bond pdb=" O5 LPP C1005 " pdb=" P1 LPP C1005 " ideal model delta sigma weight residual 2.278 1.605 0.673 2.00e-02 2.50e+03 1.13e+03 bond pdb=" O5 LPP C1001 " pdb=" P1 LPP C1001 " ideal model delta sigma weight residual 2.278 1.606 0.672 2.00e-02 2.50e+03 1.13e+03 bond pdb=" O5 LPP B1001 " pdb=" P1 LPP B1001 " ideal model delta sigma weight residual 2.278 1.606 0.672 2.00e-02 2.50e+03 1.13e+03 bond pdb=" O5 LPP A 801 " pdb=" P1 LPP A 801 " ideal model delta sigma weight residual 2.278 1.609 0.669 2.00e-02 2.50e+03 1.12e+03 bond pdb=" O4 LPP C1001 " pdb=" P1 LPP C1001 " ideal model delta sigma weight residual 1.764 1.508 0.256 2.00e-02 2.50e+03 1.64e+02 ... (remaining 22586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.42: 30514 8.42 - 16.84: 24 16.84 - 25.26: 4 25.26 - 33.68: 4 33.68 - 42.10: 8 Bond angle restraints: 30554 Sorted by residual: angle pdb=" O4 LPP C1005 " pdb=" P1 LPP C1005 " pdb=" O5 LPP C1005 " ideal model delta sigma weight residual 62.99 105.09 -42.10 3.00e+00 1.11e-01 1.97e+02 angle pdb=" O4 LPP C1001 " pdb=" P1 LPP C1001 " pdb=" O5 LPP C1001 " ideal model delta sigma weight residual 62.99 104.85 -41.86 3.00e+00 1.11e-01 1.95e+02 angle pdb=" O4 LPP B1001 " pdb=" P1 LPP B1001 " pdb=" O5 LPP B1001 " ideal model delta sigma weight residual 62.99 104.65 -41.66 3.00e+00 1.11e-01 1.93e+02 angle pdb=" O4 LPP A 801 " pdb=" P1 LPP A 801 " pdb=" O5 LPP A 801 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" C6 LPP B1001 " pdb=" O5 LPP B1001 " pdb=" P1 LPP B1001 " ideal model delta sigma weight residual 82.33 119.89 -37.56 3.00e+00 1.11e-01 1.57e+02 ... (remaining 30549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.26: 12461 24.26 - 48.51: 1092 48.51 - 72.77: 141 72.77 - 97.03: 22 97.03 - 121.29: 7 Dihedral angle restraints: 13723 sinusoidal: 5820 harmonic: 7903 Sorted by residual: dihedral pdb=" CB CYS D 549 " pdb=" SG CYS D 549 " pdb=" SG CYS D 554 " pdb=" CB CYS D 554 " ideal model delta sinusoidal sigma weight residual -86.00 -159.29 73.29 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CA MET D 644 " pdb=" C MET D 644 " pdb=" N SER D 645 " pdb=" CA SER D 645 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CBC Y01 B1002 " pdb=" CAR Y01 B1002 " pdb=" CAT Y01 B1002 " pdb=" CBH Y01 B1002 " ideal model delta sinusoidal sigma weight residual -57.13 64.16 -121.29 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 13720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3067 0.065 - 0.131: 328 0.131 - 0.196: 34 0.196 - 0.262: 8 0.262 - 0.327: 2 Chirality restraints: 3439 Sorted by residual: chirality pdb=" CB ILE C 401 " pdb=" CA ILE C 401 " pdb=" CG1 ILE C 401 " pdb=" CG2 ILE C 401 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ALA C 725 " pdb=" N ALA C 725 " pdb=" C ALA C 725 " pdb=" CB ALA C 725 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CG LEU C 89 " pdb=" CB LEU C 89 " pdb=" CD1 LEU C 89 " pdb=" CD2 LEU C 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3436 not shown) Planarity restraints: 3793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 619 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C MET C 619 " 0.058 2.00e-02 2.50e+03 pdb=" O MET C 619 " -0.022 2.00e-02 2.50e+03 pdb=" N MET C 620 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 607 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C ILE C 607 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE C 607 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 608 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 67 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO C 68 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " 0.035 5.00e-02 4.00e+02 ... (remaining 3790 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5065 2.79 - 3.31: 20693 3.31 - 3.84: 37799 3.84 - 4.37: 43752 4.37 - 4.90: 76520 Nonbonded interactions: 183829 Sorted by model distance: nonbonded pdb=" O ILE B 209 " pdb=" OG SER B 213 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR C 523 " pdb=" OH TYR C 604 " model vdw 2.290 3.040 nonbonded pdb=" O THR D 563 " pdb=" OG1 THR D 567 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR C 315 " pdb=" OAH Y01 C1002 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR C 538 " pdb=" O THR C 584 " model vdw 2.318 3.040 ... (remaining 183824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 16 through 754) selection = (chain 'C' and (resid 16 through 458 or resid 465 through 543 or resid 547 throu \ gh 659 or resid 695 through 754)) selection = (chain 'D' and (resid 16 through 274 or resid 286 through 385 or resid 391 throu \ gh 458 or resid 465 through 543 or resid 547 through 754)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.500 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.011 0.673 22611 Z= 0.533 Angle : 1.051 42.099 30574 Z= 0.460 Chirality : 0.043 0.327 3439 Planarity : 0.005 0.063 3793 Dihedral : 17.450 121.285 8557 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.42 % Allowed : 21.73 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 2626 helix: 0.31 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.73 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 360 TYR 0.028 0.001 TYR A 342 PHE 0.035 0.002 PHE A 540 TRP 0.028 0.001 TRP B 321 HIS 0.012 0.001 HIS A 646 Details of bonding type rmsd covalent geometry : bond 0.01058 (22591) covalent geometry : angle 1.05083 (30554) SS BOND : bond 0.00090 ( 4) SS BOND : angle 1.06029 ( 8) hydrogen bonds : bond 0.12690 ( 1449) hydrogen bonds : angle 5.02227 ( 4275) metal coordination : bond 0.00380 ( 16) metal coordination : angle 0.87895 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 342 time to evaluate : 0.934 Fit side-chains REVERT: A 267 MET cc_start: 0.7945 (tpp) cc_final: 0.7591 (tpp) REVERT: A 305 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6349 (ptm) REVERT: A 349 LYS cc_start: 0.7321 (mmtm) cc_final: 0.6465 (mttt) REVERT: A 440 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7469 (mtmm) REVERT: A 535 GLN cc_start: 0.7207 (mp10) cc_final: 0.6661 (tp-100) REVERT: B 186 ASP cc_start: 0.7678 (t0) cc_final: 0.7452 (m-30) REVERT: B 243 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: B 272 ARG cc_start: 0.7216 (ttt-90) cc_final: 0.6890 (tpp-160) REVERT: B 404 TRP cc_start: 0.7068 (m100) cc_final: 0.6542 (m100) REVERT: B 470 MET cc_start: 0.6832 (ptt) cc_final: 0.6367 (ptt) REVERT: B 540 TYR cc_start: 0.7901 (m-80) cc_final: 0.6811 (m-80) REVERT: B 620 MET cc_start: 0.8329 (mtt) cc_final: 0.8096 (mtt) REVERT: C 156 GLU cc_start: 0.7916 (mp0) cc_final: 0.7599 (mp0) REVERT: C 266 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 437 MET cc_start: 0.8098 (ttm) cc_final: 0.7698 (ttm) REVERT: C 511 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7573 (mtm180) REVERT: C 704 HIS cc_start: 0.8055 (m90) cc_final: 0.7825 (m90) REVERT: C 723 ARG cc_start: 0.6736 (mpt180) cc_final: 0.6352 (ttp80) REVERT: D 324 ARG cc_start: 0.5929 (mtt180) cc_final: 0.5666 (ttm-80) REVERT: D 393 ASN cc_start: 0.8037 (t0) cc_final: 0.7601 (m-40) REVERT: D 409 TRP cc_start: 0.6232 (m100) cc_final: 0.5979 (m100) REVERT: D 520 LEU cc_start: 0.7755 (mt) cc_final: 0.7554 (mp) REVERT: D 536 GLN cc_start: 0.7640 (tp40) cc_final: 0.7322 (tp40) REVERT: D 738 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6005 (mp0) outliers start: 10 outliers final: 5 residues processed: 347 average time/residue: 0.1702 time to fit residues: 89.8721 Evaluate side-chains 300 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 293 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.0670 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 94 ASN A 96 ASN A 109 GLN A 181 GLN A 287 ASN A 328 GLN A 390 HIS A 456 ASN A 478 ASN A 581 ASN A 732 GLN A 760 ASN B 80 ASN B 117 ASN B 118 HIS B 163 GLN B 192 HIS B 247 GLN B 307 GLN B 308 GLN B 472 HIS B 499 ASN B 557 GLN B 559 ASN B 569 GLN B 614 ASN B 621 ASN B 699 ASN C 102 HIS C 154 ASN C 250 GLN C 442 ASN C 472 HIS C 485 ASN C 569 GLN C 621 ASN C 735 ASN C 741 GLN D 135 GLN D 154 ASN D 485 ASN D 532 ASN D 580 ASN D 590 HIS D 735 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.178031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124603 restraints weight = 22834.327| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.24 r_work: 0.3138 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 22611 Z= 0.233 Angle : 0.597 10.546 30574 Z= 0.306 Chirality : 0.041 0.179 3439 Planarity : 0.005 0.058 3793 Dihedral : 9.459 90.172 3292 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.46 % Allowed : 18.72 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.16), residues: 2626 helix: 1.16 (0.11), residues: 1981 sheet: None (None), residues: 0 loop : -0.52 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 701 TYR 0.021 0.002 TYR D 523 PHE 0.022 0.002 PHE A 544 TRP 0.019 0.002 TRP A 335 HIS 0.005 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00560 (22591) covalent geometry : angle 0.59536 (30554) SS BOND : bond 0.00175 ( 4) SS BOND : angle 1.95951 ( 8) hydrogen bonds : bond 0.04863 ( 1449) hydrogen bonds : angle 3.99314 ( 4275) metal coordination : bond 0.00618 ( 16) metal coordination : angle 1.88000 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 316 time to evaluate : 0.845 Fit side-chains REVERT: A 158 MET cc_start: 0.7398 (ppp) cc_final: 0.6225 (tpt) REVERT: A 211 ARG cc_start: 0.7565 (mtp85) cc_final: 0.7364 (mtp85) REVERT: A 231 GLU cc_start: 0.8093 (mp0) cc_final: 0.7540 (mt-10) REVERT: A 267 MET cc_start: 0.8357 (tpp) cc_final: 0.7946 (tpt) REVERT: A 305 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6788 (ptm) REVERT: A 349 LYS cc_start: 0.7071 (mmtm) cc_final: 0.6256 (mttt) REVERT: A 438 ASP cc_start: 0.6518 (t0) cc_final: 0.5709 (m-30) REVERT: A 535 GLN cc_start: 0.7563 (mp10) cc_final: 0.6780 (tp-100) REVERT: A 553 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8280 (tt) REVERT: B 65 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7403 (p) REVERT: B 81 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7419 (mt-10) REVERT: B 154 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8919 (t0) REVERT: B 186 ASP cc_start: 0.7856 (t0) cc_final: 0.7406 (m-30) REVERT: B 232 LYS cc_start: 0.7741 (mttp) cc_final: 0.7376 (mtpt) REVERT: B 243 GLU cc_start: 0.8231 (pt0) cc_final: 0.7490 (mm-30) REVERT: B 272 ARG cc_start: 0.7505 (ttt-90) cc_final: 0.6832 (tpp-160) REVERT: B 470 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6236 (ptt) REVERT: B 478 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6453 (mt-10) REVERT: C 154 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8567 (t0) REVERT: C 243 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7764 (tt0) REVERT: C 266 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8221 (mt-10) REVERT: C 403 GLU cc_start: 0.5923 (tm-30) cc_final: 0.5579 (tm-30) REVERT: C 511 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7609 (mtm180) REVERT: C 704 HIS cc_start: 0.8266 (m90) cc_final: 0.8035 (m90) REVERT: C 723 ARG cc_start: 0.6840 (mpt180) cc_final: 0.6231 (ttp80) REVERT: D 250 GLN cc_start: 0.8731 (tp40) cc_final: 0.8523 (tp-100) REVERT: D 393 ASN cc_start: 0.7968 (t0) cc_final: 0.7489 (m-40) REVERT: D 549 CYS cc_start: 0.5464 (OUTLIER) cc_final: 0.4820 (p) REVERT: D 649 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6903 (pt0) REVERT: D 738 GLU cc_start: 0.6326 (mm-30) cc_final: 0.5765 (mp0) outliers start: 83 outliers final: 45 residues processed: 365 average time/residue: 0.1636 time to fit residues: 92.0346 Evaluate side-chains 350 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 554 CYS Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 701 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 232 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 457 GLN B 117 ASN B 499 ASN B 699 ASN C 154 ASN C 250 GLN ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN D 154 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.178763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130788 restraints weight = 22866.751| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.95 r_work: 0.3206 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22611 Z= 0.177 Angle : 0.529 8.808 30574 Z= 0.270 Chirality : 0.039 0.160 3439 Planarity : 0.004 0.054 3793 Dihedral : 8.373 79.112 3284 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.75 % Allowed : 18.89 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2626 helix: 1.53 (0.11), residues: 1980 sheet: None (None), residues: 0 loop : -0.49 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 322 TYR 0.018 0.001 TYR D 523 PHE 0.022 0.002 PHE A 544 TRP 0.017 0.001 TRP A 335 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00419 (22591) covalent geometry : angle 0.52766 (30554) SS BOND : bond 0.00150 ( 4) SS BOND : angle 1.63302 ( 8) hydrogen bonds : bond 0.04488 ( 1449) hydrogen bonds : angle 3.87080 ( 4275) metal coordination : bond 0.00447 ( 16) metal coordination : angle 1.34904 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 316 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 211 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7295 (mtp85) REVERT: A 259 GLU cc_start: 0.8077 (tt0) cc_final: 0.7869 (mt-10) REVERT: A 267 MET cc_start: 0.8373 (tpp) cc_final: 0.7963 (tpt) REVERT: A 349 LYS cc_start: 0.7082 (mmtm) cc_final: 0.6314 (mttt) REVERT: A 438 ASP cc_start: 0.6745 (t0) cc_final: 0.5955 (m-30) REVERT: A 535 GLN cc_start: 0.7464 (mp10) cc_final: 0.6738 (tp-100) REVERT: A 546 LEU cc_start: 0.8658 (tp) cc_final: 0.8438 (tt) REVERT: B 65 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7465 (p) REVERT: B 186 ASP cc_start: 0.7835 (t0) cc_final: 0.7348 (m-30) REVERT: B 232 LYS cc_start: 0.7747 (mttp) cc_final: 0.7386 (mtpt) REVERT: B 243 GLU cc_start: 0.8227 (pt0) cc_final: 0.7532 (mm-30) REVERT: B 272 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.6796 (tpp-160) REVERT: B 470 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6228 (ptt) REVERT: B 478 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6309 (mt-10) REVERT: B 715 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7809 (ttpt) REVERT: C 243 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7725 (tt0) REVERT: C 403 GLU cc_start: 0.5929 (tm-30) cc_final: 0.5616 (tm-30) REVERT: C 511 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7654 (mtm180) REVERT: C 704 HIS cc_start: 0.8222 (m90) cc_final: 0.7998 (m90) REVERT: C 723 ARG cc_start: 0.6783 (mpt180) cc_final: 0.6145 (ttp80) REVERT: D 228 GLN cc_start: 0.8155 (tp40) cc_final: 0.7872 (tp40) REVERT: D 393 ASN cc_start: 0.7945 (t0) cc_final: 0.7457 (m-40) REVERT: D 549 CYS cc_start: 0.5494 (OUTLIER) cc_final: 0.4824 (p) outliers start: 90 outliers final: 58 residues processed: 367 average time/residue: 0.1608 time to fit residues: 91.7434 Evaluate side-chains 361 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 299 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 701 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 172 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN B 117 ASN B 499 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN C 250 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN D 154 ASN ** D 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.177617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124187 restraints weight = 22862.280| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.33 r_work: 0.3129 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22611 Z= 0.186 Angle : 0.525 8.000 30574 Z= 0.270 Chirality : 0.039 0.159 3439 Planarity : 0.004 0.053 3793 Dihedral : 8.105 59.797 3281 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.05 % Allowed : 19.14 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.16), residues: 2626 helix: 1.65 (0.11), residues: 1980 sheet: None (None), residues: 0 loop : -0.49 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 322 TYR 0.017 0.001 TYR D 523 PHE 0.022 0.002 PHE A 544 TRP 0.017 0.001 TRP A 335 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00444 (22591) covalent geometry : angle 0.52298 (30554) SS BOND : bond 0.00523 ( 4) SS BOND : angle 2.85037 ( 8) hydrogen bonds : bond 0.04453 ( 1449) hydrogen bonds : angle 3.83257 ( 4275) metal coordination : bond 0.00439 ( 16) metal coordination : angle 1.22658 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 307 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.8530 (tpp) cc_final: 0.8163 (tpt) REVERT: A 305 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6935 (ptm) REVERT: A 349 LYS cc_start: 0.7041 (mmtm) cc_final: 0.6281 (mttt) REVERT: A 438 ASP cc_start: 0.6720 (t0) cc_final: 0.5907 (m-30) REVERT: A 540 PHE cc_start: 0.8355 (t80) cc_final: 0.8048 (t80) REVERT: B 44 ASP cc_start: 0.6643 (t70) cc_final: 0.6287 (t0) REVERT: B 65 CYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7488 (p) REVERT: B 186 ASP cc_start: 0.7839 (t0) cc_final: 0.7371 (m-30) REVERT: B 232 LYS cc_start: 0.7963 (mttp) cc_final: 0.7642 (mtpt) REVERT: B 243 GLU cc_start: 0.8324 (pt0) cc_final: 0.7713 (mm-30) REVERT: B 272 ARG cc_start: 0.7537 (ttt-90) cc_final: 0.6921 (tpp-160) REVERT: B 470 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6262 (ptt) REVERT: B 478 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6521 (mt-10) REVERT: B 540 TYR cc_start: 0.7978 (m-80) cc_final: 0.7223 (m-80) REVERT: B 715 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7955 (ttpt) REVERT: C 266 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8257 (mt-10) REVERT: C 403 GLU cc_start: 0.6135 (tm-30) cc_final: 0.5827 (tm-30) REVERT: C 511 ARG cc_start: 0.8382 (mtp85) cc_final: 0.7805 (mtm180) REVERT: C 549 CYS cc_start: 0.5601 (OUTLIER) cc_final: 0.5086 (p) REVERT: C 591 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 723 ARG cc_start: 0.6885 (mpt180) cc_final: 0.6236 (ttp80) REVERT: D 228 GLN cc_start: 0.8207 (tp40) cc_final: 0.7941 (tp40) REVERT: D 549 CYS cc_start: 0.5489 (OUTLIER) cc_final: 0.4941 (p) outliers start: 97 outliers final: 65 residues processed: 370 average time/residue: 0.1591 time to fit residues: 91.5163 Evaluate side-chains 369 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 297 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 549 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 170 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 45 optimal weight: 0.0980 chunk 146 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN B 154 ASN B 499 ASN B 621 ASN B 699 ASN C 250 GLN ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 ASN ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN D 154 ASN D 325 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.179177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130033 restraints weight = 22476.561| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.92 r_work: 0.3203 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22611 Z= 0.182 Angle : 0.515 8.714 30574 Z= 0.267 Chirality : 0.039 0.155 3439 Planarity : 0.004 0.052 3793 Dihedral : 7.957 59.677 3281 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.79 % Allowed : 19.60 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.16), residues: 2626 helix: 1.72 (0.11), residues: 1979 sheet: None (None), residues: 0 loop : -0.42 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 322 TYR 0.017 0.001 TYR C 315 PHE 0.022 0.002 PHE A 544 TRP 0.016 0.001 TRP A 335 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00433 (22591) covalent geometry : angle 0.51323 (30554) SS BOND : bond 0.00480 ( 4) SS BOND : angle 2.12092 ( 8) hydrogen bonds : bond 0.04420 ( 1449) hydrogen bonds : angle 3.79124 ( 4275) metal coordination : bond 0.00417 ( 16) metal coordination : angle 1.19763 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 305 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.5468 (OUTLIER) cc_final: 0.4401 (p0) REVERT: A 231 GLU cc_start: 0.8161 (mp0) cc_final: 0.7621 (mt-10) REVERT: A 267 MET cc_start: 0.8426 (tpp) cc_final: 0.8032 (tpt) REVERT: A 305 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6986 (ptm) REVERT: A 438 ASP cc_start: 0.6847 (t0) cc_final: 0.5972 (m-30) REVERT: A 540 PHE cc_start: 0.8241 (t80) cc_final: 0.7966 (t80) REVERT: A 546 LEU cc_start: 0.8683 (tp) cc_final: 0.8464 (tt) REVERT: B 65 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7488 (p) REVERT: B 79 GLU cc_start: 0.7707 (mp0) cc_final: 0.7187 (mp0) REVERT: B 186 ASP cc_start: 0.7827 (t0) cc_final: 0.7338 (m-30) REVERT: B 232 LYS cc_start: 0.7892 (mttp) cc_final: 0.7550 (mtpt) REVERT: B 234 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7085 (mp0) REVERT: B 243 GLU cc_start: 0.8273 (pt0) cc_final: 0.7645 (mm-30) REVERT: B 272 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.6767 (tpp-160) REVERT: B 470 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6082 (ptt) REVERT: B 478 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6405 (mt-10) REVERT: B 540 TYR cc_start: 0.7926 (m-80) cc_final: 0.7091 (m-80) REVERT: B 715 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7846 (ttpt) REVERT: C 266 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8190 (mt-10) REVERT: C 348 LEU cc_start: 0.8389 (tp) cc_final: 0.8179 (tp) REVERT: C 403 GLU cc_start: 0.6074 (tm-30) cc_final: 0.5762 (tm-30) REVERT: C 549 CYS cc_start: 0.5280 (OUTLIER) cc_final: 0.5065 (p) REVERT: C 591 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: C 723 ARG cc_start: 0.6801 (mpt180) cc_final: 0.6059 (ttp80) REVERT: D 228 GLN cc_start: 0.8115 (tp40) cc_final: 0.7835 (tp40) REVERT: D 549 CYS cc_start: 0.5492 (OUTLIER) cc_final: 0.4941 (p) outliers start: 91 outliers final: 67 residues processed: 362 average time/residue: 0.1632 time to fit residues: 92.2906 Evaluate side-chains 371 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 296 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 549 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 18 optimal weight: 0.0570 chunk 126 optimal weight: 0.0470 chunk 72 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN C 250 GLN ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN D 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.184297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135296 restraints weight = 22576.130| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.92 r_work: 0.3248 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22611 Z= 0.107 Angle : 0.455 8.226 30574 Z= 0.238 Chirality : 0.036 0.209 3439 Planarity : 0.004 0.053 3793 Dihedral : 7.520 59.851 3278 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.54 % Allowed : 20.35 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.16), residues: 2626 helix: 2.05 (0.11), residues: 1974 sheet: None (None), residues: 0 loop : -0.28 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 296 TYR 0.022 0.001 TYR A 742 PHE 0.021 0.001 PHE A 450 TRP 0.015 0.001 TRP D 409 HIS 0.002 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00230 (22591) covalent geometry : angle 0.45409 (30554) SS BOND : bond 0.00100 ( 4) SS BOND : angle 1.27307 ( 8) hydrogen bonds : bond 0.03844 ( 1449) hydrogen bonds : angle 3.63473 ( 4275) metal coordination : bond 0.00297 ( 16) metal coordination : angle 1.15437 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 316 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.5450 (OUTLIER) cc_final: 0.4401 (p0) REVERT: A 267 MET cc_start: 0.8295 (tpp) cc_final: 0.7911 (tpt) REVERT: A 305 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6778 (ptm) REVERT: A 438 ASP cc_start: 0.6794 (t0) cc_final: 0.5988 (m-30) REVERT: A 535 GLN cc_start: 0.7386 (mp10) cc_final: 0.6857 (mm-40) REVERT: A 540 PHE cc_start: 0.8061 (t80) cc_final: 0.7853 (t80) REVERT: B 79 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: B 81 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7526 (mt-10) REVERT: B 186 ASP cc_start: 0.7720 (t0) cc_final: 0.7234 (m-30) REVERT: B 232 LYS cc_start: 0.7678 (mttp) cc_final: 0.7327 (mtpt) REVERT: B 243 GLU cc_start: 0.8166 (pt0) cc_final: 0.7548 (mm-30) REVERT: B 272 ARG cc_start: 0.7351 (ttt-90) cc_final: 0.6676 (tpp-160) REVERT: B 470 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6108 (ptt) REVERT: B 478 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6284 (mt-10) REVERT: B 715 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7708 (ttpt) REVERT: C 266 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8113 (mt-10) REVERT: C 403 GLU cc_start: 0.5917 (tm-30) cc_final: 0.5642 (tm-30) REVERT: C 549 CYS cc_start: 0.5009 (OUTLIER) cc_final: 0.4747 (p) REVERT: C 591 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: C 723 ARG cc_start: 0.6651 (mpt180) cc_final: 0.5898 (ttp80) REVERT: D 228 GLN cc_start: 0.8023 (tp40) cc_final: 0.7756 (tp40) REVERT: D 549 CYS cc_start: 0.5421 (OUTLIER) cc_final: 0.4895 (p) REVERT: D 556 LYS cc_start: 0.8031 (tptt) cc_final: 0.7764 (tptt) outliers start: 85 outliers final: 52 residues processed: 365 average time/residue: 0.1591 time to fit residues: 90.4406 Evaluate side-chains 359 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 299 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 549 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 5 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 242 optimal weight: 3.9990 chunk 199 optimal weight: 0.2980 chunk 146 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN C 250 GLN ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN D 325 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.182185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133958 restraints weight = 22524.692| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.90 r_work: 0.3223 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22611 Z= 0.153 Angle : 0.487 6.763 30574 Z= 0.254 Chirality : 0.038 0.207 3439 Planarity : 0.004 0.052 3793 Dihedral : 7.530 58.631 3278 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.38 % Allowed : 20.48 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.16), residues: 2626 helix: 1.98 (0.11), residues: 1979 sheet: None (None), residues: 0 loop : -0.22 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 196 TYR 0.017 0.001 TYR D 523 PHE 0.020 0.001 PHE A 544 TRP 0.014 0.001 TRP A 335 HIS 0.004 0.001 HIS D 704 Details of bonding type rmsd covalent geometry : bond 0.00361 (22591) covalent geometry : angle 0.48561 (30554) SS BOND : bond 0.00143 ( 4) SS BOND : angle 1.76596 ( 8) hydrogen bonds : bond 0.04126 ( 1449) hydrogen bonds : angle 3.66476 ( 4275) metal coordination : bond 0.00333 ( 16) metal coordination : angle 1.03156 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.5452 (OUTLIER) cc_final: 0.4374 (p0) REVERT: A 231 GLU cc_start: 0.8090 (mp0) cc_final: 0.7613 (mt-10) REVERT: A 267 MET cc_start: 0.8414 (tpp) cc_final: 0.8033 (tpt) REVERT: A 305 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6885 (ptm) REVERT: A 438 ASP cc_start: 0.6824 (t0) cc_final: 0.5996 (m-30) REVERT: A 535 GLN cc_start: 0.7510 (mp10) cc_final: 0.6988 (mm-40) REVERT: A 540 PHE cc_start: 0.8173 (t80) cc_final: 0.7951 (t80) REVERT: A 765 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5150 (mtt-85) REVERT: B 79 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 81 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 186 ASP cc_start: 0.7731 (t0) cc_final: 0.7260 (m-30) REVERT: B 232 LYS cc_start: 0.7764 (mttp) cc_final: 0.7431 (mtpt) REVERT: B 243 GLU cc_start: 0.8203 (pt0) cc_final: 0.7616 (mm-30) REVERT: B 272 ARG cc_start: 0.7353 (ttt-90) cc_final: 0.6675 (tpp-160) REVERT: B 470 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6142 (ptt) REVERT: B 478 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6412 (mt-10) REVERT: B 715 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7799 (ttpt) REVERT: C 266 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8198 (mt-10) REVERT: C 403 GLU cc_start: 0.6076 (tm-30) cc_final: 0.5754 (tm-30) REVERT: C 549 CYS cc_start: 0.5014 (OUTLIER) cc_final: 0.4756 (p) REVERT: C 591 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: C 723 ARG cc_start: 0.6755 (mpt180) cc_final: 0.6018 (ttp80) REVERT: D 228 GLN cc_start: 0.8093 (tp40) cc_final: 0.7834 (tp40) REVERT: D 549 CYS cc_start: 0.5468 (OUTLIER) cc_final: 0.4933 (p) REVERT: D 556 LYS cc_start: 0.8164 (tptt) cc_final: 0.7877 (tptt) REVERT: D 704 HIS cc_start: 0.8375 (m170) cc_final: 0.8161 (m90) REVERT: D 740 LYS cc_start: 0.6139 (mtpp) cc_final: 0.5939 (ttmt) outliers start: 81 outliers final: 62 residues processed: 354 average time/residue: 0.1661 time to fit residues: 91.1868 Evaluate side-chains 367 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 296 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 549 CYS Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 0.0050 chunk 128 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 250 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN C 250 GLN ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN D 325 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.184382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135396 restraints weight = 22359.526| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.87 r_work: 0.3258 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22611 Z= 0.119 Angle : 0.466 9.787 30574 Z= 0.242 Chirality : 0.037 0.218 3439 Planarity : 0.004 0.051 3793 Dihedral : 7.304 57.359 3278 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.29 % Allowed : 20.56 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.16), residues: 2626 helix: 2.14 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -0.17 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 322 TYR 0.016 0.001 TYR B 523 PHE 0.018 0.001 PHE A 544 TRP 0.018 0.001 TRP D 409 HIS 0.003 0.000 HIS D 704 Details of bonding type rmsd covalent geometry : bond 0.00268 (22591) covalent geometry : angle 0.46483 (30554) SS BOND : bond 0.00108 ( 4) SS BOND : angle 1.36522 ( 8) hydrogen bonds : bond 0.03871 ( 1449) hydrogen bonds : angle 3.61196 ( 4275) metal coordination : bond 0.00304 ( 16) metal coordination : angle 1.06769 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 308 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.5428 (OUTLIER) cc_final: 0.4352 (p0) REVERT: A 231 GLU cc_start: 0.8074 (mp0) cc_final: 0.7579 (mt-10) REVERT: A 267 MET cc_start: 0.8384 (tpp) cc_final: 0.8023 (tpt) REVERT: A 305 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6851 (ptm) REVERT: A 438 ASP cc_start: 0.6762 (t0) cc_final: 0.5962 (m-30) REVERT: A 535 GLN cc_start: 0.7516 (mp10) cc_final: 0.6978 (mm-40) REVERT: A 765 ARG cc_start: 0.5779 (OUTLIER) cc_final: 0.5073 (mtt-85) REVERT: B 79 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: B 81 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7441 (mt-10) REVERT: B 186 ASP cc_start: 0.7688 (t0) cc_final: 0.7222 (m-30) REVERT: B 232 LYS cc_start: 0.7734 (mttp) cc_final: 0.7382 (mtpt) REVERT: B 243 GLU cc_start: 0.8200 (pt0) cc_final: 0.7635 (mm-30) REVERT: B 272 ARG cc_start: 0.7318 (ttt-90) cc_final: 0.6669 (tpp-160) REVERT: B 470 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6075 (ptt) REVERT: B 478 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6280 (mt-10) REVERT: B 639 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7379 (ttp-110) REVERT: B 715 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7761 (ttpt) REVERT: C 266 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8163 (mt-10) REVERT: C 403 GLU cc_start: 0.6097 (tm-30) cc_final: 0.5801 (tm-30) REVERT: C 591 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: C 723 ARG cc_start: 0.6662 (mpt180) cc_final: 0.5906 (ttp80) REVERT: D 228 GLN cc_start: 0.8060 (tp40) cc_final: 0.7804 (tp40) REVERT: D 471 TRP cc_start: 0.8409 (m100) cc_final: 0.8188 (m100) REVERT: D 549 CYS cc_start: 0.5364 (OUTLIER) cc_final: 0.4854 (p) REVERT: D 556 LYS cc_start: 0.8130 (tptt) cc_final: 0.7851 (tptt) REVERT: D 704 HIS cc_start: 0.8344 (m170) cc_final: 0.8120 (m90) REVERT: D 740 LYS cc_start: 0.6100 (mtpp) cc_final: 0.5882 (ttmt) outliers start: 79 outliers final: 60 residues processed: 358 average time/residue: 0.1613 time to fit residues: 89.7689 Evaluate side-chains 366 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 126 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN C 250 GLN ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN D 325 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.180614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132194 restraints weight = 22542.592| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.90 r_work: 0.3201 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22611 Z= 0.190 Angle : 0.525 9.181 30574 Z= 0.272 Chirality : 0.039 0.191 3439 Planarity : 0.004 0.050 3793 Dihedral : 7.420 59.716 3278 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.46 % Allowed : 20.64 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.16), residues: 2626 helix: 1.90 (0.11), residues: 1981 sheet: None (None), residues: 0 loop : -0.27 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 196 TYR 0.018 0.001 TYR C 315 PHE 0.022 0.002 PHE A 544 TRP 0.019 0.001 TRP D 409 HIS 0.003 0.001 HIS D 704 Details of bonding type rmsd covalent geometry : bond 0.00457 (22591) covalent geometry : angle 0.52399 (30554) SS BOND : bond 0.00283 ( 4) SS BOND : angle 1.59561 ( 8) hydrogen bonds : bond 0.04396 ( 1449) hydrogen bonds : angle 3.71756 ( 4275) metal coordination : bond 0.00372 ( 16) metal coordination : angle 1.04638 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 305 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.5410 (OUTLIER) cc_final: 0.4325 (p0) REVERT: A 231 GLU cc_start: 0.8081 (mp0) cc_final: 0.7597 (mt-10) REVERT: A 267 MET cc_start: 0.8448 (tpp) cc_final: 0.8090 (tpt) REVERT: A 305 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6906 (ptm) REVERT: A 438 ASP cc_start: 0.6738 (t0) cc_final: 0.5956 (m-30) REVERT: A 535 GLN cc_start: 0.7526 (mp10) cc_final: 0.7004 (mm-40) REVERT: A 765 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5044 (mtt-85) REVERT: B 44 ASP cc_start: 0.6611 (t0) cc_final: 0.6344 (t0) REVERT: B 79 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: B 81 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7531 (mt-10) REVERT: B 186 ASP cc_start: 0.7769 (t0) cc_final: 0.7279 (m-30) REVERT: B 232 LYS cc_start: 0.7775 (mttp) cc_final: 0.7445 (mtpt) REVERT: B 243 GLU cc_start: 0.8251 (pt0) cc_final: 0.7652 (mm-30) REVERT: B 470 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6050 (ptt) REVERT: B 478 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6415 (mt-10) REVERT: B 639 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7623 (ttp-110) REVERT: B 715 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7824 (ttpt) REVERT: C 156 GLU cc_start: 0.8208 (mp0) cc_final: 0.7929 (mp0) REVERT: C 266 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8193 (mt-10) REVERT: C 403 GLU cc_start: 0.6101 (tm-30) cc_final: 0.5738 (tm-30) REVERT: C 591 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: C 723 ARG cc_start: 0.6715 (mpt180) cc_final: 0.5963 (ttp80) REVERT: D 228 GLN cc_start: 0.8122 (tp40) cc_final: 0.7859 (tp40) REVERT: D 549 CYS cc_start: 0.5503 (OUTLIER) cc_final: 0.5015 (p) REVERT: D 556 LYS cc_start: 0.8268 (tptt) cc_final: 0.8032 (tptt) REVERT: D 704 HIS cc_start: 0.8343 (m170) cc_final: 0.8102 (m90) outliers start: 83 outliers final: 65 residues processed: 357 average time/residue: 0.1635 time to fit residues: 89.9947 Evaluate side-chains 372 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 298 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 35 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 222 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.182628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134434 restraints weight = 22567.934| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.86 r_work: 0.3235 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22611 Z= 0.132 Angle : 0.481 6.900 30574 Z= 0.252 Chirality : 0.037 0.169 3439 Planarity : 0.004 0.052 3793 Dihedral : 7.256 59.987 3278 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.04 % Allowed : 21.06 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2626 helix: 2.04 (0.11), residues: 1980 sheet: None (None), residues: 0 loop : -0.20 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 322 TYR 0.017 0.001 TYR B 523 PHE 0.019 0.001 PHE A 544 TRP 0.021 0.001 TRP D 409 HIS 0.003 0.000 HIS D 704 Details of bonding type rmsd covalent geometry : bond 0.00304 (22591) covalent geometry : angle 0.48015 (30554) SS BOND : bond 0.00277 ( 4) SS BOND : angle 1.87658 ( 8) hydrogen bonds : bond 0.04022 ( 1449) hydrogen bonds : angle 3.64887 ( 4275) metal coordination : bond 0.00318 ( 16) metal coordination : angle 1.07723 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 300 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.5409 (OUTLIER) cc_final: 0.4306 (p0) REVERT: A 231 GLU cc_start: 0.8085 (mp0) cc_final: 0.7663 (mt-10) REVERT: A 305 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6856 (ptm) REVERT: A 438 ASP cc_start: 0.6775 (t0) cc_final: 0.5953 (m-30) REVERT: A 535 GLN cc_start: 0.7505 (mp10) cc_final: 0.6982 (mm-40) REVERT: A 765 ARG cc_start: 0.5739 (OUTLIER) cc_final: 0.5025 (mtt-85) REVERT: B 79 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: B 81 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 106 LYS cc_start: 0.8156 (tptp) cc_final: 0.7949 (tptt) REVERT: B 186 ASP cc_start: 0.7687 (t0) cc_final: 0.7214 (m-30) REVERT: B 232 LYS cc_start: 0.7755 (mttp) cc_final: 0.7424 (mtpt) REVERT: B 243 GLU cc_start: 0.8213 (pt0) cc_final: 0.7632 (mm-30) REVERT: B 470 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6083 (ptt) REVERT: B 478 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6335 (mt-10) REVERT: B 715 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7794 (ttpt) REVERT: C 156 GLU cc_start: 0.8192 (mp0) cc_final: 0.7910 (mp0) REVERT: C 243 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7605 (tt0) REVERT: C 266 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 403 GLU cc_start: 0.6047 (tm-30) cc_final: 0.5734 (tm-30) REVERT: C 591 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: C 723 ARG cc_start: 0.6691 (mpt180) cc_final: 0.5956 (ttp80) REVERT: D 228 GLN cc_start: 0.8078 (tp40) cc_final: 0.7826 (tp40) REVERT: D 549 CYS cc_start: 0.5479 (OUTLIER) cc_final: 0.4971 (p) REVERT: D 556 LYS cc_start: 0.8225 (tptt) cc_final: 0.7974 (tptt) REVERT: D 704 HIS cc_start: 0.8350 (m170) cc_final: 0.8112 (m90) outliers start: 73 outliers final: 60 residues processed: 345 average time/residue: 0.1590 time to fit residues: 84.8329 Evaluate side-chains 362 residues out of total 2398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 294 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 701 ARG Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 625 GLN Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 118 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.182213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134145 restraints weight = 22571.816| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.89 r_work: 0.3212 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22611 Z= 0.145 Angle : 0.491 9.998 30574 Z= 0.256 Chirality : 0.038 0.157 3439 Planarity : 0.004 0.051 3793 Dihedral : 7.230 59.449 3278 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.21 % Allowed : 20.93 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2626 helix: 2.03 (0.11), residues: 1980 sheet: None (None), residues: 0 loop : -0.19 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.017 0.001 TYR D 523 PHE 0.019 0.001 PHE A 544 TRP 0.019 0.001 TRP D 409 HIS 0.003 0.000 HIS D 704 Details of bonding type rmsd covalent geometry : bond 0.00340 (22591) covalent geometry : angle 0.49076 (30554) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.19468 ( 8) hydrogen bonds : bond 0.04071 ( 1449) hydrogen bonds : angle 3.65962 ( 4275) metal coordination : bond 0.00323 ( 16) metal coordination : angle 1.05105 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.41 seconds wall clock time: 111 minutes 28.63 seconds (6688.63 seconds total)